RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 10 (RBM10); This subgroup corresponds to the RRM1 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1306253120 128 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS 207
Cdd:cd12753     1 SNIIMLRMLPQSATENDIRGQLQAHGVQPREVRLMRNKSSGQSRGFAFVEFNHLQDATRWMEANQHSLTILGQKVSMHYS 80

                  ....
gi 1306253120 208 DPKP 211
Cdd:cd12753    81 DPKP 84

OCRE domain found in RNA-binding protein 10 (RBM10) and similar proteins; RBM10, also called G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), is a paralogue of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, and a G-patch/D111 domain.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1306253120 563 YPVPDVSTYQYDETSGYYYDPQTGLYYDPNSQYYYNAQSQQYLYWDGERRTYIPALEQSADGHK 626
Cdd:cd16167     1 YPVPDVSTYQYDETSGYYYDPQTGLYYDPNSQYYYNAQTQQYLYWDGERRTYVPASEQGADGHK 64

Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.

                           10        20
                   ....*....|....*....|....*
gi 1306253120  215 EDWLCNKCGVQNFKRREKCFKCGVP 239
Cdd:smart00547   1 GDWECPACTFLNFASRSKCFACGAP 25

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 10 (RBM10); This subgroup corresponds to the RRM1 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1306253120 128 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS 207
Cdd:cd12753     1 SNIIMLRMLPQSATENDIRGQLQAHGVQPREVRLMRNKSSGQSRGFAFVEFNHLQDATRWMEANQHSLTILGQKVSMHYS 80

                  ....
gi 1306253120 208 DPKP 211
Cdd:cd12753    81 DPKP 84

OCRE domain found in RNA-binding protein 10 (RBM10) and similar proteins; RBM10, also called G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), is a paralogue of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, and a G-patch/D111 domain.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1306253120 563 YPVPDVSTYQYDETSGYYYDPQTGLYYDPNSQYYYNAQSQQYLYWDGERRTYIPALEQSADGHK 626
Cdd:cd16167     1 YPVPDVSTYQYDETSGYYYDPQTGLYYDPNSQYYYNAQTQQYLYWDGERRTYVPASEQGADGHK 64

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1306253120 857 SDNIGSRMLQAMGWKEGSGLGRKKQGIVTPIEAQTRVRGSGLGAR 901
Cdd:pfam01585   1 TSNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLGAE 45

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1306253120  131 VMLRMLPQAATEDDIRGQLQSHGvQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANqHSLNILGQKV 202
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFG-KVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEAL-NGKELDGRPL 71

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1306253120 301 TIILRNLNPHSTMDSILGALAPY-AVLSssnVRVIKDKQTQLNRGFAFIQLSTIEAAQllQILQALHpPLTIDGKTINVE 379
Cdd:COG0724     3 KIYVGNLPYSVTEEDLRELFSEYgEVTS---VKLITDRETGRSRGFGFVEMPDDEEAQ--AAIEALN-GAELMGRTLKVN 76

                  ...
gi 1306253120 380 FAK 382
Cdd:COG0724    77 EAR 79

Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.

                           10        20
                   ....*....|....*....|....*
gi 1306253120  215 EDWLCNKCGVQNFKRREKCFKCGVP 239
Cdd:smart00547   1 GDWECPACTFLNFASRSKCFACGAP 25

ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1306253120 136 LPQAATEDDIRGQLQSHGvQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEAnQHSLNILGQKVSMHYSDPKPKINE 215
Cdd:TIGR01661  11 LPQTMTQEEIRSLFTSIG-EIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNS-LNGLRLQNKTIKVSYARPSSDSIK 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1306253120 216 DwlcnkcgvqnfkrrEKCFKCGVPKSEAEQKL-----PLGTRLDQQALPLGGRELSQGL--LPLPQPYQAQGVLtsQALS 288
Cdd:TIGR01661  89 G--------------ANLYVSGLPKTMTQHELesifsPFGQIITSRILSDNVTGLSKGVgfIRFDKRDEADRAI--KTLN 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1306253120 289 qGSEPSSENANDTIILRNLNPHSTMDSILGALapYAVLSSSNVRVIKDKQ------TQLNRGFAFIQLSTIEAAQLLQIL 362
Cdd:TIGR01661 153 -GTTPSGCTEPITVKFANNPSSSNSKGLLSQL--EAVQNPQTTRVPLSTIltaagiGPMHHAAARFRPSAGDFTAVLAHQ 229

                         250       260
                  ....*....|....*....|....
gi 1306253120 363 QALHP-----------PLTIDGKT 375
Cdd:TIGR01661 230 QQQHAvaqqhaaqrasPPATDGQT 253

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 10 (RBM10); This subgroup corresponds to the RRM1 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1306253120 128 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS 207
Cdd:cd12753     1 SNIIMLRMLPQSATENDIRGQLQAHGVQPREVRLMRNKSSGQSRGFAFVEFNHLQDATRWMEANQHSLTILGQKVSMHYS 80

                  ....
gi 1306253120 208 DPKP 211
Cdd:cd12753    81 DPKP 84

RNA recognition motif 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins; This subgroup corresponds to the RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1306253120 298 ANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLST-IEAAQLLQILQALHPPLTIDGKTI 376
Cdd:cd12562     1 ANDTIILRNINPHTTVDSILGALAPYAVLSSSNVRLIKDKQTQLNRGFAFVQLSSpIEASQLLQILQSLHPPLTIDGKTI 80

                  ....*.
gi 1306253120 377 NVEFAK 382
Cdd:cd12562    81 NVDFAK 86

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 5 (RBM5); This subgroup corresponds to the RRM2 of RBM5, also termed protein G15, or putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9, a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both, RBM5 and RBM6, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1306253120 300 DTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLST-IEAAQLLQILQALHPPLTIDGKTINV 378
Cdd:cd12755     3 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSaLEASQLLQILQSLHPPLKIDGKTIGV 82

                  ....
gi 1306253120 379 EFAK 382
Cdd:cd12755    83 DFAK 86

OCRE domain found in RNA-binding protein 5 (RBM5) and similar proteins; RBM5 is also called protein G15, H37, putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9. It is a known modulator of apoptosis. It acts as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both of them specifically binds poly(G) RNA. RBM5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1306253120 565 VPDVSTYQYDETSGYYYDPQTGLYYDPNSQYYYNAQSQQYLYWDGERRTYIPALE 619
Cdd:cd16168     2 VPDTSTYQYDESSGYYYDPITGLYYDPNSQYYYNSLTQQYLYWDGEKQTYLPAAE 56

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins; This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1306253120 299 NDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKTIN 377
Cdd:cd12313     2 TNVLILRGLDVLTTEEDILSALQAHADLPIKDVRLIRDKLTGTSRGFAFVEFSSLeDATQVMDALQNLLPPFKIDGRVVS 81

                  ....
gi 1306253120 378 VEFA 381
Cdd:cd12313    82 VSYA 85

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 5 (RBM5); This subgroup corresponds to the RRM1 of RBM5, also termed protein G15, or putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9, a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both, RBM5 and RBM6, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1306253120 126 KASNIVMLRMLPQAATEDDIRGQLQS-HGVQAREVRLMRNKSsGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSM 204
Cdd:cd12752     3 KESKTIMLRGLPINITENDIRELIESfEGPQPADVRLMKRKT-GVSRGFAFVEFYHLQDATSWMEANQKKLVIQGKTIAM 81

                  ....*.
gi 1306253120 205 HYSDPK 210
Cdd:cd12752    82 HYSNPR 87

OCRE domain; The OCRE (OCtamer REpeat) domain contains 5 repeats of an 8-residue motif, which were shown to form beta-strands. Based on the architectures of proteins containing OCRE domains, a role in RNA metabolism and/or signalling has been proposed.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1306253120 566 PDVSTYQYDETSGYYYDPQTGLYYDPNSQYYYNAQSQQYLYWDGERRTYIP 616
Cdd:cd16074     3 PDPSGFVFDPNSGYYYDPSTGLYYDPNTGYYYDPTSGTYYIWDDELGAYVP 53

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 6 (RBM6); This subgroup corresponds to the RRM2 of RBM6, also termed lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, which has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both, RBM6 and RBM5, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has two additional unique domains: the decamer repeat occurring more than 20 times, and the POZ (poxvirus and zinc finger) domain. The POZ domain may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1306253120 301 TIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQL-STIEAAQLLQILQALHPPLTIDGKTINVE 379
Cdd:cd12563     4 TIMLKRIYRSTPPEVIVEVLEPYVRLTTANVRIIKNKTGPMGHTYGFIDLdSHAEALRLVKLLQNLDPPLYIDGRRVYVN 83

                  ....
gi 1306253120 380 FAKG 383
Cdd:cd12563    84 VATG 87

OCRE domain found in Suppressor of ABI3-5 (SUA) and similar proteins; SUA is an RNA-binding protein located in the nucleus and expressed in all plant tissues. It functions as a splicing factor that influences seed maturation by controlling alternative splicing of ABI3. The suppression of the cryptic ABI3 intron indicates a role of SUA in mRNA processing. SUA also interacts with the prespliceosomal component U2AF65, the larger subunit of the conserved pre-mRNA splicing factor U2AF. SUA contains two RNA recognition motifs surrounding a zinc finger domain, an OCtamer REpeat (OCRE) domain, and a Gly-rich domain close to the C-terminus.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1306253120 568 VSTYQYDETSGYYYDPQTGLYYDPNSQYYYNAQSQQYLYWDGERRTYIPA 617
Cdd:cd16166     5 PSGFVYDPASGYYYDASSGYYYDANTGLYYDAASGRWYSYDEETGQYVEV 54

OCRE domain found in RNA-binding protein 6 (RBM6) and similar proteins; RBM6, also called lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both specifically binds poly(G) RNA. RBM6 contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has an additional unique domain, the POZ (poxvirus and zinc finger) domain, which may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1306253120 568 VSTYQYDETSGYYYDPQTGLYYDPNSQYYYNAQSQQYLYWDGERRTYIPA 617
Cdd:cd16163     6 APTYRSDPDSGYIYDPETGYYYDPVTGLYYDPATGEYVDPDTGTLPYDPS 55

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 6 (RBM6); This subfamily corresponds to the RRM1 of RBM6, also termed lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, which has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both, RBM6 and RBM5, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has two additional unique domains: the decamer repeat occurring more than 20 times, and the POZ (poxvirus and zinc finger) domain. The POZ domain may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1306253120 129 NIVMLRMLPQAATEDDIRGQLQS-HGVQAREVRLmRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHY 206
Cdd:cd12314     1 NLIRLIGVPETATKEQILNAFRVpDGMPVKNLKL-KNYVPGYDYDYVCVEFSLLEDAIGCMEANQGTLKIGTKEVTLEY 78

OCRE domain found in angiogenic factor VG5Q and similar proteins; VG5Q, also called angiogenic factor with G patch and FHA domains 1 (AGGF1), or G patch domain-containing protein 7, or vasculogenesis gene on 5q protein, functions as a potent angiogenic factor in promoting angiogenesis through interacting with TWEAK (also known as TNFSF12), which is a member of the tumor necrosis factor (TNF) superfamily that induces angiogenesis in vivo. VG5Q can bind to the surface of endothelial cells and promote cell proliferation, suggesting that it may act in an autocrine fashion. The chromosomal translocation t(5;11) and the E133K variant in VG5Q are associated with Klippel-Trenaunay syndrome (KTS), a disorder characterized by diverse effects in the vascular system. In addition to a forkhead-associated (FHA) domain and a G-patch motif, VG5Q contains an N-terminal OCtamer REpeat (OCRE) domain that is characterized by a 5-fold, imperfectly repeated octameric sequence.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1306253120 573 YDETSGYYYDPQTGLYYDPNS--QYYYNAQSQQYLY 606
Cdd:cd16164    18 YDPSTGYYYDSETQLYYDPNTgtYYYYDEESGSYQF 53

RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 (RRM5) found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1306253120 129 NIVMLRMLPQAATEDDIRGQLQSHGvQAREVRLMRnKSSGQSRGFAFVEFSHLQDATRWMEANQHS 194
Cdd:cd12320     1 TKLIVKNVPFEATRKEIRELFSPFG-QLKSVRLPK-KFDGSHRGFAFVEFVTKQEAQNAMEALKST 64

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1306253120 136 LPQAATEDDIRGQLQSHGvQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEA 190
Cdd:COG0724     9 LPYSVTEEDLRELFSEYG-EVTSVKLITDRETGRSRGFGFVEMPDDEEAQAAIEA 62

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA; This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1306253120 135 MLPQAATEDDIRGQLQSHGVqAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEA 190
Cdd:cd12361     6 MIPKTASEEDVRPLFEQFGN-IEEVQILRDKQTGQSKGCAFVTFSTREEALRAIEA 60

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1306253120 136 LPQAATEDDIRGQLQSHGvQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEAN 191
Cdd:cd21608     7 LSWDTTEDDLRDLFSEFG-EVESAKVITDRETGRSRGFGFVTFSTAEAAEAAIDAL 61

RNA recognition motif 1 (RRM1) found in RNA-binding protein 5 (RBM5) and similar proteins; This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1306253120 298 ANDTIILRNLNPHSTMDSILGALAPYAVlSSSNVRVIKDKQTQLNRGFAFIQLSTIEAA 356
Cdd:cd12561     1 PNNTIMLRGLPLSVTEEDIRNALVSHGV-QPKDVRLMRRKTTGASRGFAFVEFMSLEEA 58

OCRE domain found in Zinc-finger and OCRE domain-containing Protein 1 (ZOP1) and similar proteins found in plant; ZOP1 is a novel plant-specific nucleic acid-binding protein required for both RNA-directed DNA methylation (RdDM) and pre-mRNA splicing. It promotes RNA polymerase IV (Pol IV)-dependent siRNA accumulation, DNA methylation, and transcriptional silencing. As a pre-mRNA splicing factor, ZOP1 associates with several typical splicing proteins as well as with RNA polymerase II (RNAP II and Pol II). It also shows both RdDM-dependent and -independent roles in transcriptional silencing. ZOP1 contains an N-terminal C2H2-type ZnF domain and an OCtamer REpeat (OCRE) domain that is usually related to RNA processing.

                          10        20        30
                  ....*....|....*....|....*....|.
gi 1306253120 568 VSTYQYDETSGYYYDPQTGLYYDPNSQYYYN 598
Cdd:cd16165     5 AGDWVLDSKSGYYYNAATRYYYDPKTGMYYS 35

RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins; This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1306253120 129 NIVMLRMLPQAATEDDIRGQLQSHGvQAREVRLMRNKSSGQSRGFAFVEFShlqDATRWMEA-NQHSLNILGQKV 202
Cdd:cd12400     1 YILFVGNLPYDTTAEDLKEHFKKAG-EPPSVRLLTDKKTGKSKGCAFVEFD---NQKALQKAlKLHHTSLGGRKI 71

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1306253120 302 IILRNLNPHSTMDSILGALAPYAVLSSsnVRVIKDKQTQlNRGFAFIQLSTIEAAQllQILQALHpPLTIDGKTINVE 379
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFGEVVS--VRIVRDRDGK-SKGFAFVEFESPEDAE--KALEALN-GTELGGRPLKVS 72

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1306253120 306 NLNPHSTMDSILGALAPY-AVLSssnVRVIKDKQTQLNRGFAFIQLSTIEAAQLLqiLQALHpPLTIDGKTINVEFA 381
Cdd:cd21608     6 NLSWDTTEDDLRDLFSEFgEVES---AKVITDRETGRSRGFGFVTFSTAEAAEAA--IDALN-GKELDGRSIVVNEA 76

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins; This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1306253120 141 TEDDIRGQLQSHGvQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWME 189
Cdd:cd12284    11 TEDMLRGIFEPFG-KIEFVQLQKDPETGRSKGYGFIQFRDAEDAKKALE 58

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins; The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1306253120 130 IVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKsSGQSRGFAFVEFSHLQDATRWMEANQHSL 195
Cdd:cd12254     1 VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDD-DGRPTGEAYVEFASEEDAQRALRRHKGKM 65

Zn-finger in Ran binding protein and others;

                          10        20
                  ....*....|....*....|....*...
gi 1306253120 214 NEDWLCNKCGVQNFKRREKCFKCGVPKS 241
Cdd:pfam00641   2 EGDWDCSKCLVQNFATSTKCVACQAPKP 29

RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins; This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1306253120 141 TEDDIRGQLQSHGV-QAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEA-NQHSLNilGQKVSMHY 206
Cdd:cd12372    11 TDEDLEGACASFGVvDVKEIKFFEHKANGKSKGYAYVEFASPAAAAAVKEKlEKREFN--GRPCVVTP 76

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins; This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1306253120 136 LPQAATEDDIRGQLQSHGvqarEVR---LMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNilGQKVsmhysDPK 210
Cdd:cd12325     6 LSWETTEESLREYFSKYG----EVVdcvVMKDPATGRSRGFGFVTFKDPSSVDAVLAARPHTLD--GRTI-----DPK 72

RNA recognition motif 4 (RRM4) found in RNA-binding protein RBM12, RBM12B and similar proteins; This subfamily corresponds to the RRM4 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B show high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1306253120 131 VMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKsSGQSRGFAFVEFSHLQDATRWMEANQHSLN 196
Cdd:cd12514     2 IRITNLPYDATPVDIQRFFEDHGVRPEDVHLLRNK-KGRGNGEALVTFKSEGDAREVLKLNGKKLG 66

RNA recognition motif 1 (RRM1) found in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1306253120 136 LPQAATEDDIRGQLQSHGvQAREVRLMRNKSSGQSRGFAFVEFSHLQDATR 186
Cdd:cd12649     8 LPQDLTDREFRALFRAIG-PVNTCKIVRDKKTGYSYGFGFVDFTSEEDAQR 57

RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1306253120 133 LRMLPQAATEDDIRGQLQSHGvQAREVRLMRNKSSGQSRGFAFVEFSHLQDATR 186
Cdd:cd12566     7 LRNLPYSTKEDDLQKLFSKFG-EVSEVHVPIDKKTKKSKGFAYVLFLDPEDAVQ 59

RNA recognition motif (RRM) found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins; This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1306253120 134 RMLPQAaTEDDIRGQLQSHGvQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSL 195
Cdd:cd12237    11 RLSLQT-TEEKLKEVFSRYG-DIRRLRLVRDIVTGFSKRYAFIEYKEERDALHAYRDAKKLV 70

RNA recognition motif 2 (RRM2) found in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins; This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1306253120 128 SNIVMLRMLPQAATEDDIRGQLQSHGVqAREVRLMRNKSSGQSRGFAFVEFSHLQDATRwmEANQHSLNILGQKVSMHYS 207
Cdd:cd12327     2 SKKVFVGGIPHNCGETELRDYFKRYGV-VTEVVMMYDAEKQRSRGFGFITFEDEQSVDQ--AVNMHFHDIMGKKVEVKRA 78

                  ..
gi 1306253120 208 DP 209
Cdd:cd12327    79 EP 80

RNA recognition motif 4 (RRM4) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1306253120 133 LRMLPQAATEDDIRGQLQSH--------GVQAREVRLMRNK------SSGQSRGFAFVEFSHLQDA 184
Cdd:cd12416     5 VRNLPKSVDDKKLKKLFLKAvkerakkkGVKIKEVKVMRDKkrlnsdGKGRSKGYGFVEFTEHEHA 70

RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins; This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1306253120 130 IVMLRMLPQAATEDDIRGQLQSHGVQAReVRLMRNKSSGQSRGFAFVEFSHLQDA 184
Cdd:cd12307     1 VVYIGHLPHGFYEPELRKYFSQFGTVTR-LRLSRSKKTGKSKGYAFVEFEDPEVA 54

ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1306253120 136 LPQAATEDDIRGQLQSHGvQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEAnQHSLNILGQKVSMHYSDPKPKINE 215
Cdd:TIGR01661  11 LPQTMTQEEIRSLFTSIG-EIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNS-LNGLRLQNKTIKVSYARPSSDSIK 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1306253120 216 DwlcnkcgvqnfkrrEKCFKCGVPKSEAEQKL-----PLGTRLDQQALPLGGRELSQGL--LPLPQPYQAQGVLtsQALS 288
Cdd:TIGR01661  89 G--------------ANLYVSGLPKTMTQHELesifsPFGQIITSRILSDNVTGLSKGVgfIRFDKRDEADRAI--KTLN 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1306253120 289 qGSEPSSENANDTIILRNLNPHSTMDSILGALapYAVLSSSNVRVIKDKQ------TQLNRGFAFIQLSTIEAAQLLQIL 362
Cdd:TIGR01661 153 -GTTPSGCTEPITVKFANNPSSSNSKGLLSQL--EAVQNPQTTRVPLSTIltaagiGPMHHAAARFRPSAGDFTAVLAHQ 229