RNA recognition motif 2 (RRM2) found in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins; This subfamily corresponds to the RRM2 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528 264 ERVVILKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFREPEEADHCIQTLDGRWFGGRQI 343
Cdd:cd12282    1 EKVVILKNMFHPKEFEEDPELINEIKEDLREECEKFGQVKKVVVFDRHPDGVASVKFKEPEEADKCIQALNGRWFAGRKL 80

                         90
                 ....*....|.
gi 321267528 344 TAQAWDGTTDY 354
Cdd:cd12282   81 EAETWDGKTDY 91

RNA recognition motif 2 (RRM2) found in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins; This subfamily corresponds to the RRM2 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528 264 ERVVILKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFREPEEADHCIQTLDGRWFGGRQI 343
Cdd:cd12282    1 EKVVILKNMFHPKEFEEDPELINEIKEDLREECEKFGQVKKVVVFDRHPDGVASVKFKEPEEADKCIQALNGRWFAGRKL 80

                         90
                 ....*....|.
gi 321267528 344 TAQAWDGTTDY 354
Cdd:cd12282   81 EAETWDGKTDY 91

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528  134 TNVYVSGLPPDITVDEFIQLMSKFGIIMrdpqteefKVKLYKDDQGNLKGDGLCCYLKKESVELALKLLDEDEI----RG 209
Cdd:TIGR01628 179 TNLYVKNLDPSVNEDKLRELFAKFGEIT--------SAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIglakEG 250

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528  210 YKLHveVAKFQLKGEYDASKKKKkckdykkklsLQQKQLDwRPERRAGPNrlrhervVILKNMfhpmdfedDPLVLNeir 289
Cdd:TIGR01628 251 KKLY--VGRAQKRAEREAELRRK----------FEELQQE-RKMKAQGVN-------LYVKNL--------DDTVTD--- 299

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 321267528  290 EDLRVECSKFGQIR--KLLLFD-RHPDGVASVSFREPEEADHCIQTLDGRWFGGR 341
Cdd:TIGR01628 300 EKLRELFSECGEITsaKVMLDEkGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGK 354

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 321267528  136 VYVSGLPPDITVDEFIQLMSKFGIIMRdpqteefkVKLYKDDQGNLKGDGLCCYLKKESVELALKLLDEDEIRGYKLH 213
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKS--------IRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying compounds]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528   404 SEHPSMSNMKAQEATTGMAFEETIDENKFEkAEEGGESEGDASEKDAkEGGSDGdhpEREGGEgcsKKENEEGCPERALE 483
Cdd:TIGR00927  704 ADHKGETEAEEVEHEGETEAEGTEDEGEIE-TGEEGEEVEDEGEGEA-EGKHEV---ETEGDR---KETEHEGETEAEGK 775

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528   484 PEEGNPQTEAQENGPEREARKKSKMDYEKNGFSKESEDNDLGKESEGEDSLKKESEDDDSEEESEEDSSEKQSQDGSDKE 563
Cdd:TIGR00927  776 EDEDEGEIQAGEDGEMKGDEGAEGKVEHEGETEAGEKDEHEGQSETQADDTEVKDETGEQELNAENQGEAKQDEKGVDGG 855

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 321267528   564 IEENGvkkdvdQDVSDKEFPEDVEKESEENETDKSEFDEGSERVL 608
Cdd:TIGR00927  856 GGSDG------GDSEEEEEEEEEEEEEEEEEEEEEEEEEENEEPL 894

RNA recognition motif 2 (RRM2) found in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins; This subfamily corresponds to the RRM2 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528 264 ERVVILKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFREPEEADHCIQTLDGRWFGGRQI 343
Cdd:cd12282    1 EKVVILKNMFHPKEFEEDPELINEIKEDLREECEKFGQVKKVVVFDRHPDGVASVKFKEPEEADKCIQALNGRWFAGRKL 80

                         90
                 ....*....|.
gi 321267528 344 TAQAWDGTTDY 354
Cdd:cd12282   81 EAETWDGKTDY 91

RNA recognition motif 3 (RRM3) found in UHM domain of poly(U)-binding-splicing factor PUF60 and similar proteins; This subgroup corresponds to the RRM3 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1), an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. The research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528 265 RVVILKNMFHPMDFEDDplvlneIREDLRVECSKFGQIRKLLLF------DRHPDGVAS--VSFREPEEADHCIQTLDGR 336
Cdd:cd12648    2 RVMVLRNMVGPEDIDDD------LEGEVTEECGKFGAVNRVIIYqekqgeEEDAEIIVKifVEFSMPSEAEKAIQALNGR 75

                         90
                 ....*....|....*
gi 321267528 337 WFGGRQITAQAWDGT 351
Cdd:cd12648   76 WFGGRKVVAELYDQT 90

RNA recognition motif (RRM) found in the FET family of RNA-binding proteins; This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528 136 VYVSGLPPDITVDEFIQLMSKFGIIMRDPQTEEFKVKLYKDDQ-GNLKGDGLCCYLKKESVELALKLLDEDEIRGYKLHV 214
Cdd:cd12280    1 IFVSGLPPDVTIDELADLFGQIGIIKRYKDTWPPKIKIYTDKEtGKPKGEATLTYEDPSAAKAAIEWFNGKEFRGNKIKV 80

                 .
gi 321267528 215 E 215
Cdd:cd12280   81 S 81

RNA recognition motif 3 (RRM3) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins; This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528 265 RVVILKNMFHPMDFEDDPLVlNEIREDLRVECSKFGQIRKLLLFDRHPDGVAS-------VSFREPEEADHCIQTLDGRW 337
Cdd:cd12232    2 RVLCLLNMVTPEELEDDEEY-EEILEDVKEECSKYGKVLSVVIPRPEAEGVDVpgvgkvfVEFEDVEDAQKAQKALAGRK 80

                 ....*....
gi 321267528 338 FGGRQITAQ 346
Cdd:cd12232   81 FDGRTVVAS 89

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528  134 TNVYVSGLPPDITVDEFIQLMSKFGIIMrdpqteefKVKLYKDDQGNLKGDGLCCYLKKESVELALKLLDEDEI----RG 209
Cdd:TIGR01628 179 TNLYVKNLDPSVNEDKLRELFAKFGEIT--------SAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIglakEG 250

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528  210 YKLHveVAKFQLKGEYDASKKKKkckdykkklsLQQKQLDwRPERRAGPNrlrhervVILKNMfhpmdfedDPLVLNeir 289
Cdd:TIGR01628 251 KKLY--VGRAQKRAEREAELRRK----------FEELQQE-RKMKAQGVN-------LYVKNL--------DDTVTD--- 299

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 321267528  290 EDLRVECSKFGQIR--KLLLFD-RHPDGVASVSFREPEEADHCIQTLDGRWFGGR 341
Cdd:TIGR01628 300 EKLRELFSECGEITsaKVMLDEkGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGK 354

RNA recognition motif;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528   135 NVYVSGLPPDITVDEFIQLMSKFGIIMRdpqteefkVKLYKD-DQGNLKGDGLCCYLKKESVELALKLLDEDEIRGYKLH 213
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVES--------VRLVRDkETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLK 72

                   .
gi 321267528   214 V 214
Cdd:smart00360  73 V 73

RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins; This subgroup corresponds to the RRM of SPF45, also termed RNA-binding motif protein 17 (RBM17), an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528 265 RVVILKNMFHPMDFEDDplvlneIREDLRVECSKFGQIRKLLLFD--RHPDGVAS---VSFREPEEADHCIQTLDGRWFG 339
Cdd:cd12647    3 KVVLLRNMVGPGEVDED------LEPEVKEECEKYGKVTKVVIFEipGAPDDEAVrifVEFERVESAIKAVVDLNGRFFG 76

                         90
                 ....*....|
gi 321267528 340 GRQITAQAWD 349
Cdd:cd12647   77 GRTVKASFYD 86

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 321267528  136 VYVSGLPPDITVDEFIQLMSKFGIIMRdpqteefkVKLYKDDQGNLKGDGLCCYLKKESVELALKLLDEDEIRGYKLH 213
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKS--------IRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528  129 EEDRntnVYVSGLPPDITVDEFIQLMSKFGIIMrdpqteefKVKLYKD-DQGNLKGDGLCCYLKKESVELALKLLDEDEI 207
Cdd:TIGR01642 294 SKDR---IYIGNLPLYLGEDQIKELLESFGDLK--------AFNLIKDiATGLSKGYAFCEYKDPSVTDVAIAALNGKDT 362

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528  208 RGYKLHVEVAKFQLK-GEYDASKKKKKCKDYKKKLSLQQKQLDWRPERragpnrlrherVVILKNMFHPMDFEDDPlVLN 286
Cdd:TIGR01642 363 GDNKLHVQRACVGANqATIDTSNGMAPVTLLAKALSQSILQIGGKPTK-----------VVQLTNLVTGDDLMDDE-EYE 430

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 321267528  287 EIREDLRVECSKFGQIRKLLLFDRHPDGVAS-------VSFREPEEADHCIQTLDGRWFGGRQITA 345
Cdd:TIGR01642 431 EIYEDVKTEFSKYGPLINIVIPRPNGDRNSTpgvgkvfLEYADVRSAEKAMEGMNGRKFNDRVVVA 496

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 321267528  289 REDLRVECSKFGQIRKLLLF---DRHPDGVASVSFREPEEADHCIQTLDGRWFGGRQIT 344
Cdd:pfam00076  12 EEDLKDLFSKFGPIKSIRLVrdeTGRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

RNA recognition motif 1 (RRM1) found in the c-myc gene single-strand binding proteins (MSSP) family; This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528 134 TNVYVSGLPPDITVDEFIQLMSKFGIIMrdpqteefKVKLYKDDQGNL-KGDGLCCYLKKESVELALKLL 202
Cdd:cd12243    1 TNVYIRGLPPNTTDEDLLLLCQSFGKII--------STKAIIDKQTNKcKGYGFVDFDSPEAALKAIEGL 62

RNA recognition motif (RRM) found in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins; This subfamily corresponds to the RRM of NOT4, also termed CCR4-associated factor 4, or E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4Hp, a component of the CCR4-NOT complex, a global negative regulator of RNA polymerase II transcription. NOT4 functions as an ubiquitin-protein ligase (E3). It contains an N-terminal C4C4 type RING finger motif, followed by a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RING fingers may interact with a subset of ubiquitin-conjugating enzymes (E2s), including UbcH5B, and mediate protein-protein interactions. T

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 321267528 298 KFGQIRKLLLFDRHPDGV-------ASVSFREPEEADHCIQTLDGRWFGGRQITAQAwdGTTDY 354
Cdd:cd12438   31 QYGKIKKIVINRSTSYAGsqgpsasAYVTYSRKEDALRAIQAVDGFVLDGRTLKASF--GTTKY 92

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins; This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 321267528 290 EDLRVECSKFGQIRK----LLLFDRHPDGVASVSFREPEEADHCIQTLDGRWFGGRQITAQ 346
Cdd:cd12312   15 DDLRREFGRYGPIVDvyipLDFYTRRPRGFAYIQFEDVRDAEDALYYLDRTRFLGREIEIQ 75

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 25 and similar proteins; This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528 134 TNVYVSGLPPDITvDEFI-QLMSKFGIIMRdpqteefkVKLYKDDQGNLKGDGLCCYLKKESVELALKLLDEDEIRGYKL 212
Cdd:cd12446    1 TTVFVGNIPDDVS-DDFIrQLLEKCGKVLS--------WKRVQDPSGKLKAFGFCEFEDPEGALRALRLLNGLELGGKKL 71

                 ....
gi 321267528 213 HVEV 216
Cdd:cd12446   72 LVKV 75

RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases; This subfamily corresponds to the RRM of the Set1-like family of histone-lysine N-methyltransferases which includes Set1A and Set1B that are ubiquitously expressed vertebrates histone methyltransferases exhibiting high homology to yeast Set1. Set1A and Set1B proteins exhibit a largely non-overlapping subnuclear distribution in euchromatic nuclear speckles, strongly suggesting that they bind to a unique set of target genes and thus make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. With the exception of the catalytic component, the subunit composition of the Set1A and Set1B histone methyltransferase complexes are identical. Each complex contains six human homologs of the yeast Set1/COMPASS complex, including Set1A or Set1B, Ash2 (homologous to yeast Bre2), CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). The genomic targeting of these complexes is determined by the identity of the catalytic subunit present in each histone methyltransferase complex. Thus, the Set1A and Set1B complexes may exhibit both overlapping and non-redundant properties. Both Set1A and Set1B contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. In contrast to Set1B, Set1A additionally contains an HCF-1 binding motif that interacts with HCF-1 in vivo.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 321267528 285 LNE-IRED-LRVECSKFGQIRKLLLFdRHPD-----GVASVSFREPEEADHCIQTLDGRWFGGRQITAQ 346
Cdd:cd12304   10 LNDnINEGfLKDMCKKYGEVEEVKIY-FHPKtgkhlGLARVVFDTTKGAKDCVEKLNQTSVMGNIIHVF 77

K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying compounds]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528   404 SEHPSMSNMKAQEATTGMAFEETIDENKFEKAEEGGESEGDASEK------------DAKEGGSDGDHPEREGGEGCSKK 471
Cdd:TIGR00927  636 AEAEHTGERTGEEGERPTEAEGENGEESGGEAEQEGETETKGENEsegeipaerkgeQEGEGEIEAKEADHKGETEAEEV 715

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528   472 ENEEGCPERALEPE-EGNPQTEAQENGPEREARKKSKMDYEKNGFSKESE----DNDLGKESEGEDSLKKESEDDDSEEE 546
Cdd:TIGR00927  716 EHEGETEAEGTEDEgEIETGEEGEEVEDEGEGEAEGKHEVETEGDRKETEhegeTEAEGKEDEDEGEIQAGEDGEMKGDE 795

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528   547 SEEDSSEKQSQDGSDKEIEENGVkkdvDQDVSDKEFPEDVEKESEENETDKSEFDEGSERVLDEEGSEREFEEDSDEKEE 626
Cdd:TIGR00927  796 GAEGKVEHEGETEAGEKDEHEGQ----SETQADDTEVKDETGEQELNAENQGEAKQDEKGVDGGGGSDGGDSEEEEEEEE 871

                   ...
gi 321267528   627 EGD 629
Cdd:TIGR00927  872 EEE 874

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins; This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 321267528 289 REDLRVECSKFGQIRKLLLfDRHPDGVASVSFREPEEADHCIQTLDGRWFGGRQIT 344
Cdd:cd12373   13 KRELEDAFEKYGPLRNVWV-ARNPPGFAFVEFEDPRDAEDAVRALDGRRICGSRVR 67

RNA recognition motif (RRM) found in vertebrate Ewing Sarcoma Protein (EWS); This subgroup corresponds to the RRM of EWS, also termed Ewing sarcoma breakpoint region 1 protein, a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multifunctional protein and may play roles in transcription and RNA processing. EWS is involved in transcriptional regulation by interacting with the preinitiation complex TFIID and the RNA polymerase II (RNAPII) complexes. It is also associated with splicing factors, such as the U1 snRNP protein U1C, suggesting its implication in pre-mRNA splicing. Additionally, EWS has been shown to regulate DNA damage-induced alternative splicing (AS). Like other members in the FET family, EWS contains an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. EWS specifically binds to poly G and poly U RNA. It also binds to the proximal-element DNA of the macrophage-specific promoter of the CSF-1 receptor gene.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528 136 VYVSGLPPDITVDEFIQLMSKFGIIMRDPQTEEFKVKLYKD-DQGNLKGDGLCCYLKKESVELALKLLDEDEIRGYKLHV 214
Cdd:cd12533    3 IYVQGLNENVTLEELADFFKHCGVVKINKRTGQPMINIYTDkETGKPKGDATVSYEDPPAAKAAVEWFDGKDFQGNKLKV 82

RNA recognition motif;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 321267528   295 ECSKFGQIRKLLLF-------DRHPDGVASVSFREPEEADHCIQTLDGRWFGGRQITA 345
Cdd:smart00361  12 EEEYFGEVGKINKIyiddvgyENHKRGNVYITFERSEDAARAIVDLNGRYFDGRLVKA 69

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins; This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528 136 VYVSGLPPDITVDEFIQLMSKFGIIMRdpqteeFKVkLYKDDQGNLKGDGLCCYLKKESVELALKLLDEDEIRGYKLHVE 215
Cdd:cd12398    3 VFVGNIPYDATEEQLKEIFSEVGPVVS------FRL-VTDRETGKPKGYGFCEFRDAETALSAVRNLNGYELNGRPLRVD 75

                 ..
gi 321267528 216 VA 217
Cdd:cd12398   76 FA 77

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528 136 VYVSGLPPDITVDEFIQLMSKFGIImrdpqteeFKVKLYKDDQGNLKGDGLCCYLKKESVELALKLLDEDEIRGYKlHVE 215
Cdd:cd12249    4 VFVGKIPRDVFEDELVPLFEKCGKI--------YELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKTLNNYEIRPGK-LLG 74

                 .
gi 321267528 216 V 216
Cdd:cd12249   75 V 75

RNA recognition motif 2 (RRM2) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. 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 RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 321267528 134 TNVYVSGLPPDITVDEFIQLMSKFGI-----IMRDPQTeefkvklykddqGNLKGDGLCCYLKKESVELALKLLD 203
Cdd:cd12376    1 ANLYVSGLPKTMTQKELEQLFSQYGRiitsrILRDQLT------------GVSRGVGFIRFDKRIEAEEAIKGLN 63

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 321267528 290 EDLRVECSKFGQIRKL-LLFDRH---PDGVASVSFREPEEADHCIQTLDGRWFGGRQI 343
Cdd:cd12353   14 EDLKEAFAPFGEISDArVVKDTQtgkSKGYGFVSFVKKEDAENAIQGMNGQWLGGRNI 71

RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528 136 VYVSGLPPDITVDEFIQLMSKFGIIMRdpqteefkVKLYKDDQGNL-KGDGLCCYLKKESVELALKlLDEDEIRGYKLHV 214
Cdd:cd12395    2 VFVGNLPFDIEEEELRKHFEDCGDVEA--------VRIVRDRETGIgKGFGYVLFKDKDSVDLALK-LNGSKLRGRKLRV 72

                 .
gi 321267528 215 E 215
Cdd:cd12395   73 K 73

K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying compounds]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 321267528   421 MAFEETIDENKFEkAEEGGESEGDASEKdakEGGSDGDHPEREGGEgcskKENEEGCPERALEPEEGNPQTEAQ-ENGPE 499
Cdd:TIGR00927  625 MALGDLSKGDVAE-AEHTGERTGEEGER---PTEAEGENGEESGGE----AEQEGETETKGENESEGEIPAERKgEQEGE 696