NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1907182432|ref|XP_036009113|]
View 

RNA exonuclease 5 isoform X4 [Mus musculus]

Protein Classification

REX1_like and RRM_SF domain-containing protein( domain architecture ID 10150244)

protein containing domains REX1_like, and RRM_SF

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 225-373 1.34e-69

DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.


:

Pssm-ID: 99848  Cd Length: 150  Bit Score: 226.21  E-value: 1.34e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907182432 225 FGLDCEVCLTSMGKELTRISLVTEGGYCLIDELVKPDLKILDYLTSFTGITKEILNPVTTKLKDVQKLLRELLPPDAVLV 304
Cdd:cd06145     1 FALDCEMCYTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTILV 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907182432 305 GHCLDLDLRVLKMIHPYVIDTSLLYAGKQGRRFK--LTFLARVILGKDIQCpNKLGRDGIEDARAALELLQ 373
Cdd:cd06145    81 GHSLENDLKALKLIHPRVIDTAILFPHPRGPPYKpsLKNLAKKYLGRDIQQ-GEGGHDSVEDARAALELVK 150
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 555-625 2.15e-21

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).


The actual alignment was detected with superfamily member cd12274:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 71  Bit Score: 88.38  E-value: 2.15e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907182432 555 IYVAGIGETFKEHLLEQS-NLFPDLEAVILPKEVKSRKQKNYCFLKFKTVNSAQVALEILKGkDWKLKGRNA 625
Cdd:cd12274     1 IYVSGFKKSLTEEDLQERfSQLSDLEAVFLPKDLQSGKHKKYCFLKFRSSQSAQAALDIITG-EWKLKGRRA 71
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 490-544 1.06e-10

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).


The actual alignment was detected with superfamily member cd12273:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 71  Bit Score: 58.32  E-value: 1.06e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1907182432 490 TVYAGPFSKDCNVGALKKVFSSLGPVHSITLVLETYRVRRLVTELTLECDTLVRE 544
Cdd:cd12273     1 TVYAGPFEKSFCLKSVKRLFRSCGPVQSLTVVTETYQPYVCVQYEVLEAAQLAVE 55
 
Name Accession Description Interval E-value
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 225-373 1.34e-69

DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.


Pssm-ID: 99848  Cd Length: 150  Bit Score: 226.21  E-value: 1.34e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907182432 225 FGLDCEVCLTSMGKELTRISLVTEGGYCLIDELVKPDLKILDYLTSFTGITKEILNPVTTKLKDVQKLLRELLPPDAVLV 304
Cdd:cd06145     1 FALDCEMCYTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTILV 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907182432 305 GHCLDLDLRVLKMIHPYVIDTSLLYAGKQGRRFK--LTFLARVILGKDIQCpNKLGRDGIEDARAALELLQ 373
Cdd:cd06145    81 GHSLENDLKALKLIHPRVIDTAILFPHPRGPPYKpsLKNLAKKYLGRDIQQ-GEGGHDSVEDARAALELVK 150
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 224-380 7.86e-27

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 107.39  E-value: 7.86e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907182432  224 LFGLDCE-VCLTSMGKELTRISLV-TEGG--YCLIDELVKPDLKILDYLTSFTGITKEILNPvTTKLKDVQKLLRELLPP 299
Cdd:smart00479   2 LVVIDCEtTGLDPGKDEIIEIAAVdVDGGeiIEVFDTYVKPDRPITDYATEIHGITPEMLDD-APTFEEVLEELLEFLRG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907182432  300 DAVLVGHCLDLDLRVLKMIHP----------YVIDTSLLYAGKQGRRFK--LTFLARVILGKDIQCPNklgrDGIEDARA 367
Cdd:smart00479  81 RILVAGNSAHFDLRFLKLEHPrlgikqppklPVIDTLKLARATNPGLPKysLKKLAKRLLLEVIQRAH----RALDDARA 156

                          170
                   ....*....|...
gi 1907182432  368 ALELLQYFLKYGP 380
Cdd:smart00479 157 TAKLFKKLLERLE 169
RRM2_NEFsp cd12274
RNA recognition motif 2 (RRM2) found in vertebrate putative RNA exonuclease NEF-sp; This ...
 555-625 2.15e-21

RNA recognition motif 2 (RRM2) found in vertebrate putative RNA exonuclease NEF-sp; This subfamily corresponds to the RRM2 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities.


Pssm-ID: 409717 [Multi-domain]  Cd Length: 71  Bit Score: 88.38  E-value: 2.15e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907182432 555 IYVAGIGETFKEHLLEQS-NLFPDLEAVILPKEVKSRKQKNYCFLKFKTVNSAQVALEILKGkDWKLKGRNA 625
Cdd:cd12274     1 IYVSGFKKSLTEEDLQERfSQLSDLEAVFLPKDLQSGKHKKYCFLKFRSSQSAQAALDIITG-EWKLKGRRA 71
RRM1_NEFsp cd12273
RNA recognition motif 1 (RRM1) found in vertebrate putative RNA exonuclease NEF-sp; This ...
 490-544 1.06e-10

RNA recognition motif 1 (RRM1) found in vertebrate putative RNA exonuclease NEF-sp; This subfamily corresponds to the RRM1 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities.


Pssm-ID: 409716 [Multi-domain]  Cd Length: 71  Bit Score: 58.32  E-value: 1.06e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1907182432 490 TVYAGPFSKDCNVGALKKVFSSLGPVHSITLVLETYRVRRLVTELTLECDTLVRE 544
Cdd:cd12273     1 TVYAGPFEKSFCLKSVKRLFRSCGPVQSLTVVTETYQPYVCVQYEVLEAAQLAVE 55
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 227-372 1.60e-08

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 54.66  E-value: 1.60e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907182432 227 LDCE-VCLTSMGKELTRISLV-TEGGYCLIDE----LVKPDL--KILDYLTSFTGITKEILnPVTTKLKDVQKLLRELLP 298
Cdd:pfam00929   3 IDLEtTGLDPEKDEIIEIAAVvIDGGENEIGEtfhtYVKPTRlpKLTDECTKFTGITQAML-DNKPSFEEVLEEFLEFLR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907182432 299 PDAVLVGH-------CLDLDLRVLKMIH----PYVIDT-SLLYAGKQGRRF-KLTFLARVILGKDIQCPNklgrDGIEDA 365
Cdd:pfam00929  82 KGNLLVAHnasfdvgFLRYDDKRFLKKPmpklNPVIDTlILDKATYKELPGrSLDALAEKLGLEHIGRAH----RALDDA 157


                  ....*..
gi 1907182432 366 RAALELL 372
Cdd:pfam00929 158 RATAKLF 164
RRM smart00360
RNA recognition motif;
554-623 9.65e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 46.82  E-value: 9.65e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907182432  554 TIYVAGIGETFKEHLLEQ--SNlFPDLEAVILPKEVKSRKQKNYCFLKFKTVNSAQVALEILKGKdwKLKGR 623
Cdd:smart00360   1 TLFVGNLPPDTTEEELRElfSK-FGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGK--ELDGR 69
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 255-377 1.07e-05

DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 46.68  E-value: 1.07e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907182432 255 DELVKPDLKILDYLTSFTGITKEILN--PvttKLKDVQKLLRELLpPDAVLVGHCLDLDLRVLKM--------IHPYVID 324
Cdd:COG2176    45 STLVNPGRPIPPFITELTGITDEMVAdaP---PFEEVLPEFLEFL-GDAVLVAHNASFDLGFLNAalkrlglpFDNPVLD 120

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907182432 325 TSLL--YAGKQGRRFKLTFLARViLGKDIQcpnklGR-DGIEDARAALELLQYFLK 377
Cdd:COG2176   121 TLELarRLLPELKSYKLDTLAER-LGIPLE-----DRhRALGDAEATAELFLKLLE 170
 
Name Accession Description Interval E-value
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 225-373 1.34e-69

DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.


Pssm-ID: 99848  Cd Length: 150  Bit Score: 226.21  E-value: 1.34e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907182432 225 FGLDCEVCLTSMGKELTRISLVTEGGYCLIDELVKPDLKILDYLTSFTGITKEILNPVTTKLKDVQKLLRELLPPDAVLV 304
Cdd:cd06145     1 FALDCEMCYTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTILV 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907182432 305 GHCLDLDLRVLKMIHPYVIDTSLLYAGKQGRRFK--LTFLARVILGKDIQCpNKLGRDGIEDARAALELLQ 373
Cdd:cd06145    81 GHSLENDLKALKLIHPRVIDTAILFPHPRGPPYKpsLKNLAKKYLGRDIQQ-GEGGHDSVEDARAALELVK 150
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 227-371 5.34e-30

DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins; This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherchia coli RNase T.


Pssm-ID: 99847  Cd Length: 152  Bit Score: 116.08  E-value: 5.34e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907182432 227 LDCE-VCLTSMGKE--LTRISLVTEGGYCLIDELVKPDLKILDYLTSFTGITKEILNPVTTkLKDVQKLLRELLpPDAVL 303
Cdd:cd06144     3 LDCEmVGVGPDGSEsaLARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPD-FEEVQKKVAELL-KGRIL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907182432 304 VGHCLDLDLRVLKMIHPYVI--DTS----LLYAGKqGRRFKLTFLARVILGKDIQCpnkLGRDGIEDARAALEL 371
Cdd:cd06144    81 VGHALKNDLKVLKLDHPKKLirDTSkykpLRKTAK-GKSPSLKKLAKQLLGLDIQE---GEHSSVEDARAAMRL 150
DEDDh_RNase cd06137
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX) ...
 226-373 1.20e-29

DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins; This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong preference for single-stranded RNA.


Pssm-ID: 99840  Cd Length: 161  Bit Score: 115.46  E-value: 1.20e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907182432 226 GLDCEVCLTSMGK-ELTRISLV-TEGGYCLIDELVKPDLKILDYLTSFTGITKEILNPVTTKLKDVQ------KLLRELL 297
Cdd:cd06137     2 ALDCEMVGLADGDsEVVRISAVdVLTGEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEAAKAGKTIFgweaarAALWKFI 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907182432 298 PPDAVLVGHCLDLDLRVLKMIHPYVIDTSLLYAG-----KQGRRFKLTFLARVILGKDIQCPNKlGRDGIEDARAALELL 372
Cdd:cd06137    82 DPDTILVGHSLQNDLDALRMIHTRVVDTAILTREavkgpLAKRQWSLRTLCRDFLGLKIQGGGE-GHDSLEDALAAREVV 160


                  .
gi 1907182432 373 Q 373
Cdd:cd06137   161 L 161
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 224-380 7.86e-27

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 107.39  E-value: 7.86e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907182432  224 LFGLDCE-VCLTSMGKELTRISLV-TEGG--YCLIDELVKPDLKILDYLTSFTGITKEILNPvTTKLKDVQKLLRELLPP 299
Cdd:smart00479   2 LVVIDCEtTGLDPGKDEIIEIAAVdVDGGeiIEVFDTYVKPDRPITDYATEIHGITPEMLDD-APTFEEVLEELLEFLRG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907182432  300 DAVLVGHCLDLDLRVLKMIHP----------YVIDTSLLYAGKQGRRFK--LTFLARVILGKDIQCPNklgrDGIEDARA 367
Cdd:smart00479  81 RILVAGNSAHFDLRFLKLEHPrlgikqppklPVIDTLKLARATNPGLPKysLKKLAKRLLLEVIQRAH----RALDDARA 156

                          170
                   ....*....|...
gi 1907182432  368 ALELLQYFLKYGP 380
Cdd:smart00479 157 TAKLFKKLLERLE 169
RRM2_NEFsp cd12274
RNA recognition motif 2 (RRM2) found in vertebrate putative RNA exonuclease NEF-sp; This ...
 555-625 2.15e-21

RNA recognition motif 2 (RRM2) found in vertebrate putative RNA exonuclease NEF-sp; This subfamily corresponds to the RRM2 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities.


Pssm-ID: 409717 [Multi-domain]  Cd Length: 71  Bit Score: 88.38  E-value: 2.15e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907182432 555 IYVAGIGETFKEHLLEQS-NLFPDLEAVILPKEVKSRKQKNYCFLKFKTVNSAQVALEILKGkDWKLKGRNA 625
Cdd:cd12274     1 IYVSGFKKSLTEEDLQERfSQLSDLEAVFLPKDLQSGKHKKYCFLKFRSSQSAQAALDIITG-EWKLKGRRA 71
PAN2_exo cd06143
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic ...
 240-373 4.30e-21

DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.


Pssm-ID: 99846  Cd Length: 174  Bit Score: 91.14  E-value: 4.30e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907182432 240 LTRISLV----TEGGYCLIDELVKPDLKILDYLTSFTGITKEILNPVT-----TKLKDVQKLLRELLPPDAVLVGHCLDL 310
Cdd:cd06143    33 LARVSVVrgegELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLDPKTssknlTTLKSAYLKLRLLVDLGCIFVGHGLAK 112

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907182432 311 DLRVLKMIHP--YVIDTSLLYAGKQGRRFKLTFLARVILGKDIQCPNklgRDGIEDARAALELLQ 373
Cdd:cd06143   113 DFRVINIQVPkeQVIDTVELFHLPGQRKLSLRFLAWYLLGEKIQSET---HDSIEDARTALKLYR 174
ISG20 cd06149
DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar ...
 227-373 6.30e-16

DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins; Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and replication. It may carry out its function by degrading viral RNAs as part of the IFN-regulated antiviral response.


Pssm-ID: 99852  Cd Length: 157  Bit Score: 75.94  E-value: 6.30e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907182432 227 LDCEVCLTSMG---KELTRISLVTEGGYCLIDELVKPDLKILDYLTSFTGITKEIL---NPVTTKLKDVQKLLRellppD 300
Cdd:cd06149     3 IDCEMVGTGPGgreSELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLvnaTPFAVAQKEILKILK-----G 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907182432 301 AVLVGHCLDLDLRVLKMIHP--YVIDTS---LL---YAGKQGRRFKLTFLARVILGKDIQCpNKLGRDGIEDARAALELL 372
Cdd:cd06149    78 KVVVGHAIHNDFKALKYFHPkhMTRDTStipLLnrkAGFPENCRVSLKVLAKRLLHRDIQV-GRQGHSSVEDARATMELY 156


                  .
gi 1907182432 373 Q 373
Cdd:cd06149   157 K 157
RRM1_NEFsp cd12273
RNA recognition motif 1 (RRM1) found in vertebrate putative RNA exonuclease NEF-sp; This ...
 490-544 1.06e-10

RNA recognition motif 1 (RRM1) found in vertebrate putative RNA exonuclease NEF-sp; This subfamily corresponds to the RRM1 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities.


Pssm-ID: 409716 [Multi-domain]  Cd Length: 71  Bit Score: 58.32  E-value: 1.06e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1907182432 490 TVYAGPFSKDCNVGALKKVFSSLGPVHSITLVLETYRVRRLVTELTLECDTLVRE 544
Cdd:cd12273     1 TVYAGPFEKSFCLKSVKRLFRSCGPVQSLTVVTETYQPYVCVQYEVLEAAQLAVE 55
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 227-372 1.60e-08

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 54.66  E-value: 1.60e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907182432 227 LDCE-VCLTSMGKELTRISLV-TEGGYCLIDE----LVKPDL--KILDYLTSFTGITKEILnPVTTKLKDVQKLLRELLP 298
Cdd:pfam00929   3 IDLEtTGLDPEKDEIIEIAAVvIDGGENEIGEtfhtYVKPTRlpKLTDECTKFTGITQAML-DNKPSFEEVLEEFLEFLR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907182432 299 PDAVLVGH-------CLDLDLRVLKMIH----PYVIDT-SLLYAGKQGRRF-KLTFLARVILGKDIQCPNklgrDGIEDA 365
Cdd:pfam00929  82 KGNLLVAHnasfdvgFLRYDDKRFLKKPmpklNPVIDTlILDKATYKELPGrSLDALAEKLGLEHIGRAH----RALDDA 157


                  ....*..
gi 1907182432 366 RAALELL 372
Cdd:pfam00929 158 RATAKLF 164
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 255-373 8.01e-08

DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.


Pssm-ID: 176648 [Multi-domain]  Cd Length: 159  Bit Score: 52.69  E-value: 8.01e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907182432 255 DELVKPDLKILDYLTSFTGITKEILNPVTTkLKDVQKLLRELLPpDAVLVGHCLDLDLRVLK---------MIHPYVIDT 325
Cdd:cd06127    36 ETLVNPGRPIPPEATAIHGITDEMLADAPP-FEEVLPEFLEFLG-GRVLVAHNASFDLRFLNrelrrlggpPLPNPWIDT 113

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1907182432 326 SLLYA--GKQGRRFKLTFLARVILGkdiqCPNKLGRDGIEDARAALELLQ 373
Cdd:cd06127   114 LRLARrlLPGLRSHRLGLLLAERYG----IPLEGAHRALADALATAELLL 159
RRM smart00360
RNA recognition motif;
554-623 9.65e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 46.82  E-value: 9.65e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907182432  554 TIYVAGIGETFKEHLLEQ--SNlFPDLEAVILPKEVKSRKQKNYCFLKFKTVNSAQVALEILKGKdwKLKGR 623
Cdd:smart00360   1 TLFVGNLPPDTTEEELRElfSK-FGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGK--ELDGR 69
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 255-377 1.07e-05

DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 46.68  E-value: 1.07e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907182432 255 DELVKPDLKILDYLTSFTGITKEILN--PvttKLKDVQKLLRELLpPDAVLVGHCLDLDLRVLKM--------IHPYVID 324
Cdd:COG2176    45 STLVNPGRPIPPFITELTGITDEMVAdaP---PFEEVLPEFLEFL-GDAVLVAHNASFDLGFLNAalkrlglpFDNPVLD 120

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907182432 325 TSLL--YAGKQGRRFKLTFLARViLGKDIQcpnklGR-DGIEDARAALELLQYFLK 377
Cdd:COG2176   121 TLELarRLLPELKSYKLDTLAER-LGIPLE-----DRhRALGDAEATAELFLKLLE 170
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 257-377 2.97e-05

DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 45.17  E-value: 2.97e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907182432 257 LVKPDLKILDYLTSFTGITKEILN--PvttKLKDVQKLLRELLpPDAVLVGHCLDLDLRVL---------KMIHPYVIDT 325
Cdd:COG0847    39 LVNPERPIPPEATAIHGITDEDVAdaP---PFAEVLPELLEFL-GGAVLVAHNAAFDLGFLnaelrraglPLPPFPVLDT 114

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1907182432 326 SLLYAGK--QGRRFKLTFLARViLGKDIQcpnklGR-DGIEDARAALELLQYFLK 377
Cdd:COG0847   115 LRLARRLlpGLPSYSLDALCER-LGIPFD-----ERhRALADAEATAELFLALLR 163
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 555-623 2.58e-04

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).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 39.96  E-value: 2.58e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907182432 555 IYVAGIGETFKEHLLEQ--SNlFPDLEAVILPKEvKSRKQKNYCFLKFKTVNSAQVALEILKGKdwKLKGR 623
Cdd:cd00590     1 LFVGNLPPDTTEEDLRElfSK-FGEVVSVRIVRD-RDGKSKGFAFVEFESPEDAEKALEALNGT--ELGGR 67
RRM2_hnRNPD cd12583
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) ...
 555-601 2.43e-03

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically.


Pssm-ID: 241027 [Multi-domain]  Cd Length: 75  Bit Score: 37.29  E-value: 2.43e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1907182432 555 IYVAGIG-ETFKEHLLEQSNLFPDLEAVILPKEVKSRKQKNYCFLKFK 601
Cdd:cd12583     2 IFVGGLSpDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFK 49
RRM1_PUF60 cd12370
RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins; ...
 555-624 7.35e-03

RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM1 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). PUF60 is 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. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.


Pssm-ID: 409805 [Multi-domain]  Cd Length: 76  Bit Score: 36.24  E-value: 7.35e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907182432 555 IYVAGIGETFKEHLLEQS-NLFPDLEAVILPKEVKSRKQKNYCFLKFKTVNSAQVALEILKGkdWKLKGRN 624
Cdd:cd12370     3 VYVGSIYFELGEDTIRQAfAPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQMNG--VMLGGRN 71
RRM_TRMT2A cd12439
RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and ...
 584-619 7.98e-03

RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins; This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases.


Pssm-ID: 409873 [Multi-domain]  Cd Length: 79  Bit Score: 36.07  E-value: 7.98e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1907182432 584 PKEVKSRKQKNYCFLKFKTVNSAQVALEILKGKDWK 619
Cdd:cd12439    33 PHKIKLIGRQTFAFVTFRNEEDRDKALKVLNGHKWK 68
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH