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Conserved domains on  [gi|1958659325|ref|XP_038942181|]
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poly(A)-specific ribonuclease PARN isoform X11 [Rattus norvegicus]

Protein Classification

RNA-binding protein( domain architecture ID 10522120)

RNA-binding protein containing an RNA recognition motif (RRM)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CAF1 pfam04857
CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with ...
 5-383 1.18e-137

CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with shortening of the polyA tail. CAF1 encodes a critical component of the major cytoplasmic deadenylase in yeast. Both Caf1p is required for normal mRNA deadenylation in vivo and localizes to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent polyA-specific exonuclease activity. Some members of this family include and inserted RNA binding domain pfam01424. This family of proteins is related to other exonucleases pfam00929 (Bateman A pers. obs.). The crystal structure of Saccharomyces cerevisiae Pop2 has been resolved at 2.3 Angstrom resolution.


:

Pssm-ID: 461457  Cd Length: 375  Bit Score: 401.79  E-value: 1.18e-137
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659325   5 RSNFKINLPKVYQAIEEADFFAIDGEFSGISdgpSVTALTSGFDTPEERYQKLKKHSMDFLLFQFGLCAFKYDHANSKHV 84
Cdd:pfam04857   3 RSNFKELLPEILKAIKEADFVAIDLEFTGLG---SPWRKSSLFDTPEERYLKLRDAAERFSILQFGLCCFREDEEKSKYT 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659325  85 TKSFNFYVFPKPFSrsSPDVKFVCQSSSIDFLASQGFDFNKVFCSGIPYLNQEEERQLREQFDEKRsqangaGALTKCPV 164
Cdd:pfam04857  80 AKPYNFYLFPRTEL--DPDRDFSCQASSLQFLAKHGFDFNKLFYEGIPYLSRAEEEKLRERLEERQ------QASPSDIP 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659325 165 TIPEDQKKFIDQVIEKIEGFLQREEKRTLELNPCTGFQRKLIYQTLSWKYPKGIHVETLETDKKERHIVISKVDEEERKR 244
Cdd:pfam04857 152 LLDVEDKEFVERVRSKIKEWLDSGEDKGEKLNIDNPVSRLLLQQLLKHQLVRVLLVELLSRGKQKVVQVVKKSSEDEELL 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659325 245 REQEKYAKEQEELNDAVGFSRVIHAIANSGKLVVGHNMLLDVMHTIHQFYCPLPVDLNEFKEMTTCVFPRLLDTKLMAST 324
Cdd:pfam04857 232 EKEEKKDEEEERLESAVGFRLVFDALSKSRKPIVGHNGLLDLLFLYQQFYGPLPETLEEFKALIHELFPGIYDTKYLATT 311

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958659325 325 Q-PFKDIINNTSLAELEKRLKETPFDPPKVESAEGFPSYDT----ASEQLHEAGYDAYITGLCF 383
Cdd:pfam04857 312 DaEFKVRLPSSSLEELFEKLCKENFSSPSVETPPFESDYHDesskYGGKAHEAGYDAYMTGYVF 375
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 431-463 4.91e-14

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 pfam08675:

Pssm-ID: 473069  Cd Length: 75  Bit Score: 66.99  E-value: 4.91e-14
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1958659325 431 PDLQPKRDHVLHVTFPKEWKTSDLYQLFSAFGS 463
Cdd:pfam08675   1 KDPNPSREHVFHVTFPKEWKTSDILQLFSPFGG 33
 
Name Accession Description Interval E-value
CAF1 pfam04857
CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with ...
 5-383 1.18e-137

CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with shortening of the polyA tail. CAF1 encodes a critical component of the major cytoplasmic deadenylase in yeast. Both Caf1p is required for normal mRNA deadenylation in vivo and localizes to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent polyA-specific exonuclease activity. Some members of this family include and inserted RNA binding domain pfam01424. This family of proteins is related to other exonucleases pfam00929 (Bateman A pers. obs.). The crystal structure of Saccharomyces cerevisiae Pop2 has been resolved at 2.3 Angstrom resolution.


Pssm-ID: 461457  Cd Length: 375  Bit Score: 401.79  E-value: 1.18e-137
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659325   5 RSNFKINLPKVYQAIEEADFFAIDGEFSGISdgpSVTALTSGFDTPEERYQKLKKHSMDFLLFQFGLCAFKYDHANSKHV 84
Cdd:pfam04857   3 RSNFKELLPEILKAIKEADFVAIDLEFTGLG---SPWRKSSLFDTPEERYLKLRDAAERFSILQFGLCCFREDEEKSKYT 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659325  85 TKSFNFYVFPKPFSrsSPDVKFVCQSSSIDFLASQGFDFNKVFCSGIPYLNQEEERQLREQFDEKRsqangaGALTKCPV 164
Cdd:pfam04857  80 AKPYNFYLFPRTEL--DPDRDFSCQASSLQFLAKHGFDFNKLFYEGIPYLSRAEEEKLRERLEERQ------QASPSDIP 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659325 165 TIPEDQKKFIDQVIEKIEGFLQREEKRTLELNPCTGFQRKLIYQTLSWKYPKGIHVETLETDKKERHIVISKVDEEERKR 244
Cdd:pfam04857 152 LLDVEDKEFVERVRSKIKEWLDSGEDKGEKLNIDNPVSRLLLQQLLKHQLVRVLLVELLSRGKQKVVQVVKKSSEDEELL 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659325 245 REQEKYAKEQEELNDAVGFSRVIHAIANSGKLVVGHNMLLDVMHTIHQFYCPLPVDLNEFKEMTTCVFPRLLDTKLMAST 324
Cdd:pfam04857 232 EKEEKKDEEEERLESAVGFRLVFDALSKSRKPIVGHNGLLDLLFLYQQFYGPLPETLEEFKALIHELFPGIYDTKYLATT 311

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958659325 325 Q-PFKDIINNTSLAELEKRLKETPFDPPKVESAEGFPSYDT----ASEQLHEAGYDAYITGLCF 383
Cdd:pfam04857 312 DaEFKVRLPSSSLEELFEKLCKENFSSPSVETPPFESDYHDesskYGGKAHEAGYDAYMTGYVF 375
R3H_PARN cd02637
R3H domain of Poly(A)-specific ribonuclease (PARN). PARN is a poly(A)-specific 3' exonuclease ...
 174-238 1.21e-24

R3H domain of Poly(A)-specific ribonuclease (PARN). PARN is a poly(A)-specific 3' exonuclease from the RNase D family that, in Xenopus, deadenylates a specific class of maternal mRNAs which results in their translational repression. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.


Pssm-ID: 100066 [Multi-domain]  Cd Length: 65  Bit Score: 96.62  E-value: 1.21e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958659325 174 IDQVIEKIEGFLQREEKRtLELNPCTGFQRKLIYQTLSWKYPKGIHVETLETDKKERHIVISKVD 238
Cdd:cd02637     1 IDEVIERIEAFLESEEDD-LELEPCNGFQRKLIYQTLEQKYPKGIHVETLETEKKERLIVIEKGD 64
RNA_bind pfam08675
RNA binding domain; This domain corresponds to the RNA binding domain of Poly(A)-specific ...
 431-463 4.91e-14

RNA binding domain; This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN).


Pssm-ID: 400835  Cd Length: 75  Bit Score: 66.99  E-value: 4.91e-14
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1958659325 431 PDLQPKRDHVLHVTFPKEWKTSDLYQLFSAFGS 463
Cdd:pfam08675   1 KDPNPSREHVFHVTFPKEWKTSDILQLFSPFGG 33
RRM_PARN cd12428
RNA recognition motif (RRM) found in poly(A)-specific ribonuclease PARN and similar proteins; ...
 437-462 5.49e-12

RNA recognition motif (RRM) found in poly(A)-specific ribonuclease PARN and similar proteins; The subfamily corresponds to the RRM of PARN, also termed deadenylating nuclease, or deadenylation nuclease, or polyadenylate-specific ribonuclease, a processive poly(A)-specific 3'-exoribonuclease involved in the decay of eukaryotic mRNAs. It specifically binds both, the poly(A) tail at the 3' end and the 7-methylguanosine (m7G) cap located at the 5' end of eukaryotic mRNAs, and catalyzes the 3'- to 5'-end deadenylation of single-stranded mRNA with a free 3' hydroxyl group both in the nucleus and in the cytoplasm. PARN belongs to the DEDD superfamily of exonucleases. It contains a nuclease domain, an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an R3H domain. PARN exists as a homodimer. The nuclease domain is involved in the dimerization. RRM and R3H domains are essential for the RNA-binding.


Pssm-ID: 409862 [Multi-domain]  Cd Length: 66  Bit Score: 60.78  E-value: 5.49e-12
                          10        20
                  ....*....|....*....|....*.
gi 1958659325 437 RDHVLHVTFPKEWKTSDLYQLFSAFG 462
Cdd:cd12428     1 RDHVFHLTFPKEWKTSDLYQLFSPFG 26
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 255-388 9.99e-03

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 37.08  E-value: 9.99e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659325 255 EELNDAVGFSRVIHAIAN--SGKLVVGHNMLLDV---MHTIHQFYCPLPVdlnefkemttcvfPRLLDTKLMAsTQPFKD 329
Cdd:COG0847    59 EDVADAPPFAEVLPELLEflGGAVLVAHNAAFDLgflNAELRRAGLPLPP-------------FPVLDTLRLA-RRLLPG 124

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958659325 330 IINNtSLAELEKRLketpfdppkvesaeGFPSYDTaseqlHEAGYDAYITGLCFISMAN 388
Cdd:COG0847   125 LPSY-SLDALCERL--------------GIPFDER-----HRALADAEATAELFLALLR 163
 
Name Accession Description Interval E-value
CAF1 pfam04857
CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with ...
 5-383 1.18e-137

CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with shortening of the polyA tail. CAF1 encodes a critical component of the major cytoplasmic deadenylase in yeast. Both Caf1p is required for normal mRNA deadenylation in vivo and localizes to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent polyA-specific exonuclease activity. Some members of this family include and inserted RNA binding domain pfam01424. This family of proteins is related to other exonucleases pfam00929 (Bateman A pers. obs.). The crystal structure of Saccharomyces cerevisiae Pop2 has been resolved at 2.3 Angstrom resolution.


Pssm-ID: 461457  Cd Length: 375  Bit Score: 401.79  E-value: 1.18e-137
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659325   5 RSNFKINLPKVYQAIEEADFFAIDGEFSGISdgpSVTALTSGFDTPEERYQKLKKHSMDFLLFQFGLCAFKYDHANSKHV 84
Cdd:pfam04857   3 RSNFKELLPEILKAIKEADFVAIDLEFTGLG---SPWRKSSLFDTPEERYLKLRDAAERFSILQFGLCCFREDEEKSKYT 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659325  85 TKSFNFYVFPKPFSrsSPDVKFVCQSSSIDFLASQGFDFNKVFCSGIPYLNQEEERQLREQFDEKRsqangaGALTKCPV 164
Cdd:pfam04857  80 AKPYNFYLFPRTEL--DPDRDFSCQASSLQFLAKHGFDFNKLFYEGIPYLSRAEEEKLRERLEERQ------QASPSDIP 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659325 165 TIPEDQKKFIDQVIEKIEGFLQREEKRTLELNPCTGFQRKLIYQTLSWKYPKGIHVETLETDKKERHIVISKVDEEERKR 244
Cdd:pfam04857 152 LLDVEDKEFVERVRSKIKEWLDSGEDKGEKLNIDNPVSRLLLQQLLKHQLVRVLLVELLSRGKQKVVQVVKKSSEDEELL 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659325 245 REQEKYAKEQEELNDAVGFSRVIHAIANSGKLVVGHNMLLDVMHTIHQFYCPLPVDLNEFKEMTTCVFPRLLDTKLMAST 324
Cdd:pfam04857 232 EKEEKKDEEEERLESAVGFRLVFDALSKSRKPIVGHNGLLDLLFLYQQFYGPLPETLEEFKALIHELFPGIYDTKYLATT 311

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958659325 325 Q-PFKDIINNTSLAELEKRLKETPFDPPKVESAEGFPSYDT----ASEQLHEAGYDAYITGLCF 383
Cdd:pfam04857 312 DaEFKVRLPSSSLEELFEKLCKENFSSPSVETPPFESDYHDesskYGGKAHEAGYDAYMTGYVF 375
R3H_PARN cd02637
R3H domain of Poly(A)-specific ribonuclease (PARN). PARN is a poly(A)-specific 3' exonuclease ...
 174-238 1.21e-24

R3H domain of Poly(A)-specific ribonuclease (PARN). PARN is a poly(A)-specific 3' exonuclease from the RNase D family that, in Xenopus, deadenylates a specific class of maternal mRNAs which results in their translational repression. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.


Pssm-ID: 100066 [Multi-domain]  Cd Length: 65  Bit Score: 96.62  E-value: 1.21e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958659325 174 IDQVIEKIEGFLQREEKRtLELNPCTGFQRKLIYQTLSWKYPKGIHVETLETDKKERHIVISKVD 238
Cdd:cd02637     1 IDEVIERIEAFLESEEDD-LELEPCNGFQRKLIYQTLEQKYPKGIHVETLETEKKERLIVIEKGD 64
RNA_bind pfam08675
RNA binding domain; This domain corresponds to the RNA binding domain of Poly(A)-specific ...
 431-463 4.91e-14

RNA binding domain; This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN).


Pssm-ID: 400835  Cd Length: 75  Bit Score: 66.99  E-value: 4.91e-14
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1958659325 431 PDLQPKRDHVLHVTFPKEWKTSDLYQLFSAFGS 463
Cdd:pfam08675   1 KDPNPSREHVFHVTFPKEWKTSDILQLFSPFGG 33
RRM_PARN cd12428
RNA recognition motif (RRM) found in poly(A)-specific ribonuclease PARN and similar proteins; ...
 437-462 5.49e-12

RNA recognition motif (RRM) found in poly(A)-specific ribonuclease PARN and similar proteins; The subfamily corresponds to the RRM of PARN, also termed deadenylating nuclease, or deadenylation nuclease, or polyadenylate-specific ribonuclease, a processive poly(A)-specific 3'-exoribonuclease involved in the decay of eukaryotic mRNAs. It specifically binds both, the poly(A) tail at the 3' end and the 7-methylguanosine (m7G) cap located at the 5' end of eukaryotic mRNAs, and catalyzes the 3'- to 5'-end deadenylation of single-stranded mRNA with a free 3' hydroxyl group both in the nucleus and in the cytoplasm. PARN belongs to the DEDD superfamily of exonucleases. It contains a nuclease domain, an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an R3H domain. PARN exists as a homodimer. The nuclease domain is involved in the dimerization. RRM and R3H domains are essential for the RNA-binding.


Pssm-ID: 409862 [Multi-domain]  Cd Length: 66  Bit Score: 60.78  E-value: 5.49e-12
                          10        20
                  ....*....|....*....|....*.
gi 1958659325 437 RDHVLHVTFPKEWKTSDLYQLFSAFG 462
Cdd:cd12428     1 RDHVFHLTFPKEWKTSDLYQLFSPFG 26
R3H cd02325
R3H domain. The name of the R3H domain comes from the characteristic spacing of the most ...
 174-236 2.54e-08

R3H domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. R3H domains are found in proteins together with ATPase domains, SF1 helicase domains, SF2 DEAH helicase domains, Cys-rich repeats, ring-type zinc fingers, and KH domains. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100064  Cd Length: 59  Bit Score: 50.31  E-value: 2.54e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958659325 174 IDQVIEKIEGFLQREEKRTLELNPCTGFQRKLIYQTLSWkypKGIHVETLETDKKeRHIVISK 236
Cdd:cd02325     1 REEREEELEAFAKDAAGKSLELPPMNSYERKLIHDLAEY---YGLKSESEGEGPN-RRVVITK 59
R3H pfam01424
R3H domain; The name of the R3H domain comes from the characteriztic spacing of the most ...
 172-236 1.31e-03

R3H domain; The name of the R3H domain comes from the characteriztic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to be binding ssDNA.


Pssm-ID: 460206  Cd Length: 60  Bit Score: 37.09  E-value: 1.31e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958659325 172 KFIDQVIEKIEGFLQREeKRTLELNPCTGFQRKLIYQTLSwKYPkgihVETLETDK-KERHIVISK 236
Cdd:pfam01424   1 EFLEQLAEKLAEFVKDT-GKSLELPPMSSYERRIIHELAQ-KYG----LESESEGEePNRRVVVYK 60
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 255-388 9.99e-03

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 37.08  E-value: 9.99e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659325 255 EELNDAVGFSRVIHAIAN--SGKLVVGHNMLLDV---MHTIHQFYCPLPVdlnefkemttcvfPRLLDTKLMAsTQPFKD 329
Cdd:COG0847    59 EDVADAPPFAEVLPELLEflGGAVLVAHNAAFDLgflNAELRRAGLPLPP-------------FPVLDTLRLA-RRLLPG 124

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958659325 330 IINNtSLAELEKRLketpfdppkvesaeGFPSYDTaseqlHEAGYDAYITGLCFISMAN 388
Cdd:COG0847   125 LPSY-SLDALCERL--------------GIPFDER-----HRALADAEATAELFLALLR 163
 
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.
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