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Conserved domains on  [gi|281485622|ref|NP_001164013|]
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cold shock domain-containing protein C2 [Rattus norvegicus]

Protein Classification

cold shock domain-containing protein( domain architecture ID 10138668)

cold shock domain-containing protein similar to mammalian calcium-regulated heat-stable protein 1, which binds mRNA and regulates the stability of target mRNA

CATH:  2.40.50.140
Gene Ontology:  GO:0003676
PubMed:  2184368|10377894|10322168
SCOP:  4001909

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 71-135 1.82e-19

Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.


:

Pssm-ID: 239905  Cd Length: 65  Bit Score: 76.85  E-value: 1.82e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 281485622  71 KGVCKQFSRSQGHGFITPENGSEDIFVHVSDIEGE--YVPVEGDEVTYKMCPIPpknQKFQAVEVVL 135
Cdd:cd04458    2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDgfRSLEEGDRVEFELEEGD---KGPQAVNVRL 65
 
Name Accession Description Interval E-value
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 71-135 1.82e-19

Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.


Pssm-ID: 239905  Cd Length: 65  Bit Score: 76.85  E-value: 1.82e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 281485622  71 KGVCKQFSRSQGHGFITPENGSEDIFVHVSDIEGE--YVPVEGDEVTYKMCPIPpknQKFQAVEVVL 135
Cdd:cd04458    2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDgfRSLEEGDRVEFELEEGD---KGPQAVNVRL 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 71-135 1.10e-16

Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.


Pssm-ID: 214633 [Multi-domain]  Cd Length: 64  Bit Score: 69.55  E-value: 1.10e-16
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 281485622    71 KGVCKQFSRsqGHGFITPENGSEDIFVHVSDIE-GEYVPVEGDEVTYKMCPiPPKNQKFQAVEVVL 135
Cdd:smart00357   1 TGVVKWFNK--GFGFIRPDDGGKDVFVHPSQIQgGLKSLREGDEVEFKVVS-PEGGEKPEAENVVK 63
CspC COG1278
Cold shock protein, CspA family [Transcription];
71-135 4.96e-14

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 62.90  E-value: 4.96e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 281485622  71 KGVCKQFSRSQGHGFITPENGSEDIFVHVSDIEGEYV--PVEGDEVTYKmcpIPPKNQKFQAVEVVL 135
Cdd:COG1278    3 TGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFrtLREGQRVEFE---VEQGDKGPQAVNVRV 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
71-136 7.07e-13

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 59.95  E-value: 7.07e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 281485622   71 KGVCKQFSRSQGHGFITPENGSEDIFVHVSDIEGEYVPV--EGDEVTYKmcpIPPKNQKFQAVEVVLT 136
Cdd:pfam00313   2 TGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSlqEGQKVEFE---VVEGTKGPQAANVTKP 66
cspE PRK09507
cold shock-like protein CspE;
71-118 1.25e-09

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 51.58  E-value: 1.25e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 281485622  71 KGVCKQFSRSQGHGFITPENGSEDIFVHVSDI--EGEYVPVEGDEVTYKM 118
Cdd:PRK09507   5 KGNVKWFNESKGFGFITPEDGSKDVFVHFSAIqtNGFKTLAEGQRVEFEI 54
 
Name Accession Description Interval E-value
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 71-135 1.82e-19

Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.


Pssm-ID: 239905  Cd Length: 65  Bit Score: 76.85  E-value: 1.82e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 281485622  71 KGVCKQFSRSQGHGFITPENGSEDIFVHVSDIEGE--YVPVEGDEVTYKMCPIPpknQKFQAVEVVL 135
Cdd:cd04458    2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDgfRSLEEGDRVEFELEEGD---KGPQAVNVRL 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 71-135 1.10e-16

Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.


Pssm-ID: 214633 [Multi-domain]  Cd Length: 64  Bit Score: 69.55  E-value: 1.10e-16
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 281485622    71 KGVCKQFSRsqGHGFITPENGSEDIFVHVSDIE-GEYVPVEGDEVTYKMCPiPPKNQKFQAVEVVL 135
Cdd:smart00357   1 TGVVKWFNK--GFGFIRPDDGGKDVFVHPSQIQgGLKSLREGDEVEFKVVS-PEGGEKPEAENVVK 63
CspC COG1278
Cold shock protein, CspA family [Transcription];
71-135 4.96e-14

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 62.90  E-value: 4.96e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 281485622  71 KGVCKQFSRSQGHGFITPENGSEDIFVHVSDIEGEYV--PVEGDEVTYKmcpIPPKNQKFQAVEVVL 135
Cdd:COG1278    3 TGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFrtLREGQRVEFE---VEQGDKGPQAVNVRV 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
71-136 7.07e-13

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 59.95  E-value: 7.07e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 281485622   71 KGVCKQFSRSQGHGFITPENGSEDIFVHVSDIEGEYVPV--EGDEVTYKmcpIPPKNQKFQAVEVVLT 136
Cdd:pfam00313   2 TGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSlqEGQKVEFE---VVEGTKGPQAANVTKP 66
cspE PRK09507
cold shock-like protein CspE;
71-118 1.25e-09

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 51.58  E-value: 1.25e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 281485622  71 KGVCKQFSRSQGHGFITPENGSEDIFVHVSDI--EGEYVPVEGDEVTYKM 118
Cdd:PRK09507   5 KGNVKWFNESKGFGFITPEDGSKDVFVHFSAIqtNGFKTLAEGQRVEFEI 54
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
72-116 4.07e-08

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 47.66  E-value: 4.07e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 281485622  72 GVCKQFSRSQGHGFITPENGSEDIFVHVSDIEGEYVPV--EGDEVTY 116
Cdd:PRK10354   7 GIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSldEGQKVSF 53
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 71-104 6.81e-08

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 46.99  E-value: 6.81e-08
                         10        20        30
                 ....*....|....*....|....*....|....
gi 281485622  71 KGVCKQFSRSQGHGFITPENGSEDIFVHVSDIEG 104
Cdd:PRK10943   5 KGQVKWFNESKGFGFITPADGSKDVFVHFSAIQG 38
PRK09937 PRK09937
cold shock-like protein CspD;
71-103 2.74e-06

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 42.80  E-value: 2.74e-06
                         10        20        30
                 ....*....|....*....|....*....|...
gi 281485622  71 KGVCKQFSRSQGHGFITPENGSEDIFVHVSDIE 103
Cdd:PRK09937   3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQ 35
PRK09890 PRK09890
cold shock protein CspG; Provisional
 72-103 5.89e-06

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 42.06  E-value: 5.89e-06
                         10        20        30
                 ....*....|....*....|....*....|..
gi 281485622  72 GVCKQFSRSQGHGFITPENGSEDIFVHVSDIE 103
Cdd:PRK09890   7 GLVKWFNADKGFGFITPDDGSKDVFVHFTAIQ 38
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 72-103 2.47e-05

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 40.42  E-value: 2.47e-05
                         10        20        30
                 ....*....|....*....|....*....|..
gi 281485622  72 GVCKQFSRSQGHGFITPENGSEDIFVHVSDIE 103
Cdd:PRK14998   4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQ 35
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 72-100 2.41e-03

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 34.88  E-value: 2.41e-03
                         10        20
                 ....*....|....*....|....*....
gi 281485622  72 GVCKQFSRSQGHGFITPENGSEDIFVHVS 100
Cdd:PRK15463   7 GIVKTFDGKSGKGLITPSDGRKDVQVHIS 35
PRK15464 PRK15464
cold shock-like protein CspH; Provisional
 72-100 4.16e-03

cold shock-like protein CspH; Provisional


Pssm-ID: 185361  Cd Length: 70  Bit Score: 34.30  E-value: 4.16e-03
                         10        20
                 ....*....|....*....|....*....
gi 281485622  72 GVCKQFSRSQGHGFITPENGSEDIFVHVS 100
Cdd:PRK15464   7 GIVKTFDRKSGKGFIIPSDGRKEVQVHIS 35
 
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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