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Conserved domains on  [gi|1958656740|ref|XP_006245812|]
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calcium-regulated heat stable protein 1 isoform X1 [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 ...
 63-128 1.45e-20

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: 79.16  E-value: 1.45e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958656740  63 YKGVCKCFCRSKGHGFITPADGGPDIFLHISDVEGE--YVPVEGDEVTYKMCSIPpknEKLQAVEVVI 128
Cdd:cd04458     1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDgfRSLEEGDRVEFELEEGD---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 ...
 63-128 1.45e-20

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: 79.16  E-value: 1.45e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958656740  63 YKGVCKCFCRSKGHGFITPADGGPDIFLHISDVEGE--YVPVEGDEVTYKMCSIPpknEKLQAVEVVI 128
Cdd:cd04458     1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDgfRSLEEGDRVEFELEEGD---KGPQAVNVRL 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 64-128 3.15e-18

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: 73.40  E-value: 3.15e-18
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958656740   64 KGVCKCFcrSKGHGFITPADGGPDIFLHISDVE-GEYVPVEGDEVTYKMCSiPPKNEKLQAVEVVI 128
Cdd:smart00357   1 TGVVKWF--NKGFGFIRPDDGGKDVFVHPSQIQgGLKSLREGDEVEFKVVS-PEGGEKPEAENVVK 63
CspC COG1278
Cold shock protein, CspA family [Transcription];
64-128 7.76e-14

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 62.13  E-value: 7.76e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958656740  64 KGVCKCFCRSKGHGFITPADGGPDIFLHISDVEGEYV--PVEGDEVTYkmcSIPPKNEKLQAVEVVI 128
Cdd:COG1278     3 TGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFrtLREGQRVEF---EVEQGDKGPQAVNVRV 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
64-127 3.41e-13

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 60.33  E-value: 3.41e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958656740  64 KGVCKCFCRSKGHGFITPADGGPDIFLHISDVEGEYVPV--EGDEVTYkmcSIPPKNEKLQAVEVV 127
Cdd:pfam00313   2 TGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSlqEGQKVEF---EVVEGTKGPQAANVT 64
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 64-111 3.67e-08

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 47.37  E-value: 3.67e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958656740  64 KGVCKCFCRSKGHGFITPADGGPDIFLHISDVEGE--YVPVEGDEVTYKM 111
Cdd:PRK10943    5 KGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNgfKTLAEGQNVEFEI 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 ...
 63-128 1.45e-20

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: 79.16  E-value: 1.45e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958656740  63 YKGVCKCFCRSKGHGFITPADGGPDIFLHISDVEGE--YVPVEGDEVTYKMCSIPpknEKLQAVEVVI 128
Cdd:cd04458     1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDgfRSLEEGDRVEFELEEGD---KGPQAVNVRL 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 64-128 3.15e-18

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: 73.40  E-value: 3.15e-18
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958656740   64 KGVCKCFcrSKGHGFITPADGGPDIFLHISDVE-GEYVPVEGDEVTYKMCSiPPKNEKLQAVEVVI 128
Cdd:smart00357   1 TGVVKWF--NKGFGFIRPDDGGKDVFVHPSQIQgGLKSLREGDEVEFKVVS-PEGGEKPEAENVVK 63
CspC COG1278
Cold shock protein, CspA family [Transcription];
64-128 7.76e-14

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 62.13  E-value: 7.76e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958656740  64 KGVCKCFCRSKGHGFITPADGGPDIFLHISDVEGEYV--PVEGDEVTYkmcSIPPKNEKLQAVEVVI 128
Cdd:COG1278     3 TGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFrtLREGQRVEF---EVEQGDKGPQAVNVRV 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
64-127 3.41e-13

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 60.33  E-value: 3.41e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958656740  64 KGVCKCFCRSKGHGFITPADGGPDIFLHISDVEGEYVPV--EGDEVTYkmcSIPPKNEKLQAVEVV 127
Cdd:pfam00313   2 TGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSlqEGQKVEF---EVVEGTKGPQAANVT 64
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 64-111 3.67e-08

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 47.37  E-value: 3.67e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958656740  64 KGVCKCFCRSKGHGFITPADGGPDIFLHISDVEGE--YVPVEGDEVTYKM 111
Cdd:PRK10943    5 KGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNgfKTLAEGQNVEFEI 54
cspE PRK09507
cold shock-like protein CspE;
64-111 1.08e-07

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 46.18  E-value: 1.08e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958656740  64 KGVCKCFCRSKGHGFITPADGGPDIFLHISDV--EGEYVPVEGDEVTYKM 111
Cdd:PRK09507    5 KGNVKWFNESKGFGFITPEDGSKDVFVHFSAIqtNGFKTLAEGQRVEFEI 54
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
65-109 4.72e-06

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 41.89  E-value: 4.72e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1958656740  65 GVCKCFCRSKGHGFITPADGGPDIFLHISDVEGEYVPV--EGDEVTY 109
Cdd:PRK10354    7 GIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSldEGQKVSF 53
PRK09937 PRK09937
cold shock-like protein CspD;
64-96 9.18e-05

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 38.56  E-value: 9.18e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1958656740  64 KGVCKCFCRSKGHGFITPADGGPDIFLHISDVE 96
Cdd:PRK09937    3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQ 35
PRK09890 PRK09890
cold shock protein CspG; Provisional
 65-96 1.29e-04

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 38.21  E-value: 1.29e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1958656740  65 GVCKCFCRSKGHGFITPADGGPDIFLHISDVE 96
Cdd:PRK09890    7 GLVKWFNADKGFGFITPDDGSKDVFVHFTAIQ 38
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 65-96 3.97e-04

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 36.95  E-value: 3.97e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1958656740  65 GVCKCFCRSKGHGFITPADGGPDIFLHISDVE 96
Cdd:PRK14998    4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQ 35
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 65-93 5.46e-03

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 33.72  E-value: 5.46e-03
                          10        20
                  ....*....|....*....|....*....
gi 1958656740  65 GVCKCFCRSKGHGFITPADGGPDIFLHIS 93
Cdd:PRK15463    7 GIVKTFDGKSGKGLITPSDGRKDVQVHIS 35
PRK15464 PRK15464
cold shock-like protein CspH; Provisional
 65-93 8.53e-03

cold shock-like protein CspH; Provisional


Pssm-ID: 185361  Cd Length: 70  Bit Score: 33.15  E-value: 8.53e-03
                          10        20
                  ....*....|....*....|....*....
gi 1958656740  65 GVCKCFCRSKGHGFITPADGGPDIFLHIS 93
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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