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Conserved domains on  [gi|1907082434|ref|XP_036012738|]
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Y-box-binding protein 2 isoform X2 [Mus musculus]

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

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 ...
 97-126 2.03e-12

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: 61.44  E-value: 2.03e-12
                          10        20        30
                  ....*....|....*....|....*....|
gi 1907082434  97 GTVKWFNVRNGYGFINRNDTKEDVFVHQGA 126
Cdd:cd04458     3 GTVKWFDDEKGFGFITPDDGGEDVFVHISA 32
 
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 ...
 97-126 2.03e-12

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: 61.44  E-value: 2.03e-12
                          10        20        30
                  ....*....|....*....|....*....|
gi 1907082434  97 GTVKWFNVRNGYGFINRNDTKEDVFVHQGA 126
Cdd:cd04458     3 GTVKWFDDEKGFGFITPDDGGEDVFVHISA 32
CSD pfam00313
'Cold-shock' DNA-binding domain;
95-134 2.53e-12

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 61.10  E-value: 2.53e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907082434  95 VLGTVKWFNVRNGYGFINRNDTKEDVFVHQ--------------------------GAEAANVTGP 134
Cdd:pfam00313   1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFsaiqgdgfrslqegqkvefevvegtkGPQAANVTKP 66
CspC COG1278
Cold shock protein, CspA family [Transcription];
97-123 2.47e-09

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 52.89  E-value: 2.47e-09
                          10        20
                  ....*....|....*....|....*..
gi 1907082434  97 GTVKWFNVRNGYGFINRNDTKEDVFVH 123
Cdd:COG1278     4 GTVKWFNAEKGFGFITPDDGGEDVFVH 30
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 97-126 1.72e-07

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: 47.59  E-value: 1.72e-07
                           10        20        30
                   ....*....|....*....|....*....|
gi 1907082434   97 GTVKWFNvrNGYGFINRNDTKEDVFVHQGA 126
Cdd:smart00357   2 GVVKWFN--KGFGFIRPDDGGKDVFVHPSQ 29
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
94-126 7.26e-06

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 43.43  E-value: 7.26e-06
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1907082434  94 QVLGTVKWFNVRNGYGFINRNDTKEDVFVHQGA 126
Cdd:PRK10354    4 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSA 36
 
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 ...
 97-126 2.03e-12

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: 61.44  E-value: 2.03e-12
                          10        20        30
                  ....*....|....*....|....*....|
gi 1907082434  97 GTVKWFNVRNGYGFINRNDTKEDVFVHQGA 126
Cdd:cd04458     3 GTVKWFDDEKGFGFITPDDGGEDVFVHISA 32
CSD pfam00313
'Cold-shock' DNA-binding domain;
95-134 2.53e-12

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 61.10  E-value: 2.53e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907082434  95 VLGTVKWFNVRNGYGFINRNDTKEDVFVHQ--------------------------GAEAANVTGP 134
Cdd:pfam00313   1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFsaiqgdgfrslqegqkvefevvegtkGPQAANVTKP 66
CspC COG1278
Cold shock protein, CspA family [Transcription];
97-123 2.47e-09

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 52.89  E-value: 2.47e-09
                          10        20
                  ....*....|....*....|....*..
gi 1907082434  97 GTVKWFNVRNGYGFINRNDTKEDVFVH 123
Cdd:COG1278     4 GTVKWFNAEKGFGFITPDDGGEDVFVH 30
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 97-126 1.72e-07

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: 47.59  E-value: 1.72e-07
                           10        20        30
                   ....*....|....*....|....*....|
gi 1907082434   97 GTVKWFNvrNGYGFINRNDTKEDVFVHQGA 126
Cdd:smart00357   2 GVVKWFN--KGFGFIRPDDGGKDVFVHPSQ 29
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
94-126 7.26e-06

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 43.43  E-value: 7.26e-06
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1907082434  94 QVLGTVKWFNVRNGYGFINRNDTKEDVFVHQGA 126
Cdd:PRK10354    4 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSA 36
cspE PRK09507
cold shock-like protein CspE;
94-130 1.12e-05

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 42.72  E-value: 1.12e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1907082434  94 QVLGTVKWFNVRNGYGFINRNDTKEDVFVHQGAEAAN 130
Cdd:PRK09507    3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTN 39
PRK09890 PRK09890
cold shock protein CspG; Provisional
 94-130 1.59e-05

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 42.44  E-value: 1.59e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1907082434  94 QVLGTVKWFNVRNGYGFINRNDTKEDVFVHQGAEAAN 130
Cdd:PRK09890    4 KMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSN 40
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 94-130 3.31e-04

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 38.51  E-value: 3.31e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1907082434  94 QVLGTVKWFNVRNGYGFINRNDTKEDVFVHQGAEAAN 130
Cdd:PRK10943    3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGN 39
PRK09937 PRK09937
cold shock-like protein CspD;
97-123 2.55e-03

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 36.25  E-value: 2.55e-03
                          10        20
                  ....*....|....*....|....*..
gi 1907082434  97 GTVKWFNVRNGYGFINRNDTKEDVFVH 123
Cdd:PRK09937    4 GTVKWFNNAKGFGFICPEGGGEDIFAH 30
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 96-123 8.65e-03

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 34.64  E-value: 8.65e-03
                          10        20
                  ....*....|....*....|....*...
gi 1907082434  96 LGTVKWFNVRNGYGFINRNDTKEDVFVH 123
Cdd:PRK14998    3 TGTVKWFNNAKGFGFICPEGGGEDIFAH 30
 
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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