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Conserved domains on  [gi|1907082436|ref|XP_036012739|]
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Y-box-binding protein 2 isoform X3 [Mus musculus]

Protein Classification

cold shock domain-containing protein( domain architecture ID 10448154)

cold shock domain-containing protein similar to mammalian Y-box-binding proteins, which are DNA- and RNA-binding proteins involved in various processes, such as translational repression, RNA stabilization, mRNA splicing, DNA repair and transcription regulation

CATH:  2.40.50.140
Gene Ontology:  GO:0003676

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
18-87 1.66e-26

'Cold-shock' DNA-binding domain;


:

Pssm-ID: 278729  Cd Length: 66  Bit Score: 98.85  E-value: 1.66e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907082436  18 VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEAANVTGP 87
Cdd:pfam00313   1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDG----FRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
18-87 1.66e-26

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 98.85  E-value: 1.66e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907082436  18 VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEAANVTGP 87
Cdd:pfam00313   1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDG----FRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
20-86 1.31e-23

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: 91.10  E-value: 1.31e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907082436  20 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEAANVTG 86
Cdd:cd04458     3 GTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDG----FRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
20-85 1.26e-19

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 80.62  E-value: 1.26e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907082436  20 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEAANVT 85
Cdd:COG1278     4 GTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSG----FRTLREGQRVEFEVEQGDKGPQAVNVR 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
20-87 9.10e-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: 70.32  E-value: 9.10e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907082436   20 GTVKWFNvrNGYGFINRNDTKEDVFVHQTAIKRNnprkfLRSVGDGETVEFDVV--EGEKGAEAANVTGP 87
Cdd:smart00357   2 GVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQGG-----LKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
cspE PRK09507
cold shock-like protein CspE;
17-85 3.51e-15

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 68.91  E-value: 3.51e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907082436  17 QVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEAANVT 85
Cdd:PRK09507    3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNGAKGPSAANVI 67
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
18-87 1.66e-26

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 98.85  E-value: 1.66e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907082436  18 VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEAANVTGP 87
Cdd:pfam00313   1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDG----FRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
20-86 1.31e-23

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: 91.10  E-value: 1.31e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907082436  20 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEAANVTG 86
Cdd:cd04458     3 GTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDG----FRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
20-85 1.26e-19

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 80.62  E-value: 1.26e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907082436  20 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEAANVT 85
Cdd:COG1278     4 GTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSG----FRTLREGQRVEFEVEQGDKGPQAVNVR 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
20-87 9.10e-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: 70.32  E-value: 9.10e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907082436   20 GTVKWFNvrNGYGFINRNDTKEDVFVHQTAIKRNnprkfLRSVGDGETVEFDVV--EGEKGAEAANVTGP 87
Cdd:smart00357   2 GVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQGG-----LKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
cspE PRK09507
cold shock-like protein CspE;
17-85 3.51e-15

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 68.91  E-value: 3.51e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907082436  17 QVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEAANVT 85
Cdd:PRK09507    3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNGAKGPSAANVI 67
PRK09890 PRK09890
cold shock protein CspG; Provisional
17-84 3.63e-14

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 65.94  E-value: 3.63e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907082436  17 QVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEAANV 84
Cdd:PRK09890    4 KMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNE----FRTLNENQKVEFSIEQGQRGPAAANV 67
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
17-85 6.41e-14

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 65.38  E-value: 6.41e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907082436  17 QVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEAANVT 85
Cdd:PRK10354    4 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIESGAKGPAAGNVT 68
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
17-85 7.06e-12

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 59.70  E-value: 7.06e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907082436  17 QVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEAANVT 85
Cdd:PRK10943    3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNG----FKTLAEGQNVEFEIQDGQKGPAAVNVT 67
PRK09937 PRK09937
cold shock-like protein CspD;
20-93 1.56e-09

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 53.58  E-value: 1.56e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907082436  20 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEAANVtgpggVPVK 93
Cdd:PRK09937    4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG----YRTLKAGQSVQFDVHQGPKGNHASVI-----VPVE 68
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
19-82 4.55e-08

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 49.28  E-value: 4.55e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907082436  19 LGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEAA 82
Cdd:PRK14998    3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG----YRTLKAGQSVRFDVHQGPKGNHAS 62
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
20-84 6.25e-05

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 40.27  E-value: 6.25e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907082436  20 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNPRkflrSVGDGETVEFDVVEGEKGAEAANV 84
Cdd:PRK15463    7 GIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAE----ELTTGLRVEFCRINGLRGPTAANV 67
 
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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