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Conserved domains on  [gi|1958771694|ref|XP_038964378|]
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Y-box-binding protein 3 isoform X1 [Rattus norvegicus]

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
PubMed:  12530521|10322168|17437059
SCOP:  4001909

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
83-152 1.52e-26

'Cold-shock' DNA-binding domain;


:

Pssm-ID: 278729  Cd Length: 66  Bit Score: 98.85  E-value: 1.52e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958771694  83 VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVTGP 152
Cdd:pfam00313   1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDG----FRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
83-152 1.52e-26

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 98.85  E-value: 1.52e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958771694  83 VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVTGP 152
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 ...
 85-151 8.87e-24

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: 91.49  E-value: 8.87e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958771694  85 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVTG 151
Cdd:cd04458     3 GTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDG----FRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
85-150 2.26e-19

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 79.85  E-value: 2.26e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958771694  85 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIkknnPRKYLRSVGDGETVEFDVVEGEKGAEAANVT 150
Cdd:COG1278     4 GTVKWFNAEKGFGFITPDDGGEDVFVHISAL----QRSGFRTLREGQRVEFEVEQGDKGPQAVNVR 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 85-152 1.81e-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: 72.25  E-value: 1.81e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958771694   85 GTVKWFNvrNGYGFINRNDTKEDVFVHQTAIKKNnprkyLRSVGDGETVEFDVV--EGEKGAEAANVTGP 152
Cdd:smart00357   2 GVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQGG-----LKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
cspE PRK09507
cold shock-like protein CspE;
81-150 3.18e-15

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 68.91  E-value: 3.18e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958771694  81 TKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVT 150
Cdd:PRK09507    2 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNGAKGPSAANVI 67
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
83-152 1.52e-26

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 98.85  E-value: 1.52e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958771694  83 VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVTGP 152
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 ...
 85-151 8.87e-24

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: 91.49  E-value: 8.87e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958771694  85 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVTG 151
Cdd:cd04458     3 GTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDG----FRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
85-150 2.26e-19

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 79.85  E-value: 2.26e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958771694  85 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIkknnPRKYLRSVGDGETVEFDVVEGEKGAEAANVT 150
Cdd:COG1278     4 GTVKWFNAEKGFGFITPDDGGEDVFVHISAL----QRSGFRTLREGQRVEFEVEQGDKGPQAVNVR 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 85-152 1.81e-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: 72.25  E-value: 1.81e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958771694   85 GTVKWFNvrNGYGFINRNDTKEDVFVHQTAIKKNnprkyLRSVGDGETVEFDVV--EGEKGAEAANVTGP 152
Cdd:smart00357   2 GVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQGG-----LKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
cspE PRK09507
cold shock-like protein CspE;
81-150 3.18e-15

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 68.91  E-value: 3.18e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958771694  81 TKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVT 150
Cdd:PRK09507    2 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNGAKGPSAANVI 67
PRK09890 PRK09890
cold shock protein CspG; Provisional
 79-149 3.27e-15

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 69.02  E-value: 3.27e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958771694  79 LATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANV 149
Cdd:PRK09890    1 MSNKMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNE----FRTLNENQKVEFSIEQGQRGPAAANV 67
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
79-150 4.14e-14

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 66.15  E-value: 4.14e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958771694  79 LATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVT 150
Cdd:PRK10354    1 MSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIESGAKGPAAGNVT 68
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 82-150 2.38e-12

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 61.24  E-value: 2.38e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958771694  82 KVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVT 150
Cdd:PRK10943    3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNG----FKTLAEGQNVEFEIQDGQKGPAAVNVT 67
PRK09937 PRK09937
cold shock-like protein CspD;
85-158 8.37e-10

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 54.35  E-value: 8.37e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958771694  85 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVtgpdgVPVE 158
Cdd:PRK09937    4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG----YRTLKAGQSVQFDVHQGPKGNHASVI-----VPVE 68
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 84-163 3.01e-08

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 50.05  E-value: 3.01e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958771694  84 LGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVtgpdgVPVEGSRYA 163
Cdd:PRK14998    3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG----YRTLKAGQSVRFDVHQGPKGNHASVI-----VPIEAEAVA 73
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 79-149 5.88e-06

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 43.35  E-value: 5.88e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958771694  79 LATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRkylrSVGDGETVEFDVVEGEKGAEAANV 149
Cdd:PRK15463    1 MSRKMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAE----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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