Human Gene CSDE1 (ENST00000358528.9_10) from GENCODE V47lift37
  Description: cold shock domain containing E1, transcript variant 1 (from RefSeq NM_001007553.3)
Gencode Transcript: ENST00000358528.9_10
Gencode Gene: ENSG00000009307.17_16
Transcript (Including UTRs)
   Position: hg19 chr1:115,259,537-115,300,605 Size: 41,069 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg19 chr1:115,260,790-115,282,511 Size: 21,722 Coding Exon Count: 18 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:115,259,537-115,300,605)mRNA (may differ from genome)Protein (798 aa)
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BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CSDE1_HUMAN
DESCRIPTION: RecName: Full=Cold shock domain-containing protein E1; AltName: Full=N-ras upstream gene protein; AltName: Full=Protein UNR;
FUNCTION: RNA-binding protein. Required for internal initiation of translation of human rhinovirus RNA. May be involved in translationally coupled mRNA turnover. Implicated with other RNA- binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding- region determinant of instability (mCRD) domain.
SUBUNIT: Component of a multi subunit autoregulatory ribonucleoprotein complex (ARC), at least composed of IGF2BP1, PABPC1 and CSDE1. Interacts with STRAP. Part of a complex associated with the FOS mCRD domain and consisting of PABPC1, PAIP1, HNRPD and SYNCRIP. The interaction with PABPC1 is direct and RNA-independent.
SUBCELLULAR LOCATION: Cytoplasm.
SIMILARITY: Contains 9 CSD (cold-shock) domains.
SEQUENCE CAUTION: Sequence=BAA74908.2; Type=Erroneous initiation; Sequence=CAH18231.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 363.05 RPKM in Muscle - Skeletal
Total median expression: 5221.14 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -128.80447-0.288 Picture PostScript Text
3' UTR -315.201253-0.252 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR019844 - Cold-shock_CS
IPR011129 - Cold_shock_prot
IPR002059 - CSP_DNA-bd
IPR012340 - NA-bd_OB-fold
IPR016027 - NA-bd_OB-fold-like
IPR024642 - SUZ-C

Pfam Domains:
PF00313 - 'Cold-shock' DNA-binding domain
PF12901 - SUZ-C motif

SCOP Domains:
50249 - Nucleic acid-binding proteins
49503 - Cupredoxins
55200 - Translation initiation factor IF3, C-terminal domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1WFQ - NMR MuPIT 1X65 - NMR MuPIT 2YTV - NMR MuPIT 2YTX - NMR MuPIT 2YTY - NMR MuPIT


ModBase Predicted Comparative 3D Structure on O75534
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0006355 regulation of transcription, DNA-templated
GO:0008584 male gonad development
GO:0070966 nuclear-transcribed mRNA catabolic process, no-go decay

Cellular Component:
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0070937 CRD-mediated mRNA stability complex


-  Descriptions from all associated GenBank mRNAs
  AM392858 - Synthetic construct Homo sapiens clone IMAGE:100002734 for hypothetical protein (CSDE1 gene).
X02751 - Human N-ras mRNA and flanking regions.
CR749378 - Homo sapiens mRNA; cDNA DKFZp779J1455 (from clone DKFZp779J1455).
CR749431 - Homo sapiens mRNA; cDNA DKFZp779B0247 (from clone DKFZp779B0247).
BX648780 - Homo sapiens mRNA; cDNA DKFZp686O07132 (from clone DKFZp686O07132).
AB020692 - Homo sapiens KIAA0885 mRNA for KIAA0885 protein.
JD051269 - Sequence 32293 from Patent EP1572962.
JD484298 - Sequence 465322 from Patent EP1572962.
JD302616 - Sequence 283640 from Patent EP1572962.
AL050150 - Homo sapiens mRNA; cDNA DKFZp586J0620 (from clone DKFZp586J0620); partial cds.
AK130392 - Homo sapiens cDNA FLJ26882 fis, clone PRS09202, highly similar to UNR protein.
AK022516 - Homo sapiens cDNA FLJ12454 fis, clone NT2RM1000555, highly similar to UNR PROTEIN.
AK022528 - Homo sapiens cDNA FLJ12466 fis, clone NT2RM1000826, highly similar to UNR PROTEIN.
AL110192 - Homo sapiens mRNA; cDNA DKFZp566C233 (from clone DKFZp566C233); partial cds.
BX648561 - Homo sapiens mRNA; cDNA DKFZp779L1054 (from clone DKFZp779L1054).
BC021692 - Homo sapiens cold shock domain containing E1, RNA-binding, mRNA (cDNA clone IMAGE:3961444), partial cds.
AF077054 - Homo sapiens unr protein mRNA, complete cds.
JD273381 - Sequence 254405 from Patent EP1572962.
JD171859 - Sequence 152883 from Patent EP1572962.
BC017662 - Homo sapiens cDNA clone IMAGE:3912700, containing frame-shift errors.
JD292896 - Sequence 273920 from Patent EP1572962.
JD262562 - Sequence 243586 from Patent EP1572962.
AY049788 - Homo sapiens NRAS-related protein (UNR) mRNA, complete cds.
AK290146 - Homo sapiens cDNA FLJ78375 complete cds, highly similar to Homo sapiens cold shock domain containing E1, RNA-binding (CSDE1), transcript variant 1, mRNA.
BC032446 - Homo sapiens cold shock domain containing E1, RNA-binding, mRNA (cDNA clone MGC:40318 IMAGE:5111213), complete cds.
JD491675 - Sequence 472699 from Patent EP1572962.
AM393166 - Synthetic construct Homo sapiens clone IMAGE:100003053 for hypothetical protein (CSDE1 gene).
AM393479 - Synthetic construct Homo sapiens clone IMAGE:100002983 for hypothetical protein (CSDE1 gene).
AM393616 - Synthetic construct Homo sapiens clone IMAGE:100003054 for hypothetical protein (CSDE1 gene).
AM393624 - Synthetic construct Homo sapiens clone IMAGE:100003012 for hypothetical protein (CSDE1 gene).
AB384032 - Synthetic construct DNA, clone: pF1KSDA0885, Homo sapiens CSDE1 gene for cold shock domain-containing protein E1, complete cds, without stop codon, in Flexi system.
AF070542 - Homo sapiens clone 24514 unknown mRNA.
DQ575323 - Homo sapiens piRNA piR-43435, complete sequence.
DQ586108 - Homo sapiens piRNA piR-53220, complete sequence.
AK131495 - Homo sapiens cDNA FLJ16692 fis, clone TRACH3002561.
JD332705 - Sequence 313729 from Patent EP1572962.
JD304097 - Sequence 285121 from Patent EP1572962.
DQ591464 - Homo sapiens piRNA piR-58576, complete sequence.
JD501480 - Sequence 482504 from Patent EP1572962.
JD467922 - Sequence 448946 from Patent EP1572962.
JD175141 - Sequence 156165 from Patent EP1572962.
JD462086 - Sequence 443110 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K281, CSDE1 , CSDE1_HUMAN, D1S155E, E9PGZ0, ENST00000358528.1, ENST00000358528.2, ENST00000358528.3, ENST00000358528.4, ENST00000358528.5, ENST00000358528.6, ENST00000358528.7, ENST00000358528.8, G5E9Q2, KIAA0885, NM_001007553, NRU, O75534, O94961, Q5TF04, Q5TF05, Q68DF1, Q68DI9, Q9Y2S4, uc318apj.1, uc318apj.2, UNR
UCSC ID: ENST00000358528.9_10
RefSeq Accession: NM_001007553.3
Protein: O75534 (aka CSDE1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.