Human Gene CARHSP1 (ENST00000311052.10_8) from GENCODE V47lift37
  Description: calcium regulated heat stable protein 1, transcript variant 1 (from RefSeq NM_014316.4)
Gencode Transcript: ENST00000311052.10_8
Gencode Gene: ENSG00000153048.11_15
Transcript (Including UTRs)
   Position: hg19 chr16:8,946,804-8,962,863 Size: 16,060 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr16:8,949,021-8,953,185 Size: 4,165 Coding Exon Count: 3 

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 (chr16:8,946,804-8,962,863)mRNA (may differ from genome)Protein (147 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CHSP1_HUMAN
DESCRIPTION: RecName: Full=Calcium-regulated heat stable protein 1; AltName: Full=Calcium-regulated heat-stable protein of 24 kDa; Short=CRHSP-24;
FUNCTION: Binds mRNA and regulates the stability of target mRNA. Binds single-stranded DNA (in vitro).
SUBUNIT: Homodimer. Interacts with STYX (By similarity).
SUBCELLULAR LOCATION: Cytoplasm. Cytoplasm, P-body. Cytoplasmic granule. Note=Detected at cytoplasmic stress granules and P- bodies. Detected at exosome granules where mRNA is degraded (By similarity).
PTM: Dephosphorylated by calcineurin in a Ca(2+) dependent manner (By similarity).
SIMILARITY: Contains 1 CSD (cold-shock) domain.

-  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: 64.57 RPKM in Testis
Total median expression: 752.73 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 -14.7048-0.306 Picture PostScript Text
3' UTR -828.102217-0.374 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

Pfam Domains:
PF00313 - 'Cold-shock' DNA-binding domain

SCOP Domains:
50249 - Nucleic acid-binding proteins

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3AQQ - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9Y2V2
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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:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0003730 mRNA 3'-UTR binding
GO:0005515 protein binding
GO:0019902 phosphatase binding

Biological Process:
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0035556 intracellular signal transduction
GO:0043488 regulation of mRNA stability

Cellular Component:
GO:0000177 cytoplasmic exosome (RNase complex)
GO:0000932 P-body
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0043186 P granule


-  Descriptions from all associated GenBank mRNAs
  BC108283 - Homo sapiens calcium regulated heat stable protein 1, 24kDa, mRNA (cDNA clone MGC:111446 IMAGE:4430943), complete cds.
JD074154 - Sequence 55178 from Patent EP1572962.
JD364144 - Sequence 345168 from Patent EP1572962.
AF115345 - Homo sapiens calcium-regulated heat stable protein CRHSP-24 mRNA, complete cds.
BC001333 - Homo sapiens calcium regulated heat stable protein 1, 24kDa, mRNA (cDNA clone IMAGE:3459662).
BC000782 - Homo sapiens calcium regulated heat stable protein 1, 24kDa, mRNA (cDNA clone IMAGE:3505721), containing frame-shift errors.
BC003366 - Homo sapiens calcium regulated heat stable protein 1, 24kDa, mRNA (cDNA clone MGC:5235 IMAGE:2900952), complete cds.
JD386248 - Sequence 367272 from Patent EP1572962.
JD306854 - Sequence 287878 from Patent EP1572962.
JD320488 - Sequence 301512 from Patent EP1572962.
JD459692 - Sequence 440716 from Patent EP1572962.
JD344442 - Sequence 325466 from Patent EP1572962.
JD089292 - Sequence 70316 from Patent EP1572962.
JD288833 - Sequence 269857 from Patent EP1572962.
JD480992 - Sequence 462016 from Patent EP1572962.
JD471693 - Sequence 452717 from Patent EP1572962.
JD204866 - Sequence 185890 from Patent EP1572962.
AK311777 - Homo sapiens cDNA, FLJ92038, highly similar to Homo sapiens calcium regulated heat stable protein 1, 24kDa (CARHSP1), mRNA.
KJ898517 - Synthetic construct Homo sapiens clone ccsbBroadEn_07911 CARHSP1 gene, encodes complete protein.
EU831795 - Synthetic construct Homo sapiens clone HAIB:100066824; DKFZo008E0321 calcium regulated heat stable protein 1, 24kDa protein (CARHSP1) gene, encodes complete protein.
EU831872 - Synthetic construct Homo sapiens clone HAIB:100066901; DKFZo004E0322 calcium regulated heat stable protein 1, 24kDa protein (CARHSP1) gene, encodes complete protein.
AB590833 - Synthetic construct DNA, clone: pFN21AE1632, Homo sapiens CARHSP1 gene for calcium regulated heat stable protein 1, 24kDa, without stop codon, in Flexi system.
AK093698 - Homo sapiens cDNA FLJ36379 fis, clone THYMU2008351, weakly similar to Calcium-regulated heat stable protein CRHSP-24.
JD022762 - Sequence 3786 from Patent EP1572962.
JD029884 - Sequence 10908 from Patent EP1572962.
JD335038 - Sequence 316062 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B2R4C3, CHSP1_HUMAN, D3DUF5, ENST00000311052.1, ENST00000311052.2, ENST00000311052.3, ENST00000311052.4, ENST00000311052.5, ENST00000311052.6, ENST00000311052.7, ENST00000311052.8, ENST00000311052.9, NM_014316, Q2YDX5, Q9BQ53, Q9Y2V2, uc317oxb.1, uc317oxb.2
UCSC ID: ENST00000311052.10_8
RefSeq Accession: NM_014316.4
Protein: Q9Y2V2 (aka CHSP1_HUMAN or CHS1_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.