Human Gene CD5 (ENST00000347785.8_4) from GENCODE V47lift37
  Description: CD5 molecule, transcript variant 1 (from RefSeq NM_014207.4)
Gencode Transcript: ENST00000347785.8_4
Gencode Gene: ENSG00000110448.11_7
Transcript (Including UTRs)
   Position: hg19 chr11:60,869,961-60,895,324 Size: 25,364 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr11:60,870,033-60,893,311 Size: 23,279 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:60,869,961-60,895,324)mRNA (may differ from genome)Protein (495 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CD5_HUMAN
DESCRIPTION: RecName: Full=T-cell surface glycoprotein CD5; AltName: Full=Lymphocyte antigen T1/Leu-1; AltName: CD_antigen=CD5; Flags: Precursor;
FUNCTION: May act as a receptor in regulating T-cell proliferation.
SUBUNIT: Interacts with CD72/LYB-2. Interacts with PTPN6/SHP-1 (By similarity).
SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane protein.
PTM: Phosphorylated on tyrosine residues by LYN; this creates binding sites for PTPN6/SHP-1 (By similarity).
SIMILARITY: Contains 3 SRCR domains.

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: CD5
Diseases sorted by gene-association score: thymus cancer (30), richter's syndrome (25), prolymphocytic leukemia (17), chronic lymphocytic leukemia (17), epithelial malignant thymoma (16), dendritic cell thymoma (16), marginal zone b-cell lymphoma (15), lymphoepithelioma-like thymic carcinoma (15), thymus large cell carcinoma (14), splenic marginal zone lymphoma (14), tracheal lymphoma (14), thymic epithelial tumor (12), autoimmune hemolytic anemia (12), b-cell lymphomas (10), papillary thymic adenocarcinoma (10), thymoma (9), composite lymphoma (9), type ii mixed cryoglobulinemia (9), intravascular large b-cell lymphoma (9), mediastinal cancer (9), spindle cell thymoma (9), mantle cell lymphoma (9), cryoglobulinemia, familial mixed (9), cll/sll (8), adult lymphoma (8), cryoglobulinemia (8), hairy cell leukemia (8), lymphoid leukemia (8), diffuse large b-cell lymphoma (8), lymphoma, malt, somatic (7), prostate lymphoma (7), type c thymoma (7), lymphoma, non-hodgkin (7), b cell prolymphocytic leukemia (7), b-cell expansion with nfkb and t-cell anergy (7), ileum cancer (6), mixed type thymoma (6), bladder lymphoma (6), colon lymphoma (6), epidural neoplasm (6), breast lymphoma (6), parapsoriasis (6), lymphoplasmacytic lymphoma (6), thymus adenocarcinoma (6), b cell linker protein deficiency (6), hemophagocytic lymphohistiocytosis (6), anterior scleritis (5), plasma protein metabolism disease (5), lung lymphoma (5), marantic endocarditis (5), autoimmune disease of blood (5), immune system organ benign neoplasm (5), thymus lipoma (5), lymphatic system cancer (4), necrotizing sialometaplasia (4), cd45 deficiency (4), malignant epithelial mesothelioma (4), leukemia, acute myeloid (0)

-  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: 7.61 RPKM in Spleen
Total median expression: 36.38 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 -24.1072-0.335 Picture PostScript Text
3' UTR -569.901567-0.364 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
IPR001190 - Srcr_rcpt
IPR017448 - Srcr_rcpt-rel
IPR003566 - Tcell_CD5

Pfam Domains:
PF00530 - Scavenger receptor cysteine-rich domain

SCOP Domains:
56487 - SRCR-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2JA4 - X-ray MuPIT 2JOP - NMR MuPIT 2JP0 - NMR MuPIT 2OTT - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P06127
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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    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004888 transmembrane signaling receptor activity
GO:0005044 scavenger receptor activity
GO:0005515 protein binding
GO:0038023 signaling receptor activity

Biological Process:
GO:0006898 receptor-mediated endocytosis
GO:0008037 cell recognition
GO:0008283 cell proliferation
GO:0031295 T cell costimulation
GO:0097190 apoptotic signaling pathway

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0009897 external side of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AY541703 - Homo sapiens CD5 transcript variant 1A mRNA, 5' UTR, exon 1A and partial cds.
AK292698 - Homo sapiens cDNA FLJ75280 complete cds, highly similar to Homo sapiens CD5 antigen (p56-62) (CD5), mRNA.
X04391 - Human mRNA for lymphocyte glycoprotein T1/Leu-1.
BC027901 - Homo sapiens CD5 molecule, mRNA (cDNA clone MGC:34370 IMAGE:5228913), complete cds.
GQ901015 - Homo sapiens clone HEL-T-127 epididymis secretory sperm binding protein mRNA, complete cds.
JD131510 - Sequence 112534 from Patent EP1572962.
DQ895270 - Synthetic construct Homo sapiens clone IMAGE:100009730; FLH182936.01L; RZPDo839D03139D CD5 molecule (CD5) gene, encodes complete protein.
DQ892077 - Synthetic construct clone IMAGE:100004707; FLH182940.01X; RZPDo839D03140D CD5 molecule (CD5) gene, encodes complete protein.
JD458014 - Sequence 439038 from Patent EP1572962.
JD147365 - Sequence 128389 from Patent EP1572962.
JD190405 - Sequence 171429 from Patent EP1572962.
JD534199 - Sequence 515223 from Patent EP1572962.
JD094806 - Sequence 75830 from Patent EP1572962.
JD496410 - Sequence 477434 from Patent EP1572962.
JD145619 - Sequence 126643 from Patent EP1572962.
JD226757 - Sequence 207781 from Patent EP1572962.
JD447940 - Sequence 428964 from Patent EP1572962.
JD404701 - Sequence 385725 from Patent EP1572962.
JD429733 - Sequence 410757 from Patent EP1572962.
JD087978 - Sequence 69002 from Patent EP1572962.
JD174171 - Sequence 155195 from Patent EP1572962.
JD281273 - Sequence 262297 from Patent EP1572962.
JD451671 - Sequence 432695 from Patent EP1572962.
JD199635 - Sequence 180659 from Patent EP1572962.
JD421841 - Sequence 402865 from Patent EP1572962.
JD432106 - Sequence 413130 from Patent EP1572962.
JD167037 - Sequence 148061 from Patent EP1572962.
JD089102 - Sequence 70126 from Patent EP1572962.
JD202150 - Sequence 183174 from Patent EP1572962.
JD486969 - Sequence 467993 from Patent EP1572962.
JD439313 - Sequence 420337 from Patent EP1572962.
JD272179 - Sequence 253203 from Patent EP1572962.
JD364945 - Sequence 345969 from Patent EP1572962.
JD053423 - Sequence 34447 from Patent EP1572962.
JD379307 - Sequence 360331 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_dcPathway - Dendritic cells in regulating TH1 and TH2 Development

-  Other Names for This Gene
  Alternate Gene Symbols: A0N0P4, A8K9I3, CD5_HUMAN, ENST00000347785.1, ENST00000347785.2, ENST00000347785.3, ENST00000347785.4, ENST00000347785.5, ENST00000347785.6, ENST00000347785.7, LEU1, NM_014207, P06127, uc317xos.1, uc317xos.2
UCSC ID: ENST00000347785.8_4
RefSeq Accession: NM_014207.4
Protein: P06127 (aka CD5_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.