Human Gene THY1 (ENST00000284240.10) from GENCODE V44
  Description: Homo sapiens Thy-1 cell surface antigen (THY1), transcript variant 1, mRNA. (from RefSeq NM_006288)
RefSeq Summary (NM_006288): This gene encodes a cell surface glycoprotein and member of the immunoglobulin superfamily of proteins. The encoded protein is involved in cell adhesion and cell communication in numerous cell types, but particularly in cells of the immune and nervous systems. The encoded protein is widely used as a marker for hematopoietic stem cells. This gene may function as a tumor suppressor in nasopharyngeal carcinoma. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2015]. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments.
Gencode Transcript: ENST00000284240.10
Gencode Gene: ENSG00000154096.14
Transcript (Including UTRs)
   Position: hg38 chr11:119,415,476-119,423,172 Size: 7,697 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg38 chr11:119,419,408-119,420,905 Size: 1,498 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr11:119,415,476-119,423,172)mRNA (may differ from genome)Protein (161 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Thy-1 membrane glycoprotein; AltName: Full=CDw90; AltName: Full=Thy-1 antigen; AltName: CD_antigen=CD90; Flags: Precursor;
FUNCTION: May play a role in cell-cell or cell-ligand interactions during synaptogenesis and other events in the brain.
SUBCELLULAR LOCATION: Cell membrane; Lipid-anchor, GPI-anchor (By similarity).
SIMILARITY: Contains 1 Ig-like V-type (immunoglobulin-like) 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

-  MalaCards Disease Associations
  MalaCards Gene Search: THY1
Diseases sorted by gene-association score: nasopharyngeal carcinoma (4), thymoma (4), warthin tumor (2), gerstmann-straussler disease (1), murray valley encephalitis (1), granulomatous angiitis (1), cd45 deficiency (1)

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 174.89 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 1602.08 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 -28.6084-0.340 Picture PostScript Text
3' UTR -1534.903932-0.390 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
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR003599 - Ig_sub
IPR013151 - Immunoglobulin

Pfam Domains:
PF00047 - Immunoglobulin domain

ModBase Predicted Comparative 3D Structure on P04216
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005096 GTPase activator activity
GO:0005178 integrin binding
GO:0005515 protein binding
GO:0019899 enzyme binding
GO:0019901 protein kinase binding
GO:0034235 GPI anchor binding

Biological Process:
GO:0001525 angiogenesis
GO:0001952 regulation of cell-matrix adhesion
GO:0002693 positive regulation of cellular extravasation
GO:0006469 negative regulation of protein kinase activity
GO:0007010 cytoskeleton organization
GO:0007155 cell adhesion
GO:0007229 integrin-mediated signaling pathway
GO:0007267 cell-cell signaling
GO:0030334 regulation of cell migration
GO:0030336 negative regulation of cell migration
GO:0034116 positive regulation of heterotypic cell-cell adhesion
GO:0043113 receptor clustering
GO:0043547 positive regulation of GTPase activity
GO:0046549 retinal cone cell development
GO:0046777 protein autophosphorylation
GO:0048041 focal adhesion assembly
GO:0050771 negative regulation of axonogenesis
GO:0050852 T cell receptor signaling pathway
GO:0050860 negative regulation of T cell receptor signaling pathway
GO:0050870 positive regulation of T cell activation
GO:0051281 positive regulation of release of sequestered calcium ion into cytosol
GO:0051894 positive regulation of focal adhesion assembly
GO:0061099 negative regulation of protein tyrosine kinase activity
GO:0070571 negative regulation of neuron projection regeneration
GO:0098609 cell-cell adhesion
GO:2000298 regulation of Rho-dependent protein serine/threonine kinase activity

Cellular Component:
GO:0005576 extracellular region
GO:0005783 endoplasmic reticulum
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0005925 focal adhesion
GO:0009897 external side of plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0016324 apical plasma membrane
GO:0030425 dendrite
GO:0030426 growth cone
GO:0030673 axolemma
GO:0031225 anchored component of membrane
GO:0031362 anchored component of external side of plasma membrane
GO:0032590 dendrite membrane
GO:0032809 neuronal cell body membrane
GO:0043209 myelin sheath
GO:0045121 membrane raft
GO:0046658 anchored component of plasma membrane
GO:0070062 extracellular exosome

-  Descriptions from all associated GenBank mRNAs
  JD478540 - Sequence 459564 from Patent EP1572962.
JD543230 - Sequence 524254 from Patent EP1572962.
JD537271 - Sequence 518295 from Patent EP1572962.
JD463783 - Sequence 444807 from Patent EP1572962.
JD478541 - Sequence 459565 from Patent EP1572962.
JD543231 - Sequence 524255 from Patent EP1572962.
AK094374 - Homo sapiens cDNA FLJ37055 fis, clone BRACE2014161, highly similar to Homo sapiens Thy-1 glycoprotein and Thy-1 co-transcribed protein mRNAs.
BC009328 - Homo sapiens cDNA clone IMAGE:4125908, **** WARNING: chimeric clone ****.
AK057865 - Homo sapiens cDNA FLJ25136 fis, clone CBR07030, highly similar to THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR.
AK090996 - Homo sapiens cDNA FLJ33677 fis, clone BRAWH2002125, highly similar to THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR.
AL161958 - Homo sapiens mRNA; cDNA DKFZp761B15121 (from clone DKFZp761B15121).
BC005175 - Homo sapiens Thy-1 cell surface antigen, mRNA (cDNA clone IMAGE:3507917), **** WARNING: chimeric clone ****.
AF261093 - Homo sapiens Thy-1 glycoprotein and Thy-1 co-transcribed protein mRNAs, complete cds.
BC062593 - Homo sapiens cDNA clone IMAGE:5225379, **** WARNING: chimeric clone ****.
BC037832 - Homo sapiens Thy-1 cell surface antigen, mRNA (cDNA clone IMAGE:4812471), **** WARNING: chimeric clone ****.
JD328041 - Sequence 309065 from Patent EP1572962.
JD243558 - Sequence 224582 from Patent EP1572962.
JD283593 - Sequence 264617 from Patent EP1572962.
JD283592 - Sequence 264616 from Patent EP1572962.
JD556632 - Sequence 537656 from Patent EP1572962.
JD232046 - Sequence 213070 from Patent EP1572962.
AK314018 - Homo sapiens cDNA, FLJ94676, Homo sapiens Thy-1 co-transcribed (LOC94105), mRNA.
JD456143 - Sequence 437167 from Patent EP1572962.
JD335017 - Sequence 316041 from Patent EP1572962.
JD103099 - Sequence 84123 from Patent EP1572962.
JD159923 - Sequence 140947 from Patent EP1572962.
JD326586 - Sequence 307610 from Patent EP1572962.
JD490336 - Sequence 471360 from Patent EP1572962.
JD222628 - Sequence 203652 from Patent EP1572962.
JD344221 - Sequence 325245 from Patent EP1572962.
JD098314 - Sequence 79338 from Patent EP1572962.
JD051764 - Sequence 32788 from Patent EP1572962.
JD187944 - Sequence 168968 from Patent EP1572962.
JD088390 - Sequence 69414 from Patent EP1572962.
JD088389 - Sequence 69413 from Patent EP1572962.
JD045463 - Sequence 26487 from Patent EP1572962.
BC065559 - Homo sapiens Thy-1 cell surface antigen, mRNA (cDNA clone MGC:74728 IMAGE:6137513), complete cds.
AB209209 - Homo sapiens mRNA for Thy-1 cell surface antigen variant protein.
AK090644 - Homo sapiens cDNA FLJ33325 fis, clone BNGH42008832, highly similar to THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR.
JD187963 - Sequence 168987 from Patent EP1572962.
JD399314 - Sequence 380338 from Patent EP1572962.
JD106983 - Sequence 88007 from Patent EP1572962.
JD340617 - Sequence 321641 from Patent EP1572962.
JD485998 - Sequence 467022 from Patent EP1572962.
JD295395 - Sequence 276419 from Patent EP1572962.
JD525677 - Sequence 506701 from Patent EP1572962.
JD520274 - Sequence 501298 from Patent EP1572962.
JD413161 - Sequence 394185 from Patent EP1572962.
JD126848 - Sequence 107872 from Patent EP1572962.
JD054837 - Sequence 35861 from Patent EP1572962.
JD175783 - Sequence 156807 from Patent EP1572962.
JD131356 - Sequence 112380 from Patent EP1572962.
JD023548 - Sequence 4572 from Patent EP1572962.
JD190464 - Sequence 171488 from Patent EP1572962.
JD498711 - Sequence 479735 from Patent EP1572962.
JD279168 - Sequence 260192 from Patent EP1572962.
KJ892277 - Synthetic construct Homo sapiens clone ccsbBroadEn_01671 THY1 gene, encodes complete protein.
DQ895011 - Synthetic construct Homo sapiens clone IMAGE:100009471; FLH180305.01L; RZPDo839A10133D Thy-1 cell surface antigen (THY1) gene, encodes complete protein.
DQ895013 - Synthetic construct Homo sapiens clone IMAGE:100009473; FLH263688.01L; RZPDo839A12133D Thy-1 cell surface antigen (THY1) gene, encodes complete protein.
EU176310 - Synthetic construct Homo sapiens clone IMAGE:100006411; FLH180309.01X; RZPDo839A10134D Thy-1 cell surface antigen (THY1) gene, encodes complete protein.
AB528296 - Synthetic construct DNA, clone: pF1KE0419, Homo sapiens THY1 gene for Thy-1 cell surface antigen, without stop codon, in Flexi system.
AM393032 - Synthetic construct Homo sapiens clone IMAGE:100001920 for hypothetical protein (THY1 gene).
AM393214 - Synthetic construct Homo sapiens clone IMAGE:100001915 for hypothetical protein (THY1 gene).
JD464797 - Sequence 445821 from Patent EP1572962.
JD424057 - Sequence 405081 from Patent EP1572962.
JD031520 - Sequence 12544 from Patent EP1572962.
JD322156 - Sequence 303180 from Patent EP1572962.
JD496094 - Sequence 477118 from Patent EP1572962.
JD456269 - Sequence 437293 from Patent EP1572962.
JD411167 - Sequence 392191 from Patent EP1572962.
JD474188 - Sequence 455212 from Patent EP1572962.
JD154522 - Sequence 135546 from Patent EP1572962.
JD025614 - Sequence 6638 from Patent EP1572962.
S59749 - Homo sapiens 5E10 antigen (Thy-1) mRNA, partial cds.
JD029179 - Sequence 10203 from Patent EP1572962.
JD142517 - Sequence 123541 from Patent EP1572962.
JD045941 - Sequence 26965 from Patent EP1572962.
JD333797 - Sequence 314821 from Patent EP1572962.
JD079355 - Sequence 60379 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04670 - Leukocyte transendothelial migration

BioCarta from NCI Cancer Genome Anatomy Project
h_tcytotoxicPathway - T Cytotoxic Cell Surface Molecules
h_thelperPathway - T Helper Cell Surface Molecules

Reactome (by CSHL, EBI, and GO)

Protein P04216 (Reactome details) participates in the following event(s):

R-HSA-8940388 GPLD1 hydrolyses GPI-anchors from proteins
R-HSA-163125 Post-translational modification: synthesis of GPI-anchored proteins
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000284240.1, ENST00000284240.2, ENST00000284240.3, ENST00000284240.4, ENST00000284240.5, ENST00000284240.6, ENST00000284240.7, ENST00000284240.8, ENST00000284240.9, NM_006288, P04216, Q16008, Q9NSP1, THY1_HUMAN, uc001pwr.1, uc001pwr.2, uc001pwr.3, uc001pwr.4, uc001pwr.5
UCSC ID: ENST00000284240.10
RefSeq Accession: NM_006288
Protein: P04216 (aka THY1_HUMAN)
CCDS: CCDS8424.1

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