Human Gene LY9 (ENST00000392203.8) from GENCODE V44
  Description: Homo sapiens lymphocyte antigen 9 (LY9), transcript variant 4, mRNA. (from RefSeq NM_001261457)
RefSeq Summary (NM_001261457): LY9 belongs to the SLAM family of immunomodulatory receptors (see SLAMF1; MIM 603492) and interacts with the adaptor molecule SAP (SH2D1A; MIM 300490) (Graham et al., 2006 [PubMed 16365421]).[supplied by OMIM, Mar 2008].
Gencode Transcript: ENST00000392203.8
Gencode Gene: ENSG00000122224.18
Transcript (Including UTRs)
   Position: hg38 chr1:160,796,112-160,828,255 Size: 32,144 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg38 chr1:160,796,188-160,827,816 Size: 31,629 Coding Exon Count: 9 

Page IndexSequence and LinksPrimersMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:160,796,112-160,828,255)mRNA (may differ from genome)Protein (565 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCLynxMalacardsMGIOMIMPubMed
UniProtKBWikipediaBioGrid CRISPR DB

-  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: LY9
Diseases sorted by gene-association score: systemic lupus erythematosus (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 8.13 RPKM in Spleen
Total median expression: 29.58 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 -16.6076-0.218 Picture PostScript Text
3' UTR -127.00439-0.289 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
IPR015631 - SLAM_fam_rcpts

ModBase Predicted Comparative 3D Structure on Q5VYH9
FrontTopSide
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     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  BC121049 - Homo sapiens lymphocyte antigen 9, mRNA (cDNA clone MGC:149745 IMAGE:40117946), complete cds.
AF244129 - Homo sapiens cell-surface molecule Ly-9 mRNA, complete cds.
AK292048 - Homo sapiens cDNA FLJ75340 complete cds, highly similar to Homo sapiens cell-surface molecule Ly-9 mRNA.
BC027920 - Homo sapiens lymphocyte antigen 9, mRNA (cDNA clone MGC:34782 IMAGE:5225850), complete cds.
L42621 - Homo sapiens Ly-9 mRNA, complete cds.
AY007142 - Homo sapiens clone CDABP0070 mRNA sequence.
KJ901560 - Synthetic construct Homo sapiens clone ccsbBroadEn_10954 LY9 gene, encodes complete protein.
BC062589 - Homo sapiens lymphocyte antigen 9, mRNA (cDNA clone IMAGE:5215651).
AF055708 - Homo sapiens lymphocyte antigen 9 precursor (LY9) mRNA, alternatively spliced, partial cds.
AF055709 - Homo sapiens lymphocyte antigen 9 precursor (LY9) mRNA, partial cds.
AK303403 - Homo sapiens cDNA FLJ56843 complete cds, highly similar to T-lymphocyte surface antigen Ly-9 precursor.
HQ447693 - Synthetic construct Homo sapiens clone IMAGE:100071021; CCSB013751_01 lymphocyte antigen 9 (LY9) gene, encodes complete protein.
KJ891559 - Synthetic construct Homo sapiens clone ccsbBroadEn_00953 LY9 gene, encodes complete protein.
BC042905 - Homo sapiens lymphocyte antigen 9, mRNA (cDNA clone IMAGE:5932767).
BC064485 - Homo sapiens lymphocyte antigen 9, mRNA (cDNA clone IMAGE:5483404), complete cds.
AK128573 - Homo sapiens cDNA FLJ46732 fis, clone TRACH3019807.
JD202587 - Sequence 183611 from Patent EP1572962.
JD302182 - Sequence 283206 from Patent EP1572962.
JD071629 - Sequence 52653 from Patent EP1572962.
JD544679 - Sequence 525703 from Patent EP1572962.
JD099417 - Sequence 80441 from Patent EP1572962.
JD207453 - Sequence 188477 from Patent EP1572962.
JD497309 - Sequence 478333 from Patent EP1572962.
JD289858 - Sequence 270882 from Patent EP1572962.
JD432145 - Sequence 413169 from Patent EP1572962.
JD508559 - Sequence 489583 from Patent EP1572962.
JD166340 - Sequence 147364 from Patent EP1572962.
JD039792 - Sequence 20816 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000392203.1, ENST00000392203.2, ENST00000392203.3, ENST00000392203.4, ENST00000392203.5, ENST00000392203.6, ENST00000392203.7, NM_001261457, Q5VYH9, Q5VYH9_HUMAN, RP11-312J18.1-002, uc001fww.1, uc001fww.2, uc001fww.3, uc001fww.4, uc001fww.5
UCSC ID: ENST00000392203.8
RefSeq Accession: NM_001261457
Protein: Q5VYH9 CCDS: CCDS65696.1

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