Human Gene CD48 (ENST00000368046.8_13) from GENCODE V47lift37

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Description: CD48 molecule, transcript variant 1 (from RefSeq NM_001778.4)
Gencode Transcript: ENST00000368046.8_13
Gencode Gene: ENSG00000117091.10_14
Transcript (Including UTRs)
Position: hg19 chr1:160,648,536-160,681,612 Size: 33,077 Total Exon Count: 4 Strand: -
Coding Region
Position: hg19 chr1:160,648,842-160,681,553 Size: 32,712 Coding Exon Count: 4

Page Index	Sequence and Links	UniProtKB Comments	Primers	CTD	Gene Alleles
RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species	GO Annotations
mRNA Descriptions	Pathways	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr1:160,648,536-160,681,612)			mRNA (may differ from genome)		Protein (243 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	MGI	OMIM	PubMed	Reactome	UniProtKB
Wikipedia	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: CD48_HUMAN DESCRIPTION: RecName: Full=CD48 antigen; AltName: Full=B-lymphocyte activation marker BLAST-1; AltName: Full=BCM1 surface antigen; AltName: Full=Leukocyte antigen MEM-102; AltName: Full=TCT.1; AltName: CD_antigen=CD48; Flags: Precursor; FUNCTION: Ligand for CD2. Might facilitate interaction between activated lymphocytes. Probably involved in regulating T-cell activation. INTERACTION: Q9BZW8:CD244; NbExp=2; IntAct=EBI-714770, EBI-1580565; SUBCELLULAR LOCATION: Cell membrane; Lipid-anchor, GPI-anchor. SIMILARITY: Contains 1 Ig-like C2-type (immunoglobulin-like) domain. 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

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D000082 Acetaminophen C049325 1,2-dithiol-3-thione C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl C010914 2,4-diaminotoluene C009505 4,4'-diaminodiphenylmethane C065250 4-hydroxy-equilenin C547126 AZM551248 D000643 Ammonium Chloride D001205 Ascorbic Acid D001564 Benzo(a)pyrene more ... click here to view the complete list

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 255.57 RPKM in Cells - EBV-transformed lymphocytes Total median expression: 399.30 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-14.00	59	-0.237	Picture	PostScript	Text
3' UTR	-57.30	306	-0.187	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
IPR013106 - Ig_V-set
IPR015631 - SLAM_fam_rcpts

Pfam Domains:
PF07686 - Immunoglobulin V-set domain
PF13895 - Immunoglobulin domain

SCOP Domains:
48726 - Immunoglobulin

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

2EDO - NMR MuPIT

ModBase Predicted Comparative 3D Structure on P09326


Front	Top	Side

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD	Ensembl

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0003823 antigen binding GO:0005515 protein binding GO:0038023 signaling receptor activity Biological Process: GO:0002819 regulation of adaptive immune response GO:0006952 defense response GO:0007165 signal transduction GO:0050900 leukocyte migration Cellular Component: GO:0005886 plasma membrane GO:0005887 integral component of plasma membrane GO:0016020 membrane GO:0031225 anchored component of membrane GO:0045121 membrane raft GO:0070062 extracellular exosome

Descriptions from all associated GenBank mRNAs


	M37766 - Human MEM-102 glycoprotein mRNA, complete cds. BC016182 - Homo sapiens CD48 molecule, mRNA (cDNA clone MGC:22996 IMAGE:4850933), complete cds. M59904 - Human pan-leukocyte antigen (CD48) mRNA, complete cds. X06341 - Human mRNA for lymphocte activation marker Blast-1. JD199102 - Sequence 180126 from Patent EP1572962. KJ890866 - Synthetic construct Homo sapiens clone ccsbBroadEn_00260 CD48 gene, encodes complete protein. BT019813 - Homo sapiens CD48 antigen (B-cell membrane protein) mRNA, complete cds. DQ896316 - Synthetic construct Homo sapiens clone IMAGE:100010776; FLH193218.01L; RZPDo839D1268D CD48 molecule (CD48) gene, encodes complete protein. EU176422 - Synthetic construct Homo sapiens clone IMAGE:100006500; FLH193222.01X; RZPDo839D1278D CD48 molecule (CD48) gene, encodes complete protein. AB590257 - Synthetic construct DNA, clone: pFN21AE1514, Homo sapiens CD48 gene for CD48 molecule, without stop codon, in Flexi system. CR457012 - Homo sapiens full open reading frame cDNA clone RZPDo834G095D for gene CD48, CD48 antigen (B-cell membrane protein); complete cds, incl. stopcodon. AK225636 - Homo sapiens mRNA for CD48 antigen variant, clone: SPL08742. AK310624 - Homo sapiens cDNA, FLJ17666. AK310744 - Homo sapiens cDNA, FLJ17786. BC030224 - Homo sapiens CD48 molecule, mRNA (cDNA clone MGC:34616 IMAGE:5223308), complete cds. CU688852 - Synthetic construct Homo sapiens gateway clone IMAGE:100018141 5' read CD48 mRNA. KJ901325 - Synthetic construct Homo sapiens clone ccsbBroadEn_10719 CD48 gene, encodes complete protein. JD234420 - Sequence 215444 from Patent EP1572962.

Biochemical and Signaling Pathways


	Reactome (by CSHL, EBI, and GO) Protein P09326 (Reactome details) participates in the following event(s): R-HSA-202722 CD48 binds CD244 R-HSA-202733 Cell surface interactions at the vascular wall R-HSA-109582 Hemostasis

Other Names for This Gene


	Alternate Gene Symbols: BCM1, BLAST1, CD48_HUMAN, ENST00000368046.1, ENST00000368046.2, ENST00000368046.3, ENST00000368046.4, ENST00000368046.5, ENST00000368046.6, ENST00000368046.7, NM_001778, P09326, Q5U055, Q8MGR0, uc318gks.1, uc318gks.2 UCSC ID: ENST00000368046.8_13 RefSeq Accession: NM_001778.4 Protein: P09326 (aka CD48_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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