Cd48 Gene Detail

Summary

• Symbol
  Cd48
• Name
  CD48 antigen
• Synonyms
  Bcm-1, BCM1, BLAST-1, Sgp-60

• Feature Type
  protein coding gene
• IDs
  MGI:88339
  NCBI Gene: 12506
• Alliance
  gene page
• Transcription Start Sites
  4 TSS
• Candidate for QTL
  1 QTL

Location &
Maps

• Sequence Map
  Chr1:171509577-171532826 bp, + strand

  From Ensembl annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 1, 79.54 cM
• Mapping Data
  19 experiments

Strain
Comparison

• SNPs within 2kb
  169 from dbSNP Build 142
• Strain Annotations
  18
• RFLP
  2

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_88339	protein coding gene	Chr1:171508989-171532826 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0016769	protein coding gene	Chr1:177516961-177540630 (+)
A/J	MGP_AJ_G0016748	protein coding gene	Chr1:170254108-170275715 (+)
AKR/J	MGP_AKRJ_G0016714	protein coding gene	Chr1:175398358-175422568 (+)
BALB/cJ	MGP_BALBcJ_G0016709	protein coding gene	Chr1:170798882-170820302 (+)
C3H/HeJ	MGP_C3HHeJ_G0016533	protein coding gene	Chr1:175962050-175984942 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0017171	protein coding gene	Chr1:183398374-183424530 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0014878	protein coding gene	Chr1:161996247-162005854 (+)
CAST/EiJ	MGP_CASTEiJ_G0016114	protein coding gene	Chr1:175324844-175350658 (+)
CBA/J	MGP_CBAJ_G0016507	protein coding gene	Chr1:189928486-189951243 (+)
DBA/2J	MGP_DBA2J_G0016614	protein coding gene	Chr1:169196347-169218628 (+)
FVB/NJ	MGP_FVBNJ_G0016611	protein coding gene	Chr1:167449179-167470788 (+)
LP/J	MGP_LPJ_G0016685	protein coding gene	Chr1:178588884-178614239 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0016638	protein coding gene	Chr1:197220785-197243347 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0017207	protein coding gene	Chr1:175256658-175279603 (+)
PWK/PhJ	MGP_PWKPhJ_G0015899	protein coding gene	Chr1:168560629-168583855 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0015683	protein coding gene	Chr1:174184556-174214089 (+)
WSB/EiJ	MGP_WSBEiJ_G0016175	protein coding gene	Chr1:175426551-175448890 (+)

Homology

• Human Ortholog
  CD48, CD48 molecule

• Vertebrate Orthologs
  3

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  CD48, CD48 molecule
  
• Synonyms
  BCM1, BLAST, BLAST1, hCD48, mCD48, MEM-102, SLAMF2
• Links
  HGNC:1683

  NCBI Gene ID: 962

  neXtProt AC: NX_P09326

  UniProt: P09326

  
  
• Chr Location
  1q23.3; chr1:160678746-160711831 (-)  GRCh38

---

• MGI Vertebrate Homology
  Cd48 stringent orthology
  1 human;1 mouse;1 rat;1 zebrafish
  
• HCOP
  vertebrate homology predictions: CD48
• Gene Tree
  Cd48
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  3 phenotypes from 1 allele in 1 genetic background
  17 phenotype references
  

• All Mutations and Alleles
  11
• Chemically induced (other)
  2
• Endonuclease-mediated
  3
• Targeted
  6
• Genomic Mutations
  3 involving Cd48
• Incidental Mutations
  Mutagenetix , APF
• Find Mice (IMSR)
  22 strains or lines available

Homozygous mutation of this gene results in a slight increase in CD4+CD8- thymocytes and impaired T cell proliferation in response to mitogens, anti-CD3 antibodies, and alloantigens.

Gene Ontology
(GO)
Classifications

• All GO Annotations
  10
• GO References
  7

Expression

• Assay Results
  767
• Tissues
  13
• cDNA Data
  49
• Literature Summary
  3

Images

Tissue x Stage Matrix

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas

Sequences &
Gene Models

• All Sequences
  54
• RefSeq
  8
• UniProt
  6
• CCDS
  CCDS15501.1, CCDS87923.1

• Ensembl
  ENSMUSG00000015355 (Evidence)
• NCBI Gene
  12506

Representative Sequences			Length	Strain/Species
genomic	ENSMUSG00000015355	Ensembl Gene Model | MGI Sequence Detail	23250	C57BL/6J
transcript	ENSMUST00000068584	Ensembl | MGI Sequence Detail	1186	Not Applicable
polypeptide	ENSMUSP00000064241	Ensembl | MGI Sequence Detail	240	Not Applicable

Protein
Information

• UniProt
  6 Sequences
• Protein Ontology
  PR:000001308 CD48 molecule
  (term hierarchy)
• PDB
  2PTT, 2PTV
• InterPro Domains
  IPR007110 Immunoglobulin-like domain
  IPR036179 Immunoglobulin-like domain superfamily
  IPR013783 Immunoglobulin-like fold
  IPR003599 Immunoglobulin subtype
  IPR013106 Immunoglobulin V-set domain

Molecular
Reagents

• All nucleic 69

  Genomic 17

  cDNA 49

  Primer pair 3

  
  

  Microarray probesets 3

Other
Accession IDs

MGD-MRK-1529, MGD-MRK-1865, MGI:2138248, MGI:2138623

References

• Summaries
  All 73

  Developmental Gene Expression 3

  Gene Ontology 7

  Phenotypes 17
• Earliest
  J:10552 Wong YW, et al., Structure, expression, and genetic linkage of the mouse BCM1 (OX45 or Blast-1) antigen. Evidence for genetic duplication giving rise to the BCM1 region on mouse chromosome 1 and the CD2/LFA3 region on mouse chromosome 3. J Exp Med. 1990 Jun 1;171(6):2115-30
• Latest
  J:326541 Cyagen Biosciences Inc., Cyagen Biosciences Website. 2022;

TSS for Cd48:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr10078	Chr1:171509559-171509560 (+)	-17 bp
Tssr10079	Chr1:171509572-171509639 (+)	29 bp
Tssr10080	Chr1:171509645-171509660 (+)	76 bp
Tssr10081	Chr1:171523457-171523475 (+)	13,889 bp

Cd48 is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Sle1b	Chr1, 75.10 cM		J:94686	Congenic and physical mapping was used to show that Sle1b mapped within an interval containing SLAM family members ordered as Cd244 - Ly9 - Slamf7 - Cd48 - Slamf1 - Cd84 - Slamf6. Haplotype analysis of the aformentioned region were suggestive that the markers contained within the region as contributing to the Sle1b phenotype. The strongest contribution may come from Slamf6.

*cM position of peak correlated region/marker