Cd84 Gene Detail

Summary

• Symbol
  Cd84
• Name
  CD84 antigen
• Synonyms
  A130013D22Rik, CDw84, SLAMF5

• Feature Type
  protein coding gene
• IDs
  MGI:1336885
  NCBI Gene: 12523
• Alliance
  gene page
• Transcription Start Sites
  50 TSS
• Candidate for QTL
  1 QTL

Location &
Maps

• Sequence Map
  Chr1:171667265-171718285 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
  8 experiments

Strain
Comparison

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

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1336885	protein coding gene	Chr1:171667261-171718288 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0016771	protein coding gene	Chr1:177676453-177715551 (+)
A/J	MGP_AJ_G0016750	protein coding gene	Chr1:170409476-170450989 (+)
AKR/J	MGP_AKRJ_G0016716	protein coding gene	Chr1:175560196-175598364 (+)
BALB/cJ	MGP_BALBcJ_G0016711	protein coding gene	Chr1:170963146-171002425 (+)
C3H/HeJ	MGP_C3HHeJ_G0016535	protein coding gene	Chr1:176136812-176174049 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0017173	protein coding gene	Chr1:183570421-183616879 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0014880	protein coding gene	Chr1:162129810-162163342 (+)
CAST/EiJ	MGP_CASTEiJ_G0016116	protein coding gene	Chr1:175482892-175525517 (+)
CBA/J	MGP_CBAJ_G0016509	protein coding gene	Chr1:190117860-190153801 (+)
DBA/2J	MGP_DBA2J_G0016616	protein coding gene	Chr1:169352685-169392272 (+)
FVB/NJ	MGP_FVBNJ_G0016613	protein coding gene	Chr1:167601114-167640236 (+)
LP/J	MGP_LPJ_G0016687	protein coding gene	Chr1:178754466-178798797 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0016640	protein coding gene	Chr1:197386343-197428110 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0017209	protein coding gene	Chr1:175413619-175454402 (+)
PWK/PhJ	MGP_PWKPhJ_G0015901	protein coding gene	Chr1:168721045-168764065 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0015684	protein coding gene	Chr1:174369387-174404947 (+)
WSB/EiJ	MGP_WSBEiJ_G0016177	protein coding gene	Chr1:175583115-175625129 (+)

Homology

• Human Ortholog
  CD84, CD84 molecule

• Vertebrate Orthologs
  3

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  CD84, CD84 molecule
  
• Synonyms
  hCD84, LY9B, mCD84, SLAMF5
• Links
  HGNC:1704

  NCBI Gene ID: 8832

  neXtProt AC: NX_Q9UIB8

  UniProt: Q9UIB8

  
  
• Chr Location
  1q23.3; chr1:160541095-160579516 (-)  GRCh38

---

• MGI Vertebrate Homology
  Cd84 stringent orthology
  1 human;1 mouse;1 rat;1 zebrafish
  
• HCOP
  vertebrate homology predictions: CD84
• Gene Tree
  Cd84
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  9 phenotypes from 3 alleles in 3 genetic backgrounds
  1 phenotype from multigenic genotypes
  22 phenotype references
  

• All Mutations and Alleles
  16
• Chemically induced (other)
  2
• Endonuclease-mediated
  6
• Targeted
  8
• Genomic Mutations
  3 involving Cd84
• Incidental Mutations
  Mutagenetix , APF
• Find Mice (IMSR)
  54 strains or lines available
• Comparison Matrix
  Gene Expression + Phenotype

Mice homozygous for a knock-out allele of this gene show defects in T follicular helper function and germinal center formation. Mice homozygous for a different knock-out allele display normal platelet physiology and thrombus formation.

Gene Ontology
(GO)
Classifications

• All GO Annotations
  24
• GO References
  5

Expression

• Assay Results
  714
• Tissues
  5
• cDNA Data
  18
• Literature Summary
  2

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas

Sequences &
Gene Models

• All Sequences
  61
• RefSeq
  10
• UniProt
  6
• CCDS
  CCDS15503.1, CCDS56657.1, CCDS69979.1

• Ensembl
  ENSMUSG00000038147 (Evidence)
• NCBI Gene
  12523

Representative Sequences			Length	Strain/Species
genomic	ENSMUSG00000038147	Ensembl Gene Model | MGI Sequence Detail	51021	C57BL/6J
transcript	ENSMUST00000155802	Ensembl | MGI Sequence Detail	3290	Not Applicable
polypeptide	ENSMUSP00000120881	Ensembl | MGI Sequence Detail	329	Not Applicable

Protein
Information

• UniProt
  6 Sequences
• Protein Ontology
  PR:000001319 SLAM family member 5
  (term hierarchy)
• InterPro Domains
  IPR007110 Immunoglobulin-like domain
  IPR036179 Immunoglobulin-like domain superfamily
  IPR013783 Immunoglobulin-like fold
  IPR003599 Immunoglobulin subtype
  IPR013106 Immunoglobulin V-set domain
• GlyGen
  Q18PI6 1 site

Molecular
Reagents

• All nucleic 24

  Genomic 5

  cDNA 18

  Primer pair 1

  
  

  Microarray probesets 3

Other
Accession IDs

MGI:2444272

References

• Summaries
  All 59

  Developmental Gene Expression 2

  Gene Ontology 5

  Phenotypes 22
• Earliest
  J:9401 Rathbun GA, et al., Molecular characterization of the A/J J558 family of heavy chain variable region gene segments. J Mol Biol. 1988 Aug 5;202(3):383-95
• Latest
  J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136

TSS for Cd84:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr10095	Chr1:171667262-171667267 (+)	0 bp
Tssr10096	Chr1:171667283-171667299 (+)	26 bp
Tssr10097	Chr1:171668124-171668137 (+)	866 bp
Tssr10098	Chr1:171668139-171668165 (+)	887 bp
Tssr10099	Chr1:171668174-171668208 (+)	926 bp
Tssr10100	Chr1:171668382-171668401 (+)	1,127 bp
Tssr10101	Chr1:171668418-171668436 (+)	1,162 bp
Tssr10102	Chr1:171668542-171668556 (+)	1,284 bp
Tssr10103	Chr1:171671997-171672038 (+)	4,753 bp
Tssr10104	Chr1:171672540-171672556 (+)	5,283 bp
Tssr10105	Chr1:171673246-171673251 (+)	5,984 bp
Tssr10106	Chr1:171673269-171673285 (+)	6,012 bp
Tssr10107	Chr1:171673288-171673302 (+)	6,030 bp
Tssr10108	Chr1:171673413-171673415 (+)	6,149 bp
Tssr10109	Chr1:171675614-171675627 (+)	8,356 bp
Tssr10110	Chr1:171675635-171675659 (+)	8,382 bp
Tssr10111	Chr1:171675950-171675973 (+)	8,697 bp
Tssr292	Chr1:171677221-171677223 (+)	9,957 bp
Tssr10112	Chr1:171677395-171677412 (+)	10,139 bp
Tssr10113	Chr1:171679419-171679434 (+)	12,162 bp
Tssr10114	Chr1:171679468-171679479 (+)	12,209 bp
Tssr10115	Chr1:171679527-171679540 (+)	12,269 bp
Tssr10116	Chr1:171679549-171679560 (+)	12,290 bp
Tssr10117	Chr1:171679562-171679574 (+)	12,303 bp
Tssr10118	Chr1:171679581-171679590 (+)	12,321 bp
Tssr10119	Chr1:171679597-171679608 (+)	12,338 bp
Tssr10120	Chr1:171679618-171679623 (+)	12,356 bp
Tssr10121	Chr1:171679659-171679672 (+)	12,401 bp
Tssr10122	Chr1:171681737-171681748 (+)	14,478 bp
Tssr10123	Chr1:171681761-171681787 (+)	14,509 bp
Tssr10124	Chr1:171681838-171681858 (+)	14,583 bp
Tssr10125	Chr1:171682433-171682444 (+)	15,174 bp
Tssr10126	Chr1:171682468-171682476 (+)	15,207 bp
Tssr10127	Chr1:171682596-171682604 (+)	15,335 bp
Tssr10128	Chr1:171682608-171682627 (+)	15,353 bp
Tssr10129	Chr1:171682641-171682653 (+)	15,382 bp
Tssr10130	Chr1:171683475-171683495 (+)	16,220 bp
Tssr10131	Chr1:171683645-171683656 (+)	16,386 bp
Tssr10132	Chr1:171683701-171683738 (+)	16,455 bp
Tssr10133	Chr1:171684081-171684097 (+)	16,824 bp
Tssr10134	Chr1:171684183-171684194 (+)	16,924 bp
Tssr10135	Chr1:171684217-171684238 (+)	16,963 bp
Tssr10136	Chr1:171684315-171684326 (+)	17,056 bp
Tssr10137	Chr1:171684404-171684454 (+)	17,164 bp
Tssr10138	Chr1:171684483-171684507 (+)	17,230 bp
Tssr10139	Chr1:171684556-171684593 (+)	17,310 bp
Tssr10140	Chr1:171684663-171684678 (+)	17,406 bp
Tssr10141	Chr1:171691950-171691978 (+)	24,699 bp
Tssr10142	Chr1:171692158-171692178 (+)	24,903 bp
Tssr10143	Chr1:171696376-171696400 (+)	29,123 bp

Cd84 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