Cd6 MGI Mouse Gene Detail - MGI:103566

Symbol

Cd6
Name

CD6 antigen

Feature Type

protein coding gene
IDs

MGI:103566
NCBI Gene: 12511
Alliance

gene page
Transcription Start Sites

6 TSS

Sequence Map

Chr19:10766705-10807422 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 19, 7.16 cM
Mapping Data

1 experiment

SNPs within 2kb

1107 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_103566	protein coding gene	Chr19:10766703-10807427 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0024857	protein coding gene	Chr19:8160787-8203851 (-)
A/J	MGP_AJ_G0024825	protein coding gene	Chr19:7607042-7646963 (-)
AKR/J	MGP_AKRJ_G0024800	protein coding gene	Chr19:7902118-7946764 (-)
BALB/cJ	MGP_BALBcJ_G0024825	protein coding gene	Chr19:7649603-7691966 (-)
C3H/HeJ	MGP_C3HHeJ_G0024591	protein coding gene	Chr19:7792068-7836080 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0025273	protein coding gene	Chr19:8512776-8554862 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0022700	protein coding gene	Chr19:8024250-8064609 (-)
CAST/EiJ	MGP_CASTEiJ_G0024064	protein coding gene	Chr19:7436999-7482718 (-)
CBA/J	MGP_CBAJ_G0024565	protein coding gene	Chr19:8558847-8601674 (-)
DBA/2J	MGP_DBA2J_G0024692	protein coding gene	Chr19:7611211-7651725 (-)
FVB/NJ	MGP_FVBNJ_G0024659	protein coding gene	Chr19:7655148-7696412 (-)
LP/J	MGP_LPJ_G0024779	protein coding gene	Chr19:8112809-8155035 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0024686	protein coding gene	Chr19:8462176-8504525 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0025321	protein coding gene	Chr19:7921791-7966888 (-)
PWK/PhJ	MGP_PWKPhJ_G0023809	protein coding gene	Chr19:7063005-7104338 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0023614	protein coding gene	Chr19:7101630-7146071 (-)
WSB/EiJ	MGP_WSBEiJ_G0024126	protein coding gene	Chr19:7815605-7857429 (-)

Human Ortholog

CD6, CD6 molecule

Vertebrate Orthologs

2

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

CD6, CD6 molecule
Synonyms

TP120
Links

HGNC:1691

NCBI Gene ID: 923

neXtProt AC: NX_P30203

UniProt: P30203
Chr Location

11q12.2; chr11:60971680-61020377 (+) GRCh38

MGI Vertebrate Homology

Cd6 stringent orthology
1 human;1 mouse;1 rat
HCOP

vertebrate homology predictions: CD6
Gene Tree

Cd6

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Phenotype Summary

9 phenotypes from 1 allele in 1 genetic background
13 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

10
Endonuclease-mediated

6
Gene trapped

1
Targeted

3
Incidental Mutations

APF
Find Mice (IMSR)

26 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit reduced susceptibility to insteinal ischemia/reperfusion induced injury due to reduced IgM-producing B1a cell self-renewal.

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All GO Annotations

35
GO References

6

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

706
cDNA Data

21

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas

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All Sequences

53
RefSeq

8
UniProt

5
CCDS

CCDS37917.1, CCDS50391.1

Ensembl

ENSMUSG00000024670 (Evidence)
NCBI Gene

12511

			Length	Strain/Species	Flank
genomic	ENSMUSG00000024670	Ensembl Gene Model \| MGI Sequence Detail	40718	C57BL/6J	± kb
transcript	ENSMUST00000080292	Ensembl \| MGI Sequence Detail	3032	Not Applicable
polypeptide	ENSMUSP00000079172	Ensembl \| MGI Sequence Detail	665	Not Applicable

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UniProt

5 Sequences
Protein Ontology

PR:000001837 CD6 molecule

(term hierarchy)
InterPro Domains

IPR001190 SRCR domain

IPR017448 SRCR-like domain

IPR036772 SRCR-like domain superfamily

IPR050686 SRCR-S1 Scavenger Receptor
GlyGen

Q61003 8 sites, 2 N-linked glycans (2 sites)

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All nucleic 25

Genomic 3

cDNA 22

Microarray probesets 5

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MGD-MRK-24451

Summaries

All 45

Gene Ontology 6

Phenotypes 13
Earliest

J:20989 Wee S, et al., Characterization of a CD6 ligand(s) expressed on human- and murine-derived cell lines and murine lymphoid tissues. Cell Immunol. 1994 Oct 15;158(2):353-64
Latest

J:332932 Ozawa M, et al., Efficient simultaneous double DNA knock-in in murine embryonic stem cells by CRISPR/Cas9 ribonucleoprotein-mediated circular plasmid targeting for generating gene-manipulated mice. Sci Rep. 2022 Dec 13;12(1):21558

TSS for Cd6:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr158245	Chr19:10807409-10807427 (-)	4 bp
Tssr158244	Chr19:10807285-10807406 (-)	76 bp
Tssr158243	Chr19:10807269-10807274 (-)	150 bp
Tssr158242	Chr19:10807261-10807266 (-)	158 bp
Tssr158241	Chr19:10806944-10806955 (-)	472 bp
Tssr158240	Chr19:10772020-10772042 (-)	35,391 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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