Clec9a MGI Mouse Gene Detail - MGI:2444608 - C-type lectin domain family 9, member a

Symbol

Clec9a
Name

C-type lectin domain family 9, member a
Synonyms

9830005G06Rik, DNGR-1

Feature Type

protein coding gene
IDs

MGI:2444608
NCBI Gene: 232414
Alliance

gene page
Transcription Start Sites

4 TSS

Sequence Map

Chr6:129385825-129401726 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 6, 63.30 cM
Mapping Data

2 experiments

SNPs within 2kb

630 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2444608	protein coding gene	Chr6:129385825-129401727 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0031347	protein coding gene	Chr6:133079335-133096021 (+)
A/J	MGP_AJ_G0031318	protein coding gene	Chr6:127983527-128000031 (+)
AKR/J	MGP_AKRJ_G0031246	protein coding gene	Chr6:131482004-131500059 (+)
BALB/cJ	MGP_BALBcJ_G0031325	protein coding gene	Chr6:127631487-127647232 (+)
C3H/HeJ	MGP_C3HHeJ_G0031049	protein coding gene	Chr6:131677669-131693484 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0031784	protein coding gene	Chr6:136575253-136590993 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0028930	protein coding gene	Chr6:126307489-126325823 (+)
CAST/EiJ	MGP_CASTEiJ_G0030427	protein coding gene	Chr6:131910034-131927460 (+)
CBA/J	MGP_CBAJ_G0031009	protein coding gene	Chr6:141952490-141968254 (+)
DBA/2J	MGP_DBA2J_G0031166	protein coding gene	Chr6:126936857-126952642 (+)
FVB/NJ	MGP_FVBNJ_G0031116	protein coding gene	Chr6:125819731-125835461 (+)
LP/J	MGP_LPJ_G0031246	protein coding gene	Chr6:133296490-133313557 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0031154	protein coding gene	Chr6:145794651-145811189 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0031817	protein coding gene	Chr6:131544772-131560597 (+)
PWK/PhJ	MGP_PWKPhJ_G0030145	protein coding gene	Chr6:125216344-125232375 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0029974	protein coding gene	Chr6:129564034-129580823 (+)
WSB/EiJ	MGP_WSBEiJ_G0030515	protein coding gene	Chr6:131968943-131985263 (+)

Human Ortholog

CLEC9A, C-type lectin domain containing 9A

Vertebrate Orthologs

2

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

CLEC9A, C-type lectin domain containing 9A
Synonyms

CD370, DNGR-1, DNGR1, UNQ9341
Links

HGNC:26705

NCBI Gene ID: 283420

neXtProt AC: NX_Q6UXN8

UniProt: Q6UXN8
Chr Location

12p13.2; chr12:10030678-10066031 (+) GRCh38

MGI Vertebrate Homology

Clec9a stringent orthology
1 human;1 mouse;1 rat
HCOP

vertebrate homology predictions: CLEC9A
Gene Tree

Clec9a

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Phenotype Summary

3 phenotypes from 4 alleles in 4 genetic backgrounds
50 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

17
Endonuclease-mediated

5
Targeted

12
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

29 strains or lines available
Comparison Matrix

Gene Expression + Phenotype
Recombinase Activity

Comparison Matrix Gene Expression + Recombinase Activity

Homozygous null mice have CD8alpha⁺ dendritic cells that are defective in cross-presentation of dead-cell associated antigens.

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All GO Annotations

12
GO References

8

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

6
Literature Summary

1

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas

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All Sequences

46
RefSeq

8
UniProt

1
CCDS

CCDS39658.1, CCDS57454.1, CCDS57455.1

Ensembl

ENSMUSG00000046080 (Evidence)
NCBI Gene

232414

			Length	Strain/Species	Flank
genomic	ENSMUSG00000046080	Ensembl Gene Model \| MGI Sequence Detail	15902	C57BL/6J	± kb
transcript	ENSMUST00000058352	Ensembl \| MGI Sequence Detail	3293	Not Applicable
polypeptide	ENSMUSP00000056625	Ensembl \| MGI Sequence Detail	264	Not Applicable

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UniProt

1 Sequence
Protein Ontology

PR:000026296 C-type lectin domain family 9 member A

(term hierarchy)
PDB

3J82
InterPro Domains

IPR018378 C-type lectin, conserved site

IPR043315 C-type lectin domain family 9 member A

IPR016187 C-type lectin fold

IPR001304 C-type lectin-like

IPR016186 C-type lectin-like/link domain superfamily

IPR033992 Natural killer cell receptor-like, C-type lectin-like domain
GlyGen

Q8BRU4 2 sites

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All nucleic 6

cDNA 6

Microarray probesets 1

Summaries

All 78

Developmental Gene Expression 1

Gene Ontology 8

Phenotypes 50
Earliest

J:80000 The FANTOM Consortium and The RIKEN Genome Exploration Research Group Phase I & II Team, Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002;420:563-573
Latest

J:349001 Xiao H, et al., Genomic deletion of Bcl6 differentially affects conventional dendritic cell subsets and compromises Tfh/Tfr/Th17 cell responses. Nat Commun. 2024 Apr 30;15(1):3554

TSS for Clec9a:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr59162	Chr6:129385817-129385839 (+)	3 bp
Tssr59163	Chr6:129385859-129385875 (+)	42 bp
Tssr59164	Chr6:129385879-129385890 (+)	60 bp
Tssr59165	Chr6:129385893-129385900 (+)	72 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)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 12/17/2024 MGI 6.24