Cd1d1 MGI Mouse Gene Detail - MGI:107674

Symbol

Cd1d1
Name

CD1d1 antigen
Synonyms

CD1.1, Cd1a, Cd1d, Ly-38

Feature Type

protein coding gene
IDs

MGI:107674
NCBI Gene: 12479
Member of

Cd1 cluster
Alliance

gene page
Transcription Start Sites

4 TSS

Sequence Map

Chr3:86903141-86906748 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 3, 37.91 cM
Mapping Data

15 experiments

SNPs within 2kb

205 from dbSNP Build 142
Strain Annotations

17
RFLP

6

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_107674	protein coding gene	Chr3:86903141-86919665 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0027358	protein coding gene	Chr3:87072177-87074772 (-)
A/J	MGP_AJ_G0027322	protein coding gene	Chr3:84103150-84105529 (-)
AKR/J	MGP_AKRJ_G0027288	protein coding gene	Chr3:86150515-86154805 (-)
BALB/cJ	MGP_BALBcJ_G0027331	protein coding gene	Chr3:84207353-84210205 (-)
C3H/HeJ	MGP_C3HHeJ_G0027074	protein coding gene	Chr3:86425503-86427838 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0027776	protein coding gene	Chr3:90286473-90292851 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0025130	protein coding gene	Chr3:79780642-79783372 (-)
CAST/EiJ	MGP_CASTEiJ_G0026521	protein coding gene	Chr3:86656429-86658453 (-)
CBA/J	MGP_CBAJ_G0027049	protein coding gene	Chr3:93328094-93330860 (-)
DBA/2J	MGP_DBA2J_G0027185	protein coding gene	Chr3:83614275-83617446 (-)
FVB/NJ	MGP_FVBNJ_G0027154	protein coding gene	Chr3:81930160-81932405 (-)
LP/J	MGP_LPJ_G0027293	protein coding gene	Chr3:88014025-88016390 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0027173	protein coding gene	Chr3:99618642-99621296 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0027835	protein coding gene	Chr3:85917017-85921461 (-)
PWK/PhJ	no annotation
SPRET/EiJ	MGP_SPRETEiJ_G0026071	protein coding gene	Chr3:85097250-85114504 (-)
WSB/EiJ	MGP_WSBEiJ_G0026599	protein coding gene	Chr3:86300626-86305023 (-)

Human Ortholog

CD1D, CD1d molecule

Vertebrate Orthologs

8

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

CD1D, CD1d molecule
Synonyms

CD1A, R3, R3G1
Links

HGNC:1637

NCBI Gene ID: 912

neXtProt AC: NX_P15813

UniProt: P15813
Chr Location

1q23.1; chr1:158178030-158186427 (+) GRCh38

MGI Vertebrate Homology

Cd1d1 stringent orthology
1 human;1 mouse;1 rat;6 zebrafish
HCOP

vertebrate homology predictions: CD1D
Gene Tree

Cd1d1

Diseases

1 with human CD1D associations

				Human Disease	Mouse Models
				pulmonary tuberculosis IDs pulmonary tuberculosis DOID:2957 ICD10CM:A15 ICD9CM:011 ICD9CM:011.9 ICD9CM:011.90 MESH:D014397 NCI:C26899 UMLS_CUI:C0041327

Click on a disease name to see all genes associated with that disease.

References

1 with disease annotations

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Phenotype Summary

39 phenotypes from 7 alleles in 14 genetic backgrounds
9 phenotypes from multigenic genotypes
467 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

27
Chemically induced (other)

1
Endonuclease-mediated

8
Radiation induced

1
Targeted

15
Transgenic

2
Genomic Mutations

5 involving Cd1d1
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

35 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Homozygotes for targeted null mutations lack natural killer T cells, and mutant splenocytes fail to produce interleukin 4 (IL4).

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All GO Annotations

46
GO References

15

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

744
Tissues

11
cDNA Data

48
Literature Summary

3

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas

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All Sequences

68
RefSeq

29
UniProt

5
CCDS

CCDS17449.1

Ensembl

ENSMUSG00000028076 (Evidence)
NCBI Gene

12479

			Length	Strain/Species	Flank
genomic	ENSMUSG00000028076	Ensembl Gene Model \| MGI Sequence Detail	3608	C57BL/6J	± kb
transcript	ENSMUST00000029717	Ensembl \| MGI Sequence Detail	1946	Not Applicable
polypeptide	ENSMUSP00000029717	Ensembl \| MGI Sequence Detail	336	Not Applicable

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UniProt

5 Sequences
Protein Ontology

PR:000002028 antigen-presenting glycoprotein CD1d

(term hierarchy)
PDB

1CD1, 1Z5L, 1ZHN, 2AKR, 2FIK, 2GAZ, 2Q7Y, 3ARB, 3ARD, 3ARE, 3ARF, 3ARG, 3AU1, 3G08, 3GML, 3GMM, 3GMN, 3GMO, 3GMP, 3GMQ, 3GMR, 3HE6, 3HE7, 3ILP, 3ILQ, 3MA7, 3O8X, 3O9W, 3QI9, 3QUX, 3QUY, 3QUZ, 3RTQ, 3RUG, 3RZC, 3SCM, 3SDA, 3SDC, 3SDD, 3T1F, 3TA3, 3TN0, 3TO4, 3TVM, 3UBX, 4APQ, 4EI5, 4ELM, 4IRJ, 4IRS, 4MNG, 4MQ7, 4MX7, 4Y16, 4Y2D, 4Y4F, 4Y4H, 4Y4K, 4ZAK, 5EFI, 5FKP, 5TW2, 5TW5, 5VCJ, 6BNK, 6BNL, 6C5M, 6C69, 6C6A, 6C6C, 6C6E, 6C6F, 6C6H, 6C6J, 6CW6, 6CW9, 6CWB, 6CWE, 6CX5, 6CX7, 6CX9, 6CXA, 6CXE, 6CXF, 6CYW, 6MIV, 6MIY, 6MJ4, 6MJ6, 6MJA, 6MJI, 6MJJ, 6MJQ, 6MSS, 6OJP, 6OMG, 6OOR, 6XNG, 7M72
InterPro Domains

IPR050208 Antigen-presenting and immune regulatory MHC class I-related

IPR003597 Immunoglobulin C1-set

IPR007110 Immunoglobulin-like domain

IPR036179 Immunoglobulin-like domain superfamily

IPR013783 Immunoglobulin-like fold

IPR011162 MHC classes I/II-like antigen recognition protein

IPR011161 MHC class I-like antigen recognition-like

IPR037055 MHC class I-like antigen recognition-like superfamily
GlyGen

P11609 5 sites, 4 N-linked glycans (3 sites)

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All nucleic 62

Genomic 5

cDNA 52

Primer pair 3

Other 2

Microarray probesets 4

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MGD-MRK-11979, MGD-MRK-1834, MGD-MRK-1836, MGD-MRK-36249, MGI:2139791

Summaries

All 580

Developmental Gene Expression 3

Diseases 1

Gene Ontology 15

Phenotypes 467
Earliest

J:17169 McMichael AJ, et al., A human thymocyte antigen defined by a hybrid myeloma monoclonal antibody. Eur J Immunol. 1979 Mar;9(3):205-10
Latest

J:355000 Loh L, et al., Unraveling the phenotypic states of human innate-like T cells: Comparative insights with conventional T cells and mouse models. Cell Rep. 2024 Sep 24;43(9):114705

TSS for Cd1d1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr33922	Chr3:86906654-86906679 (-)	81 bp
Tssr33921	Chr3:86906591-86906641 (-)	132 bp
Tssr33920	Chr3:86906571-86906582 (-)	171 bp
Tssr33919	Chr3:86906304-86906340 (-)	426 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 11/05/2024 MGI 6.24