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Ciita Gene Detail
Summary
  • Symbol
    Ciita
  • Name
    class II transactivator
  • Synonyms
    C2ta, Gm9475
  • Feature Type
    protein coding gene
  • IDs
    MGI:108445
    NCBI Gene: 12265
  • Alliance
    genome feature page
  • Transcription Start Sites
    15 TSS
Location &
Maps
more
  • Sequence Map
    Chr16:10297923-10346282 bp, + strand
    From Ensembl annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 16, 5.65 cM, cytoband B1
  • Mapping Data
    4 experiments
Strain
Comparison
more
  • SNPs within 2kb
    1232 from dbSNP Build 142
  • Strain Annotations
    31
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_108445
 protein coding gene Chr16:10297877-10348928 (+)
129S1/SvImJ ENSMUSG00200011099
 protein coding gene Chr16:7313925-7316376 (+)
129S1/SvImJ ENSMUSGG00200054681
 protein coding gene Chr16:7325928-7349438 (+)
A/J ENSMUSGG00195055230
 protein coding gene Chr16:6864972-6888476 (+)
A/J ENSMUSG00195010180
 protein coding gene Chr16:6852975-6855426 (+)
AKR/J ENSMUSGG00220054612
 protein coding gene Chr16:7153777-7177289 (+)
AKR/J ENSMUSG00220016627
 protein coding gene Chr16:7141774-7144226 (+)
BALB/cJ ENSMUSGG00180055266
 protein coding gene Chr16:7104173-7127671 (+)
BALB/cJ ENSMUSG00180008445
 protein coding gene Chr16:7092170-7094621 (+)
C3H/HeJ ENSMUSG00175025535
 protein coding gene Chr16:7281831-7284244 (+)
C3H/HeJ ENSMUSGG00175055125
 protein coding gene Chr16:7293766-7317090 (+)
C57BL/6NJ ENSMUSG00215010265
 protein coding gene Chr16:6957375-6959826 (+)
C57BL/6NJ ENSMUSGG00215055515
 protein coding gene Chr16:6969373-6992873 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0020444
 protein coding gene Chr16:7029957-7077753 (+)
CAST/EiJ ENSTCUG00005027430
 protein coding gene Chr16:7195679-7243387 (+)
CBA/J ENSMUSG00210011315
 protein coding gene Chr16:7299040-7301453 (+)
CBA/J ENSMUSGG00210054785
 protein coding gene Chr16:7310963-7334277 (+)
DBA/2J ENSMUSG00185009996
 protein coding gene Chr16:7244331-7246744 (+)
DBA/2J ENSMUSGG00185057653
 protein coding gene Chr16:7256269-7279582 (+)
FVB/NJ ENSMUSGG00205054351
 protein coding gene Chr16:7174205-7197706 (+)
FVB/NJ ENSMUSG00205011451
 protein coding gene Chr16:7162204-7164655 (+)
JF1/MsJ ENSUMUG00000022808
 protein coding gene Chr16:7349288-7396962 (+)
LP/J ENSMUSGG00230055730
 protein coding gene Chr16:9821725-9845236 (+)
LP/J ENSMUSG00230011188
 protein coding gene Chr16:9809705-9812156 (+)
NOD/ShiLtJ ENSMUSGG00190054581
 protein coding gene Chr16:7356410-7379909 (+)
NOD/ShiLtJ ENSMUSG00190024743
 protein coding gene Chr16:7344413-7346864 (+)
NZO/HlLtJ ENSMUSG00225030427
 protein coding gene Chr16:13028745-13031196 (+)
NZO/HlLtJ ENSMUSGG00225055348
 protein coding gene Chr16:13040740-13064240 (+)
PWK/PhJ ENSLUMG00010017138
 protein coding gene Chr16:7190832-7238425 (+)
SPRET/EiJ ENSMSPG00010015940
 protein coding gene Chr16:7168076-7213100 (+)
WSB/EiJ ENSIUOG00005015951
 protein coding gene Chr16:7299592-7343395 (+)



Homology
more
  • Human Ortholog
    CIITA, class II major histocompatibility complex transactivator
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    CIITA, class II major histocompatibility complex transactivator
  • Synonyms
    C2TA, CIITAIV, MHC2D1, MHC2TA, NLRA
  • Links
    NCBI Gene ID: 4261
    UniProt: P33076

  • Chr Location
    16p13.13; chr16:10866206-10943021 (+)  GRCh38
Human Diseases
more
  • Diseases
    2 with Ciita mouse models; 7 with human CIITA associations

Human Disease Mouse Models
      
IDs
 View 2 models
      
IDs
 View 1 model
      
IDs
IDs
IDs
IDs
IDs
IDs
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    3 with disease annotations
  • References
    5 with disease annotations
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    46 phenotypes from 7 alleles in 12 genetic backgrounds
    3 phenotypes from multigenic genotypes
    103 phenotype references
Phenotype Overview

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.
Homozygous targeted mutants are immunologically abnormal with extremely little MHC class II expression, greatly reduced serum IgG, and impaired T-dependent antigen responses.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    44
  • GO References
    13
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.
Expression
less
Expression Overview

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
    758
  • Tissues
    138
  • cDNA Data
    20
  • Literature Summary
    3
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic ENSMUSG00000022504 Ensembl Gene Model | MGI Sequence Detail 48360 C57BL/6J ±  kb
    transcript ENSMUST00000230395 Ensembl | MGI Sequence Detail 4237 Not Applicable  
    polypeptide ENSMUSP00000155517 Ensembl | MGI Sequence Detail 1155 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 23
      Genomic 2
      cDNA 20
      Primer pair 1

      Microarray probesets 4
    Other
    Accession IDs
    less
    MGD-MRK-37489, MGI:3712178
    References
    more
    • Summaries
      All 175
      Developmental Gene Expression 3
      Diseases 5
      Gene Ontology 13
      Phenotypes 103
    • Earliest
      J:65917 Elliott EA, et al., The invariant chain is required for intracellular transport and function of major histocompatibility complex class II molecules. J Exp Med. 1994 Feb 1;179(2):681-94
    • Latest
      J:371744 Castanheira FVS, et al., Bacterial type IV secretion system induces specific and nonspecific protective immunity. mBio. 2025 Aug 13;16(8):e0044825
    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
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    Send questions and comments to User Support.     		last database update
    09/01/2026
    MGI 6.24     		The Jackson Laboratory