Ciita class II transactivator [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Ciitaprovided by MGI
Official Full Name: class II transactivatorprovided by MGI
Primary source: MGI:MGI:108445
See related: Ensembl:ENSMUSG00000022504 AllianceGenome:MGI:108445
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: C2ta; Gm9475; Mhc2ta; EG669998
Summary: This gene encodes a member of the NOD-like receptor protein family. This protein acts as a transcriptional coactivator and component of the enhanceosome complex to stimulate transcription of MHC class II genes in the adaptive immune response. This protein may also regulate the transcription of MHC class I genes. Mutations in the human gene have been linked to a rare immunodeficiency, bare lymphocyte syndrome, and homozygous knockout mice exhibit many features of this disease. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2014]
Expression: Biased expression in spleen adult (RPKM 29.2), mammary gland adult (RPKM 10.6) and 7 other tissues See more
Orthologs: human all
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Genomic context

Location:: 16 A1; 16 5.65 cM

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	16	NC_000082.7 (10297877..10348928)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	16	NC_000082.6 (10480014..10531064)

Chromosome 16 - NC_000082.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

NLRC5-CIITA Fusion Protein as an Effective Inducer of MHC-I Expression and Antitumor Immunity.
Title: NLRC5-CIITA Fusion Protein as an Effective Inducer of MHC-I Expression and Antitumor Immunity.
Cancer-specific T helper shared and neo-epitopes uncovered by expression of the MHC class II master regulator CIITA.
Title: Cancer-specific T helper shared and neo-epitopes uncovered by expression of the MHC class II master regulator CIITA.
CIITA expression is regulated by histone deacetylase enzymes and has a role in alpha-synuclein pre-formed fibril-induced antigen presentation in murine microglial cell line.
Title: CIITA expression is regulated by histone deacetylase enzymes and has a role in α-synuclein pre-formed fibril-induced antigen presentation in murine microglial cell line.
Induction of CIITA by IFN-gamma in macrophages involves STAT1 activation by JAK and JNK.
Title: Induction of CIITA by IFN-γ in macrophages involves STAT1 activation by JAK and JNK.
Cannabinoid receptors modulate LPS-induced increase of class-II transactivator expression levels in a microglial cell line.
Title: Cannabinoid receptors modulate LPS-induced increase of class-II transactivator expression levels in a microglial cell line.
results uncover an NFAT5-regulated mechanism that maintains CIITA and MHCII expression in macrophages and thus modulates their T lymphocyte priming capacity.
Title: Macrophage-specific MHCII expression is regulated by a remote Ciita enhancer controlled by NFAT5.
Low CIITA expression is associated with cancer.
Title: FoxO1 is a regulator of MHC-II expression and anti-tumor effect of tumor-associated macrophages.
This study provided evidence that CIITA is required for alpha-syn-induced MHCII expression and subsequent infiltration of peripheral immune cells in to the midbrain.
Title: Targeting of the class II transactivator attenuates inflammation and neurodegeneration in an alpha-synuclein model of Parkinson's disease.
study found that CIITA exerts a highly restricted control over only the MHCII, H2-DO and H2-DM genes, in DC1 and DC2 cDC subsets, but not over other proposed targets
Title: Revisiting the specificity of the MHC class II transactivator CIITA in classical murine dendritic cells in vivo.
Decreasing CIITA expression in allogeneic MSCs abolished MHC II induction during myogenic differentiation and prevented immunorejection of these cells from the infarcted myocardium, which enhanced beneficial functional effects of MSC implantation on myocardial repair.
Title: Class II transactivator knockdown limits major histocompatibility complex II expression, diminishes immune rejection, and improves survival of allogeneic bone marrow stem cells in the infarcted heart.

Submit: New GeneRIF Correction See all GeneRIFs (51)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Chemically induced (ENU) (1)
Endonuclease-mediated (3)
Targeted (6) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables GTP binding	IEA Inferred from Electronic Annotation more info
enables acyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AS1 kinase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein serine kinase activity	IEA Inferred from Electronic Annotation more info
enables protein-containing complex binding	ISO Inferred from Sequence Orthology more info
enables protein-containing complex binding	ISS Inferred from Sequence or Structural Similarity more info
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cellular response to electrical stimulus	IEA Inferred from Electronic Annotation more info
involved_in cellular response to exogenous dsRNA	IEA Inferred from Electronic Annotation more info
involved_in cellular response to type II interferon	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of viral entry into host cell	ISO Inferred from Sequence Orthology more info
involved_in phosphorylation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of MHC class I biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of MHC class I biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of MHC class II biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of MHC class II biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of MHC class II biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to antibiotic	ISO Inferred from Sequence Orthology more info	PubMed
acts_upstream_of_or_within response to type II interferon	IDA Inferred from Direct Assay more info	PubMed
involved_in response to type II interferon	IDA Inferred from Direct Assay more info	PubMed
involved_in response to type II interferon	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in PML body	ISO Inferred from Sequence Orthology more info
located_in PML body	ISS Inferred from Sequence or Structural Similarity more info
located_in cell surface	IEA Inferred from Electronic Annotation more info
located_in cell surface	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: MHC class II transactivator

NP_001230689.1

EC 2.7.11.1

NP_001230690.1

EC 2.7.11.1

NP_001289547.1

EC 2.7.11.1

NP_001289548.1

EC 2.7.11.1

NP_031601.1

EC 2.7.11.1

XP_006521787.1

EC 2.7.11.1

XP_006521789.1

EC 2.7.11.1

XP_011244112.1

EC 2.7.11.1

XP_036015649.1

EC 2.7.11.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001243760.2 → NP_001230689.1 MHC class II transactivator isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (1) uses an alternate in-frame splice site in the 5' coding region, compared to variant 4. It encodes isoform 1, which is shorter than isoform 4.

Source sequence(s)

AI182240, AK138822, AK143956, AK153609, BC107330, BE850370

UniProtKB/TrEMBL

Q3UNW8

Conserved Domains (4) summary

cd00116
Location:813 → 1138

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

sd00033
Location:1010 → 1040

LRR_RI; leucine-rich repeat [structural motif]

sd00034
Location:981 → 1007

LRR_AMN1; leucine-rich repeat [structural motif]

pfam05729
Location:439 → 608

NACHT; NACHT domain
NM_001243761.2 → NP_001230690.1 MHC class II transactivator isoform 3

See identical proteins and their annotated locations for NP_001230690.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate start codon compared to variant 4. It encodes isoform 3, which is shorter and has a distinct N-terminus, compared to isoform 4.

Source sequence(s)

AF100710, AI182240, AK153609, BC107330, BE850370

Consensus CDS

CCDS88876.1

UniProtKB/TrEMBL

A0A2R8VHC7, Q3UU40

Related

ENSMUSP00000154946.2, ENSMUST00000230146.2

Conserved Domains (3) summary

cd00116
Location:734 → 1059

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

sd00034
Location:902 → 930

LRR_AMN1; leucine-rich repeat [structural motif]

pfam05729
Location:360 → 529

NACHT; NACHT domain
NM_001302618.1 → NP_001289547.1 MHC class II transactivator isoform 4

See identical proteins and their annotated locations for NP_001289547.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) represents the longest transcript and encodes the longest isoform (4).

Source sequence(s)

AI182240, AK138822, AK143956, AK153609, BC107330, BE850370

Consensus CDS

CCDS88875.1

UniProtKB/Swiss-Prot

O46787, O78036, O78109, P79621, Q31115, Q9TPP1

UniProtKB/TrEMBL

Q3UNW8

Related

ENSMUSP00000155517.2, ENSMUST00000230395.2

Conserved Domains (4) summary

cd00116
Location:814 → 1139

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

sd00033
Location:1011 → 1041

LRR_RI; leucine-rich repeat [structural motif]

sd00034
Location:982 → 1008

LRR_AMN1; leucine-rich repeat [structural motif]

pfam05729
Location:440 → 609

NACHT; NACHT domain
NM_001302619.1 → NP_001289548.1 MHC class II transactivator isoform 5

See identical proteins and their annotated locations for NP_001289548.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region and uses a downstream start codon compared to variant 4. It encodes isoform 5, which is shorter and has a distinct N-terminus, compared to isoform 4.

Source sequence(s)

AC122352, AI182240, AK138822, AK143956, AK153609, BC107330, BE850370

Consensus CDS

CCDS88877.1

UniProtKB/TrEMBL

Q3UU40

Related

ENSMUSP00000155002.2, ENSMUST00000230450.2

Conserved Domains (4) summary

cd00116
Location:713 → 1038

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

sd00034
Location:881 → 909

LRR_AMN1; leucine-rich repeat [structural motif]

pfam05729
Location:339 → 508

NACHT; NACHT domain

pfam17776
Location:637 → 742

NLRC4_HD2; NLRC4 helical domain HD2
NM_007575.4 → NP_031601.1 MHC class II transactivator isoform 2

See identical proteins and their annotated locations for NP_031601.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and uses an alternate start codon compared to variant 4. It encodes isoform 2, which is shorter and has a distinct N-terminus, compared to isoform 4.

Source sequence(s)

AI182240, AK040723, AK153609, BC107330, BE850370

Consensus CDS

CCDS27950.1

UniProtKB/TrEMBL

Q3U2P0, Q3U5G4

Related

ENSMUSP00000023147.7, ENSMUST00000023147.8

Conserved Domains (4) summary

cd00116
Location:737 → 1062

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

sd00033
Location:934 → 964

LRR_RI; leucine-rich repeat [structural motif]

sd00034
Location:905 → 931

LRR_AMN1; leucine-rich repeat [structural motif]

pfam05729
Location:363 → 532

NACHT; NACHT domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000082.7 Reference GRCm39 C57BL/6J

Range

10297877..10348928

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006521724.3 → XP_006521787.1 MHC class II transactivator isoform X1

UniProtKB/TrEMBL

Q3UNW8

Conserved Domains (2) summary

cd00116
Location:814 → 1045

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

pfam05729
Location:440 → 609

NACHT; NACHT domain
XM_006521726.4 → XP_006521789.1 MHC class II transactivator isoform X3

UniProtKB/TrEMBL

Q8HW99

Conserved Domains (2) summary

cd00116
Location:814 → 1045

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

pfam05729
Location:440 → 609

NACHT; NACHT domain
XM_011245810.4 → XP_011244112.1 MHC class II transactivator isoform X2

See identical proteins and their annotated locations for XP_011244112.1

UniProtKB/TrEMBL

Q3UU40

Conserved Domains (4) summary

cd00116
Location:713 → 1038

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

sd00034
Location:881 → 909

LRR_AMN1; leucine-rich repeat [structural motif]

pfam05729
Location:339 → 508

NACHT; NACHT domain

pfam17776
Location:637 → 742

NLRC4_HD2; NLRC4 helical domain HD2
XM_036159756.1 → XP_036015649.1 MHC class II transactivator isoform X2

UniProtKB/TrEMBL

Q3UU40

Conserved Domains (4) summary

cd00116
Location:713 → 1038

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

sd00034
Location:881 → 909

LRR_AMN1; leucine-rich repeat [structural motif]

pfam05729
Location:339 → 508

NACHT; NACHT domain

pfam17776
Location:637 → 742

NLRC4_HD2; NLRC4 helical domain HD2