Ciita class II, major histocompatibility complex, transactivator [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ciitaprovided by RGD
Official Full Name: class II, major histocompatibility complex, transactivatorprovided by RGD
Primary source: RGD:619813
See related: EnsemblRapid:ENSRNOG00000002659 AllianceGenome:RGD:619813
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: C2ta; Mhc2ta
Summary: Predicted to enable DNA-binding transcription factor binding activity and transcription cis-regulatory region binding activity. Involved in several processes, including cellular response to electrical stimulus; cellular response to exogenous dsRNA; and regulation of transcription by RNA polymerase II. Located in cell surface. Used to study periapical periodontitis. Human ortholog(s) of this gene implicated in Addison's disease; MHC class II deficiency; autoimmune disease (multiple); and myocardial infarction. Orthologous to human CIITA (class II major histocompatibility complex transactivator). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Spleen (RPKM 130.5), Thymus (RPKM 59.8) and 6 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 10q11

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (5646854..5694393, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (5139947..5187493, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (5212621..5260641, complement)

Chromosome 10 - NC_086028.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Ciita Regulates Local and Systemic Immune Responses in a Combined rAAV-alpha-synuclein and Preformed Fibril-Induced Rat Model for Parkinson's Disease.
Title: Ciita Regulates Local and Systemic Immune Responses in a Combined rAAV-α-synuclein and Preformed Fibril-Induced Rat Model for Parkinson's Disease.
Differential expression of the inflammatory ciita gene may be accompanied by altered bone properties in intact sex steroid-deficient female rats.
Title: Differential expression of the inflammatory ciita gene may be accompanied by altered bone properties in intact sex steroid-deficient female rats.
The MHC class II transactivator modulates seeded alpha-synuclein pathology and dopaminergic neurodegeneration in an in vivo rat model of Parkinson's disease.
Title: The MHC class II transactivator modulates seeded alpha-synuclein pathology and dopaminergic neurodegeneration in an in vivo rat model of Parkinson's disease.
Study found that natural allelic differences in the Mhc2ta gene regulating MHCII expression levels impact microglial phenotype, antigen presentation capacity and dopaminergic pathology after overexpression of human alpha-syn. These results indicate that Mhc2ta is a key upstream regulator of the inflammatory response in Parkinson's Disease pathology.
Title: Allelic difference in Mhc2ta confers altered microglial activation and susceptibility to α-synuclein-induced dopaminergic neurodegeneration.
Naturally occurring allelic variability in Mhc2ta profoundly affects the quantity of class II histocompatibility gene expression in the central nervous system and modulates susceptibility to autoimmune neuroinflammation.
Title: Vra4 congenic rats with allelic differences in the class II transactivator gene display altered susceptibility to experimental autoimmune encephalomyelitis.
Silencing of CIITA transcription is recessive in trophoblasts and involves an epigenetic mechanism other than promoter methylation. Trophoblasts may be missing a factor that regulates chromatin structure at the CIITA promoter.
Title: Class II transactivator (CIITA) promoter methylation does not correlate with silencing of CIITA transcription in trophoblasts.
mutations result in differential MHC molecule expression associated with susceptibility to inflammatory diseases
Title: MHC2TA is associated with differential MHC molecule expression and susceptibility to rheumatoid arthritis, multiple sclerosis and myocardial infarction.
possible role in IFN-gamma induction of MHC class II
Title: Failure of MHC class II expression in neonatal alveolar macrophages: potential role of class II transactivator.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D10Got7 (e-PCR)
- UniSTS:115277

D10Mgh25 (e-PCR)
- UniSTS:240371

Gene Ontology Provided by RGD

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 protein-containing complex binding	ISO Inferred from Sequence Orthology 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	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to exogenous dsRNA	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to type II interferon	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
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	IDA Inferred from Direct Assay more info	PubMed
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 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	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of MHC class II biosynthetic process	IEP Inferred from Expression Pattern more info	PubMed
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
acts_upstream_of_or_within response to type II interferon	ISO Inferred from Sequence Orthology more info
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 cell surface	IDA Inferred from Direct Assay more info	PubMed
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

Names: MHC class II transactivator type IV; class II transactivator

NP_001257732.1

EC 2.7.11.1

NP_001257733.1

EC 2.7.11.1

NP_445981.2

EC 2.7.11.1

XP_006245800.1

EC 2.7.11.1

XP_038942928.1

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_001270803.1 → NP_001257732.1 MHC class II transactivator isoform 2

See identical proteins and their annotated locations for NP_001257732.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) has an alternate first exon compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.

Source sequence(s)

JAXUCZ010000010

UniProtKB/TrEMBL

A0A0G2K9Q5, A6K4J5, Q9GJD9

Related

ENSRNOP00000075087.1, ENSRNOT00000085310.3

Conserved Domains (4) summary

cd00116
Location:732 → 1057

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:932 → 959

LRR_RI; leucine-rich repeat [structural motif]

sd00034
Location:900 → 917

LRR_AMN1; leucine-rich repeat [structural motif]

pfam05729
Location:361 → 530

NACHT; NACHT domain
NM_001270804.1 → NP_001257733.1 MHC class II transactivator isoform 3

See identical proteins and their annotated locations for NP_001257733.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) has an alternate first exon compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.

Source sequence(s)

JAXUCZ010000010

UniProtKB/TrEMBL

A6K4J8, Q9GJD8

Conserved Domains (4) summary

cd00116
Location:711 → 1036

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:911 → 938

LRR_RI; leucine-rich repeat [structural motif]

sd00034
Location:879 → 896

LRR_AMN1; leucine-rich repeat [structural motif]

pfam05729
Location:340 → 509

NACHT; NACHT domain
NM_053529.2 → NP_445981.2 MHC class II transactivator isoform 1

See identical proteins and their annotated locations for NP_445981.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

JAXUCZ010000010

UniProtKB/TrEMBL

A6K4J3, Q9GJE0

Related

ENSRNOP00000003572.4, ENSRNOT00000003572.5

Conserved Domains (5) summary

cd00116
Location:812 → 1137

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:1012 → 1039

LRR_RI; leucine-rich repeat [structural motif]

sd00034
Location:980 → 997

LRR_AMN1; leucine-rich repeat [structural motif]

pfam05729
Location:441 → 610

NACHT; NACHT domain

pfam17776
Location:736 → 841

NLRC4_HD2; NLRC4 helical domain HD2

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086028.1 Reference GRCr8

Range

5646854..5694393 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006245738.5 → XP_006245800.1 MHC class II transactivator isoform X1

See identical proteins and their annotated locations for XP_006245800.1

UniProtKB/TrEMBL

A6K4J3, Q9GJE0

Conserved Domains (5) summary

cd00116
Location:812 → 1137

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:1012 → 1039

LRR_RI; leucine-rich repeat [structural motif]

sd00034
Location:980 → 997

LRR_AMN1; leucine-rich repeat [structural motif]

pfam05729
Location:441 → 610

NACHT; NACHT domain

pfam17776
Location:736 → 841

NLRC4_HD2; NLRC4 helical domain HD2
XM_039087000.1 → XP_038942928.1 MHC class II transactivator isoform X2

UniProtKB/TrEMBL

Q9GJD8

Conserved Domains (5) summary

cd00116
Location:582 → 907

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:782 → 809

LRR_RI; leucine-rich repeat [structural motif]

sd00034
Location:750 → 767

LRR_AMN1; leucine-rich repeat [structural motif]

pfam05729
Location:211 → 380

NACHT; NACHT domain

pfam17776
Location:506 → 611

NLRC4_HD2; NLRC4 helical domain HD2