Display Settings:

Format

Send to:

Choose Destination

CIITA class II, major histocompatibility complex, transactivator [ Homo sapiens (human) ]

Gene ID: 4261, updated on 4-May-2015
Official Symbol
CIITAprovided by HGNC
Official Full Name
class II, major histocompatibility complex, transactivatorprovided by HGNC
Primary source
HGNC:HGNC:7067
See related
Ensembl:ENSG00000179583; HPRD:02475; MIM:600005; Vega:OTTHUMG00000129753
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
C2TA; NLRA; MHC2TA; CIITAIV
Summary
This gene encodes a protein with an acidic transcriptional activation domain, 4 LRRs (leucine-rich repeats) and a GTP binding domain. The protein is located in the nucleus and acts as a positive regulator of class II major histocompatibility complex gene transcription, and is referred to as the "master control factor" for the expression of these genes. The protein also binds GTP and uses GTP binding to facilitate its own transport into the nucleus. Once in the nucleus it does not bind DNA but rather uses an intrinsic acetyltransferase (AT) activity to act in a coactivator-like fashion. Mutations in this gene have been associated with bare lymphocyte syndrome type II (also known as hereditary MHC class II deficiency or HLA class II-deficient combined immunodeficiency), increased susceptibility to rheumatoid arthritis, multiple sclerosis, and possibly myocardial infarction. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2013]
Orthologs
See CIITA in MapViewer
Location:
16p13
Exon count:
29
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 16 NC_000016.10 (10866212..10941449)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (10971055..11018840)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene nucleotide binding protein 1 Neighboring gene trans-golgi network vesicle protein 23 homolog A (S. cerevisiae) Neighboring gene uncharacterized LOC105371080 Neighboring gene Rho GTPase activating protein 21 pseudogene Neighboring gene C-type lectin domain family 16, member A Neighboring gene Dexi homolog (mouse) Neighboring gene ribosomal protein L7 pseudogene 46 Neighboring gene uncharacterized LOC105371081

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Rheumatoid arthritis
MedGen: C0003873 OMIM: 180300 GeneReviews: Not available
Compare labs
SCID due to absent class II HLA antigens
MedGen: C0242583 OMIM: 209920 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Genome-wide association identifies multiple ulcerative colitis susceptibility loci.
NHGRI GWA Catalog
Multiple common variants for celiac disease influencing immune gene expression.
NHGRI GWA Catalog

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env CIITA-mediated enhancement of HIV-1 infection is gp120/gp41/CD4-dependent and occurs at the early steps in the infection cycle PubMed
Envelope transmembrane glycoprotein gp41 env CIITA-mediated enhancement of HIV-1 infection is gp120/gp41/CD4-dependent and occurs at the early steps in the infection cycle PubMed
Gag-Pol gag-pol CIITA increases the viral protease activity through increased HIV-1 Gag-Pol levels PubMed
Pr55(Gag) gag CIITA enhancement of HIV-1 Gag processing is through the viral protease activity PubMed
gag Gag production is significantly increased by fusing HIV-1-infected CD4- and CXCR4-expressing rat fibroblasts with uninfected human T-, B-, and macrophage cell lines. This process is regulated by HP68 and MHC class II transactivator (CIITA) PubMed
Tat tat HIV-1 Tat inhibits CIITA by competing with CIITA for binding to P-TEFb PubMed
tat The HLA class II transcriptional activator, CIITA, inhibits HIV-1 Tat and virus replication PubMed
tat HIV-1 Tat downregulates expression of MHC class II genes in antigen-presenting cells (APC) by inhibiting the transactivator of MHC class II genes, CIITA PubMed
capsid gag p24 production is significantly increased by fusing HIV-1-infected CD4- and CXCR4-expressing rat fibroblasts with uninfected human T-, B-, and macrophage cell lines. This process is regulated by HP68 and MHC class II transactivator (CIITA) PubMed
retropepsin gag-pol CIITA enhancement of HIV-1 Gag processing is through the viral protease activity, which results from increased levels of HIV-1 Gag-Pol by CIITA PubMed

Go to the HIV-1, Human Interaction Database

  • Antigen processing and presentation, organism-specific biosystem (from KEGG)
    Antigen processing and presentation, organism-specific biosystem
    Antigen processing and presentation
  • Antigen processing and presentation, conserved biosystem (from KEGG)
    Antigen processing and presentation, conserved biosystem
    Antigen processing and presentation
  • Cytokine Signaling in Immune system, organism-specific biosystem (from REACTOME)
    Cytokine Signaling in Immune system, organism-specific biosystemCytokines are small proteins that regulate and mediate immunity, inflammation, and hematopoiesis. They are secreted in response to immune stimuli, and usually act briefly, locally, at very low concen...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Influenza A, organism-specific biosystem (from KEGG)
    Influenza A, organism-specific biosystemInfluenza is a contagious respiratory disease caused by influenza virus infection. Influenza A virus is responsible for both annual seasonal epidemics and periodic worldwide pandemics. Novel strains ...
  • Influenza A, conserved biosystem (from KEGG)
    Influenza A, conserved biosystemInfluenza is a contagious respiratory disease caused by influenza virus infection. Influenza A virus is responsible for both annual seasonal epidemics and periodic worldwide pandemics. Novel strains ...
  • Interferon Signaling, organism-specific biosystem (from REACTOME)
    Interferon Signaling, organism-specific biosystemInterferons (IFNs) are cytokines that play a central role in initiating immune responses, especially antiviral and antitumor effects. There are three types of IFNs:Type I (IFN-alpha, -beta and others...
  • Interferon gamma signaling, organism-specific biosystem (from REACTOME)
    Interferon gamma signaling, organism-specific biosystemInterferon-gamma (IFN-gamma) belongs to the type II interferon family and is secreted by activated immune cells-primarily T and NK cells, but also B-cells and APC. INFG exerts its effect on cells by ...
  • Primary immunodeficiency, organism-specific biosystem (from KEGG)
    Primary immunodeficiency, organism-specific biosystemPrimary immunodeficiencies (PIs) are a heterogeneous group of disorders, which affect cellular and humoral immunity or non-specific host defense mechanisms mediated by complement proteins, and cells ...
  • Primary immunodeficiency, conserved biosystem (from KEGG)
    Primary immunodeficiency, conserved biosystemPrimary immunodeficiencies (PIs) are a heterogeneous group of disorders, which affect cellular and humoral immunity or non-specific host defense mechanisms mediated by complement proteins, and cells ...
  • Toxoplasmosis, organism-specific biosystem (from KEGG)
    Toxoplasmosis, organism-specific biosystemToxoplasma gondii is an obligate intracellular parasite that is prevalent worldwide. The tachyzoite form acquired by oral ingestion downmodulates proinflammatory signaling pathways via various mechan...
  • Toxoplasmosis, conserved biosystem (from KEGG)
    Toxoplasmosis, conserved biosystemToxoplasma gondii is an obligate intracellular parasite that is prevalent worldwide. The tachyzoite form acquired by oral ingestion downmodulates proinflammatory signaling pathways via various mechan...
  • Tuberculosis, organism-specific biosystem (from KEGG)
    Tuberculosis, organism-specific biosystemTuberculosis, or TB, is an infectious disease caused by Mycobacterium tuberculosis. One third of the world's population is thought to be infected with TB. About 90% of those infected result in latent...
  • Tuberculosis, conserved biosystem (from KEGG)
    Tuberculosis, conserved biosystemTuberculosis, or TB, is an infectious disease caused by Mycobacterium tuberculosis. One third of the world's population is thought to be infected with TB. About 90% of those infected result in latent...
  • Type II interferon signaling (IFNG), organism-specific biosystem (from WikiPathways)
    Type II interferon signaling (IFNG), organism-specific biosystemAdapted from Raza et al. (2008). This pathway is initiated by IFNG binding to its receptor and a subsequent phosphorylation cascade involving a number of the JAK and STAT family of proteins. Several ...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
NOT DNA binding TAS
Traceable Author Statement
more info
PubMed 
GTP binding IEA
Inferred from Electronic Annotation
more info
 
activating transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
kinase activity IEA
Inferred from Electronic Annotation
more info
 
protein C-terminus binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein complex binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription coactivator activity TAS
Traceable Author Statement
more info
PubMed 
transcription regulatory region DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transferase activity, transferring acyl groups IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
PML body IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
Preferred Names
MHC class II transactivator
Names
MHC class II transactivator
MHC class II transactivator type III
NLR family, acid domain containing
nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing
NP_000237.2
NP_001273331.1
NP_001273332.1

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.

Genomic

  1. NG_009628.1 RefSeqGene

    Range
    5001..52786
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_49

mRNA and Protein(s)

  1. NM_000246.3NP_000237.2  MHC class II transactivator isoform 2

    See identical proteins and their annotated locations for NP_000237.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (2) is 1 aa shorter compared to isoform 1.
    Source sequence(s)
    AC133065, AY699071, BE247223, X74301
    Consensus CDS
    CCDS10544.1
    UniProtKB/TrEMBL
    A0A0B4J1S1
    UniProtKB/Swiss-Prot
    P33076
    UniProtKB/TrEMBL
    Q66X48
    Conserved Domains (2) summary
    cd00116
    Location:7891114
    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:414583
    NACHT; NACHT domain
  2. NM_001286402.1NP_001273331.1  MHC class II transactivator isoform 1

    See identical proteins and their annotated locations for NP_001273331.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC133065, BC007406, BE247223, BM193016
    Consensus CDS
    CCDS73826.1
    UniProtKB/TrEMBL
    A0A087X2I7
    Related
    ENSP00000485010, ENST00000618327
    Conserved Domains (2) summary
    cd00116
    Location:7901115
    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:415584
    NACHT; NACHT domain
  3. NM_001286403.1NP_001273332.1  MHC class II transactivator isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses two alternate splice junctions and lacks two alternate coding exons compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC133065, AY084054, BC007406, BE247223, BM193016
    Consensus CDS
    CCDS66943.1
    UniProtKB/Swiss-Prot
    P33076
    Related
    ENSP00000371257, OTTHUMP00000256539, ENST00000381835, OTTHUMT00000436686
    Conserved Domains (2) summary
    cd00116
    Location:299530
    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 ...
    pfam13855
    Location:400446
    LRR_8; Leucine rich repeat

RNA

  1. NR_104444.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate splice junction and lacks an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC133065, AY084054, BC007406, BE247223, BM193016, U31931, X74301

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p2 Primary Assembly

    Range
    10866212..10941449
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011522485.1XP_011520787.1  

    See identical proteins and their annotated locations for XP_011520787.1

    Conserved Domains (2) summary
    cd00116
    Location:8881213
    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:513682
    NACHT; NACHT domain
  2. XM_006720880.2XP_006720943.2  

    See identical proteins and their annotated locations for XP_006720943.2

    Conserved Domains (2) summary
    cd00116
    Location:8881213
    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:513682
    NACHT; NACHT domain
  3. XM_011522484.1XP_011520786.1  

    See identical proteins and their annotated locations for XP_011520786.1

    Conserved Domains (2) summary
    cd00116
    Location:8881213
    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:513682
    NACHT; NACHT domain
  4. XM_011522486.1XP_011520788.1  

    Conserved Domains (3) summary
    cd00116
    Location:8881149
    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:513682
    NACHT; NACHT domain
    sd00031
    Location:10811150
    LRR_1; leucine-rich repeats
  5. XM_011522491.1XP_011520793.1  

    Conserved Domains (2) summary
    cd00116
    Location:8881119
    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:513682
    NACHT; NACHT domain
  6. XM_011522494.1XP_011520796.1  

    Conserved Domains (2) summary
    cd00116
    Location:7661091
    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:391560
    NACHT; NACHT domain
  7. XM_011522487.1XP_011520789.1  

    Conserved Domains (2) summary
    cd00116
    Location:8061131
    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:431600
    NACHT; NACHT domain
  8. XM_011522489.1XP_011520791.1  

    Conserved Domains (2) summary
    cd00116
    Location:8051130
    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:430599
    NACHT; NACHT domain
  9. XM_011522495.1XP_011520797.1  

    Conserved Domains (2) summary
    cd00116
    Location:7411066
    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:366535
    NACHT; NACHT domain
  10. XM_011522496.1XP_011520798.1  

    Conserved Domains (2) summary
    cd00116
    Location:7401065
    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:365534
    NACHT; NACHT domain
  11. XM_011522492.1XP_011520794.1  

    See identical proteins and their annotated locations for XP_011520794.1

    Conserved Domains (2) summary
    cd00116
    Location:7901115
    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:415584
    NACHT; NACHT domain
  12. XM_011522493.1XP_011520795.1  

    See identical proteins and their annotated locations for XP_011520795.1

    Conserved Domains (2) summary
    cd00116
    Location:7891114
    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:414583
    NACHT; NACHT domain
  13. XM_011522488.1XP_011520790.1  

    Conserved Domains (2) summary
    cd00116
    Location:8051130
    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:430599
    NACHT; NACHT domain
  14. XM_011522490.1XP_011520792.1  

    Conserved Domains (2) summary
    cd00116
    Location:8041129
    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:429598
    NACHT; NACHT domain

RNA

  1. XR_932842.1 RNA Sequence

  2. XR_932841.1 RNA Sequence

  3. XR_932843.1 RNA Sequence

  4. XR_932846.1 RNA Sequence

  5. XR_932847.1 RNA Sequence

  6. XR_932848.1 RNA Sequence

Alternate CHM1_1.1

Genomic

  1. NC_018927.2 Alternate CHM1_1.1

    Range
    10970985..11018760
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)