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

Gene ID: 4261, updated on 20-Dec-2019

Summary

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 MIM:600005
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]
Expression
Broad expression in spleen (RPKM 12.7), lymph node (RPKM 11.9) and 19 other tissues See more
Orthologs

Genomic context

See CIITA in Genome Data Viewer
Location:
16p13.13
Exon count:
27
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (10866208..10941562)
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 Neighboring gene uncharacterized LOC105371080 Neighboring gene Rho GTPase activating protein 21 pseudogene Neighboring gene uncharacterized LOC112267907 Neighboring gene C-type lectin domain containing 16A Neighboring gene Dexi homolog Neighboring gene ribosomal protein L7 pseudogene 46 Neighboring gene uncharacterized LOC105371081

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Bare lymphocyte syndrome 2
MedGen: C2931418 OMIM: 209920 GeneReviews: Not available
Compare labs
Rheumatoid arthritis
MedGen: C0003873 OMIM: 180300 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

HIV-1 interactions

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 transactivation is inhibited by the amino acids 64-285 in CIITA in U937 cells PubMed
tat The HLA class II transcriptional activator, CIITA, inhibits HIV-1 Tat and virus replication PubMed
tat HIV-1 Tat inhibits CIITA by competing with CIITA for binding to P-TEFb 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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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-containing 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
 
Process Evidence Code Pubs
immune response TAS
Traceable Author Statement
more info
PubMed 
inflammatory response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
interferon-gamma-mediated signaling pathway TAS
Traceable Author Statement
more info
 
negative regulation of collagen biosynthetic process IC
Inferred by Curator
more info
PubMed 
negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
phosphorylation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of MHC class I biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of MHC class I biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of MHC class II biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of MHC class II biosynthetic process IC
Inferred by Curator
more info
PubMed 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
response to antibiotic IDA
Inferred from Direct Assay
more info
PubMed 
response to interferon-gamma IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
PML body IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
MHC class II transactivator
Names
MHC class II transactivator type I
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
XP_006720943.2
XP_011520786.1
XP_011520787.1
XP_011520788.1
XP_011520789.1
XP_011520790.1
XP_011520791.1
XP_011520792.1
XP_011520793.1
XP_011520794.1
XP_011520795.1
XP_011520796.1
XP_011520797.1
XP_011520798.1
XP_024306048.1
XP_024306049.1

NCBI Reference Sequences (RefSeq)

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/Swiss-Prot
    P33076
    UniProtKB/TrEMBL
    A0A0B4J1S1, Q66X48
    Related
    ENSP00000316328.8, ENST00000324288.13
    Conserved Domains (3) 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 ...
    sd00034
    Location:9861013
    LRR_AMN1; leucine-rich repeat [structural motif]
    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
    ENSP00000485010.1, ENST00000618327.4
    Conserved Domains (3) 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 ...
    sd00034
    Location:9871014
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:415584
    NACHT; NACHT domain
  3. NM_001286403.2NP_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
    ENSP00000371257.5, ENST00000381835.9
    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 ...
    sd00034
    Location:402429
    LRR_AMN1; leucine-rich repeat [structural motif]

RNA

  1. NR_104444.2 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 Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    10866208..10941562
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011522486.2XP_011520788.1  MHC class II transactivator isoform X3

    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 ...
    sd00031
    Location:10881115
    LRR_1; leucine-rich repeat [structural motif]
    pfam05729
    Location:513682
    NACHT; NACHT domain
  2. XM_011522491.2XP_011520793.1  MHC class II transactivator isoform X9

    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
  3. XM_011522485.2XP_011520787.1  MHC class II transactivator isoform X1

    See identical proteins and their annotated locations for XP_011520787.1

    Conserved Domains (3) 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 ...
    sd00034
    Location:10851112
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:513682
    NACHT; NACHT domain
  4. XM_006720880.3XP_006720943.2  MHC class II transactivator isoform X1

    See identical proteins and their annotated locations for XP_006720943.2

    Conserved Domains (3) 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 ...
    sd00034
    Location:10851112
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:513682
    NACHT; NACHT domain
  5. XM_011522484.3XP_011520786.1  MHC class II transactivator isoform X1

    See identical proteins and their annotated locations for XP_011520786.1

    Conserved Domains (3) 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 ...
    sd00034
    Location:10851112
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:513682
    NACHT; NACHT domain
  6. XM_011522494.2XP_011520796.1  MHC class II transactivator isoform X12

    Conserved Domains (3) 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 ...
    sd00034
    Location:963990
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:391560
    NACHT; NACHT domain
  7. XM_011522487.2XP_011520789.1  MHC class II transactivator isoform X5

    Conserved Domains (3) 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 ...
    sd00034
    Location:10031030
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:431600
    NACHT; NACHT domain
  8. XM_011522489.2XP_011520791.1  MHC class II transactivator isoform X7

    Conserved Domains (3) 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 ...
    sd00034
    Location:10021029
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:430599
    NACHT; NACHT domain
  9. XM_024450281.1XP_024306049.1  MHC class II transactivator isoform X4

    Conserved Domains (4) summary
    cd00116
    Location:8211146
    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 ...
    sd00031
    Location:10211048
    LRR_1; leucine-rich repeat [structural motif]
    sd00034
    Location:11031133
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:446615
    NACHT; NACHT domain
  10. XM_024450280.1XP_024306048.1  MHC class II transactivator isoform X2

    Conserved Domains (4) summary
    cd00116
    Location:8701195
    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 ...
    sd00031
    Location:10701097
    LRR_1; leucine-rich repeat [structural motif]
    sd00034
    Location:11521182
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:495664
    NACHT; NACHT domain
  11. XM_011522495.2XP_011520797.1  MHC class II transactivator isoform X13

    Conserved Domains (3) 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 ...
    sd00034
    Location:938965
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:366535
    NACHT; NACHT domain
  12. XM_011522496.2XP_011520798.1  MHC class II transactivator isoform X14

    Conserved Domains (3) 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 ...
    sd00034
    Location:937964
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:365534
    NACHT; NACHT domain
  13. XM_011522492.2XP_011520794.1  MHC class II transactivator isoform X10

    See identical proteins and their annotated locations for XP_011520794.1

    UniProtKB/TrEMBL
    A0A087X2I7
    Conserved Domains (3) 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 ...
    sd00034
    Location:9871014
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:415584
    NACHT; NACHT domain
  14. XM_011522493.2XP_011520795.1  MHC class II transactivator isoform X11

    See identical proteins and their annotated locations for XP_011520795.1

    UniProtKB/TrEMBL
    A0A0B4J1S1
    Conserved Domains (3) 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 ...
    sd00034
    Location:9861013
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:414583
    NACHT; NACHT domain
  15. XM_011522490.2XP_011520792.1  MHC class II transactivator isoform X8

    Conserved Domains (3) 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 ...
    sd00034
    Location:10011028
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:429598
    NACHT; NACHT domain
  16. XM_011522488.2XP_011520790.1  MHC class II transactivator isoform X6

    Conserved Domains (3) 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 ...
    sd00034
    Location:10021029
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:430599
    NACHT; NACHT domain

RNA

  1. XR_001751904.1 RNA Sequence

  2. XR_932846.3 RNA Sequence

  3. XR_932847.3 RNA Sequence

  4. XR_932842.2 RNA Sequence

  5. XR_932841.3 RNA Sequence

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