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

Gene ID: 12265, updated on 18-Apr-2024

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
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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_000082.7Genomic Context describing neighboring genes Neighboring gene nucleotide binding protein 1 Neighboring gene trans-golgi network vesicle protein 23A Neighboring gene CapStarr-seq enhancer MGSCv37_chr16:10469529-10469712 Neighboring gene STARR-seq mESC enhancer starr_40087 Neighboring gene STARR-positive B cell enhancer mm9_chr16:10487992-10488292 Neighboring gene predicted gene, 41420 Neighboring gene predicted gene, 57630 Neighboring gene STARR-positive B cell enhancer ABC_E5523 Neighboring gene STARR-positive B cell enhancer ABC_E10887 Neighboring gene dexamethasone-induced transcript Neighboring gene C-type lectin domain family 16, member A Neighboring gene STARR-seq mESC enhancer starr_40088 Neighboring gene CapStarr-seq enhancer MGSCv37_chr16:10666979-10667180 Neighboring gene predicted gene, 52264 Neighboring gene CapStarr-seq enhancer MGSCv37_chr16:10668626-10668834 Neighboring gene predicted gene 15558

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (6)  1 citation
  • Endonuclease-mediated (3) 
  • Chemically induced (ENU) (1) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC130299

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 kinase activity IEA
Inferred from Electronic Annotation
more info
 
enables nucleotide binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein serine/threonine kinase activity IEA
Inferred from Electronic Annotation
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
 
enables transferase activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
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 ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of viral entry into host cell ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within 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 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
 
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
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 cell surface ISO
Inferred from Sequence Orthology
more info
 
located_in cytosol ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
MHC class II transactivator
NP_001230689.1
NP_001230690.1
NP_001289547.1
NP_001289548.1
NP_031601.1
XP_006521787.1
XP_006521789.1
XP_011244112.1
XP_036015649.1

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)

  1. NM_001243760.2NP_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:8131138
    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:10101040
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:9811007
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:439608
    NACHT; NACHT domain
  2. NM_001243761.2NP_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:7341059
    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:902930
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:360529
    NACHT; NACHT domain
  3. NM_001302618.1NP_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:8141139
    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:10111041
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:9821008
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:440609
    NACHT; NACHT domain
  4. NM_001302619.1NP_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:7131038
    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:881909
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:339508
    NACHT; NACHT domain
    pfam17776
    Location:637742
    NLRC4_HD2; NLRC4 helical domain HD2
  5. NM_007575.4NP_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:7371062
    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:934964
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:905931
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:363532
    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

  1. NC_000082.7 Reference GRCm39 C57BL/6J

    Range
    10297877..10348928
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    Q3UNW8
    Conserved Domains (2) summary
    cd00116
    Location:8141045
    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:440609
    NACHT; NACHT domain
  2. XM_006521726.4XP_006521789.1  MHC class II transactivator isoform X3

    UniProtKB/TrEMBL
    Q8HW99
    Conserved Domains (2) summary
    cd00116
    Location:8141045
    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:440609
    NACHT; NACHT domain
  3. XM_011245810.4XP_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:7131038
    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:881909
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:339508
    NACHT; NACHT domain
    pfam17776
    Location:637742
    NLRC4_HD2; NLRC4 helical domain HD2
  4. XM_036159756.1XP_036015649.1  MHC class II transactivator isoform X2

    UniProtKB/TrEMBL
    Q3UU40
    Conserved Domains (4) summary
    cd00116
    Location:7131038
    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:881909
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:339508
    NACHT; NACHT domain
    pfam17776
    Location:637742
    NLRC4_HD2; NLRC4 helical domain HD2

RNA

  1. XR_001781783.3 RNA Sequence