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

    Gene ID: 4261, updated on 3-Dec-2024

    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; AllianceGenome:HGNC:7067
    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; MHC2D1; 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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CIITA in Genome Data Viewer
    Location:
    16p13.13
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (10866206..10943021)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (10902173..10978992)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (10971055..11030251)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene NUBP iron-sulfur cluster assembly factor 1, cytosolic Neighboring gene NANOG hESC enhancer GRCh37_chr16:10883659-10884197 Neighboring gene trans-golgi network vesicle protein 23 homolog A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10387 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10389 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7194 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10390 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:10932437-10932956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10391 Neighboring gene Rho GTPase activating protein 21 pseudogene Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:10964767-10965966 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10393 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10395 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10397 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10398 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10399 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10400 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10401 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7195 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10403 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10402 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10404 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10405 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10406 Neighboring gene Sharpr-MPRA regulatory region 12638 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:11066007-11066184 Neighboring gene C-type lectin domain containing 16A Neighboring gene Dexi homolog Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11073759-11074260 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11074261-11074760 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7196 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:11099817-11100053 Neighboring gene NANOG hESC enhancer GRCh37_chr16:11101530-11102234 Neighboring gene Sharpr-MPRA regulatory region 10204 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11144189-11144765 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11144766-11145343 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10407 Neighboring gene ribosomal protein L7 pseudogene 46 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10408 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10409 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10410 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10411 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10412 Neighboring gene Sharpr-MPRA regulatory region 12604 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
    MHC class II deficiency
    MedGen: C5447452 GeneReviews: Not available
    Compare labs
    Rheumatoid arthritis
    MedGen: C0003873 OMIM: 180300 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 3-phosphoinositide-dependent protein kinase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables AMP-activated protein kinase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    NOT enables DNA binding TAS
    Traceable Author Statement
    more info
    PubMed 
    enables DNA-binding transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables DNA-dependent protein kinase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables GTP binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables Rho-dependent protein serine/threonine kinase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables acyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables eukaryotic translation initiation factor 2alpha kinase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H2AS1 kinase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H2AS121 kinase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H2AT120 kinase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H2AXS139 kinase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H2BS14 kinase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H2BS36 kinase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3S10 kinase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3S28 kinase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3S57 kinase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3T11 kinase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3T3 kinase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3T45 kinase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3T6 kinase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H4S1 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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables ribosomal protein S6 kinase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables transcription cis-regulatory region binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription coactivator activity TAS
    Traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in immune response TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of collagen biosynthetic process IC
    Inferred by Curator
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of viral entry into host cell IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 IC
    Inferred by Curator
    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 IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within response to antibiotic IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in response to type II interferon IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in PML body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in 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
    NP_001366259.1
    NP_001366260.1
    NP_001366261.1
    NP_001366262.1
    NP_001366263.1
    XP_006720943.2
    XP_011520786.1
    XP_011520787.1
    XP_011520788.1
    XP_011520792.2
    XP_011520793.1
    XP_047290070.1
    XP_047290071.1
    XP_047290072.1
    XP_047290073.1
    XP_047290074.1
    XP_047290075.1
    XP_047290076.1
    XP_047290078.1
    XP_047290079.1
    XP_047290080.1
    XP_047290081.1
    XP_047290082.1
    XP_047290083.1
    XP_047290084.1
    XP_054236303.1
    XP_054236304.1
    XP_054236305.1
    XP_054236306.1
    XP_054236307.1
    XP_054236308.1
    XP_054236309.1
    XP_054236310.1
    XP_054236311.1
    XP_054236312.1
    XP_054236313.1
    XP_054236314.1
    XP_054236315.1
    XP_054236316.1
    XP_054236317.1
    XP_054236318.1
    XP_054236319.1
    XP_054236320.1
    XP_054236321.1
    XP_054236322.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_000246.4NP_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, KF459560
      Consensus CDS
      CCDS10544.1
      UniProtKB/Swiss-Prot
      A0N0N9, D3DUG0, E9PFE0, P33076, Q29675, Q8SNB8, Q96KL4
      UniProtKB/TrEMBL
      A0A0B4J1S1
      Related
      ENSP00000316328.8, ENST00000324288.14
      Conserved Domains (4) 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 ...
      sd00031
      Location:9891016
      LRR_1; leucine-rich repeat [structural motif]
      sd00034
      Location:10711101
      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/Swiss-Prot
      A0N0N9, D3DUG0, E9PFE0, P33076, Q29675, Q8SNB8, Q96KL4
      UniProtKB/TrEMBL
      A0A087X2I7
      Related
      ENSP00000485010.1, ENST00000618327.4
      Conserved Domains (4) 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 ...
      sd00031
      Location:9901017
      LRR_1; leucine-rich repeat [structural motif]
      sd00034
      Location:10721102
      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]
    4. NM_001379330.1NP_001366259.1  MHC class II transactivator isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC133065
      UniProtKB/Swiss-Prot
      A0N0N9, D3DUG0, E9PFE0, P33076, Q29675, Q8SNB8, Q96KL4
      Conserved Domains (4) 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 ...
      sd00031
      Location:941968
      LRR_1; leucine-rich repeat [structural motif]
      sd00034
      Location:10231053
      LRR_AMN1; leucine-rich repeat [structural motif]
      pfam05729
      Location:366535
      NACHT; NACHT domain
    5. NM_001379331.1NP_001366260.1  MHC class II transactivator isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC133065
      UniProtKB/Swiss-Prot
      A0N0N9, D3DUG0, E9PFE0, P33076, Q29675, Q8SNB8, Q96KL4
      Conserved Domains (4) 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 ...
      sd00031
      Location:940967
      LRR_1; leucine-rich repeat [structural motif]
      sd00034
      Location:10221052
      LRR_AMN1; leucine-rich repeat [structural motif]
      pfam05729
      Location:365534
      NACHT; NACHT domain
    6. NM_001379332.1NP_001366261.1  MHC class II transactivator isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC133065, KF459560
      Consensus CDS
      CCDS73826.1
      UniProtKB/Swiss-Prot
      A0N0N9, D3DUG0, E9PFE0, P33076, Q29675, Q8SNB8, Q96KL4
      UniProtKB/TrEMBL
      A0A087X2I7
      Conserved Domains (4) 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 ...
      sd00031
      Location:9901017
      LRR_1; leucine-rich repeat [structural motif]
      sd00034
      Location:10721102
      LRR_AMN1; leucine-rich repeat [structural motif]
      pfam05729
      Location:415584
      NACHT; NACHT domain
    7. NM_001379333.1NP_001366262.1  MHC class II transactivator isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC133065, KF459560
      Consensus CDS
      CCDS10544.1
      UniProtKB/Swiss-Prot
      A0N0N9, D3DUG0, E9PFE0, P33076, Q29675, Q8SNB8, Q96KL4
      UniProtKB/TrEMBL
      A0A0B4J1S1
      Conserved Domains (4) 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 ...
      sd00031
      Location:9891016
      LRR_1; leucine-rich repeat [structural motif]
      sd00034
      Location:10711101
      LRR_AMN1; leucine-rich repeat [structural motif]
      pfam05729
      Location:414583
      NACHT; NACHT domain
    8. NM_001379334.1NP_001366263.1  MHC class II transactivator isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC133065, KF459560
      UniProtKB/TrEMBL
      Q66X48
      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

    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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      10866206..10943021
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

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

      See identical proteins and their annotated locations for XP_011520787.1

      UniProtKB/Swiss-Prot
      A0N0N9, D3DUG0, E9PFE0, P33076, Q29675, Q8SNB8, Q96KL4
      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
    2. XM_011522484.4XP_011520786.1  MHC class II transactivator isoform X1

      See identical proteins and their annotated locations for XP_011520786.1

      UniProtKB/Swiss-Prot
      A0N0N9, D3DUG0, E9PFE0, P33076, Q29675, Q8SNB8, Q96KL4
      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
    3. XM_006720880.4XP_006720943.2  MHC class II transactivator isoform X1

      See identical proteins and their annotated locations for XP_006720943.2

      UniProtKB/Swiss-Prot
      A0N0N9, D3DUG0, E9PFE0, P33076, Q29675, Q8SNB8, Q96KL4
      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_047434123.1XP_047290079.1  MHC class II transactivator isoform X5

      UniProtKB/TrEMBL
      Q66X48
    5. XM_011522486.3XP_011520788.1  MHC class II transactivator isoform X2

      UniProtKB/Swiss-Prot
      A0N0N9, D3DUG0, E9PFE0, P33076, Q29675, Q8SNB8, Q96KL4
      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
    6. XM_011522491.3XP_011520793.1  MHC class II transactivator isoform X7

      UniProtKB/Swiss-Prot
      A0N0N9, D3DUG0, E9PFE0, P33076, Q29675, Q8SNB8, Q96KL4
      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
    7. XM_047434115.1XP_047290071.1  MHC class II transactivator isoform X4

      UniProtKB/TrEMBL
      Q66X48
    8. XM_047434118.1XP_047290074.1  MHC class II transactivator isoform X6

      UniProtKB/TrEMBL
      Q66X48
    9. XM_047434114.1XP_047290070.1  MHC class II transactivator isoform X3

      UniProtKB/TrEMBL
      Q66X48
    10. XM_047434120.1XP_047290076.1  MHC class II transactivator isoform X8

      UniProtKB/Swiss-Prot
      A0N0N9, D3DUG0, E9PFE0, P33076, Q29675, Q8SNB8, Q96KL4
      UniProtKB/TrEMBL
      A0A087X2I7
    11. XM_047434122.1XP_047290078.1  MHC class II transactivator isoform X9

      UniProtKB/Swiss-Prot
      A0N0N9, D3DUG0, E9PFE0, P33076, Q29675, Q8SNB8, Q96KL4
      UniProtKB/TrEMBL
      A0A0B4J1S1
    12. XM_047434128.1XP_047290084.1  MHC class II transactivator isoform X11

      UniProtKB/Swiss-Prot
      A0N0N9, D3DUG0, E9PFE0, P33076, Q29675, Q8SNB8, Q96KL4
    13. XM_047434126.1XP_047290082.1  MHC class II transactivator isoform X10

      UniProtKB/Swiss-Prot
      A0N0N9, D3DUG0, E9PFE0, P33076, Q29675, Q8SNB8, Q96KL4
    14. XM_047434127.1XP_047290083.1  MHC class II transactivator isoform X11

      UniProtKB/Swiss-Prot
      A0N0N9, D3DUG0, E9PFE0, P33076, Q29675, Q8SNB8, Q96KL4
    15. XM_047434117.1XP_047290073.1  MHC class II transactivator isoform X5

      UniProtKB/TrEMBL
      Q66X48
    16. XM_047434116.1XP_047290072.1  MHC class II transactivator isoform X5

      UniProtKB/TrEMBL
      Q66X48
    17. XM_047434124.1XP_047290080.1  MHC class II transactivator isoform X4

      UniProtKB/TrEMBL
      Q66X48
    18. XM_047434125.1XP_047290081.1  MHC class II transactivator isoform X4

      UniProtKB/TrEMBL
      Q66X48
    19. XM_047434119.1XP_047290075.1  MHC class II transactivator isoform X3

      UniProtKB/TrEMBL
      Q66X48
    20. XM_011522490.3XP_011520792.2  MHC class II transactivator isoform X3

      UniProtKB/TrEMBL
      Q66X48

    RNA

    1. XR_001751904.2 RNA Sequence

    2. XR_007064880.1 RNA Sequence

    3. XR_007064879.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      10902173..10978992
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054380331.1XP_054236306.1  MHC class II transactivator isoform X2

      UniProtKB/TrEMBL
      Q66X48
    2. XM_054380339.1XP_054236314.1  MHC class II transactivator isoform X7

      UniProtKB/TrEMBL
      Q66X48
    3. XM_054380330.1XP_054236305.1  MHC class II transactivator isoform X1

      UniProtKB/TrEMBL
      Q66X48
    4. XM_054380329.1XP_054236304.1  MHC class II transactivator isoform X1

      UniProtKB/TrEMBL
      Q66X48
    5. XM_054380328.1XP_054236303.1  MHC class II transactivator isoform X1

      UniProtKB/TrEMBL
      Q66X48
    6. XM_054380342.1XP_054236317.1  MHC class II transactivator isoform X5

      UniProtKB/TrEMBL
      Q66X48
    7. XM_054380333.1XP_054236308.1  MHC class II transactivator isoform X4

      UniProtKB/TrEMBL
      Q66X48
    8. XM_054380336.1XP_054236311.1  MHC class II transactivator isoform X6

      UniProtKB/TrEMBL
      Q66X48
    9. XM_054380332.1XP_054236307.1  MHC class II transactivator isoform X3

      UniProtKB/TrEMBL
      Q66X48
    10. XM_054380340.1XP_054236315.1  MHC class II transactivator isoform X8

      UniProtKB/Swiss-Prot
      A0N0N9, D3DUG0, E9PFE0, P33076, Q29675, Q8SNB8, Q96KL4
    11. XM_054380341.1XP_054236316.1  MHC class II transactivator isoform X9

      UniProtKB/Swiss-Prot
      A0N0N9, D3DUG0, E9PFE0, P33076, Q29675, Q8SNB8, Q96KL4
    12. XM_054380347.1XP_054236322.1  MHC class II transactivator isoform X11

      UniProtKB/Swiss-Prot
      A0N0N9, D3DUG0, E9PFE0, P33076, Q29675, Q8SNB8, Q96KL4
    13. XM_054380345.1XP_054236320.1  MHC class II transactivator isoform X10

      UniProtKB/Swiss-Prot
      A0N0N9, D3DUG0, E9PFE0, P33076, Q29675, Q8SNB8, Q96KL4
    14. XM_054380346.1XP_054236321.1  MHC class II transactivator isoform X11

      UniProtKB/Swiss-Prot
      A0N0N9, D3DUG0, E9PFE0, P33076, Q29675, Q8SNB8, Q96KL4
    15. XM_054380335.1XP_054236310.1  MHC class II transactivator isoform X5

      UniProtKB/TrEMBL
      Q66X48
    16. XM_054380334.1XP_054236309.1  MHC class II transactivator isoform X5

      UniProtKB/TrEMBL
      Q66X48
    17. XM_054380343.1XP_054236318.1  MHC class II transactivator isoform X4

      UniProtKB/TrEMBL
      Q66X48
    18. XM_054380344.1XP_054236319.1  MHC class II transactivator isoform X4

      UniProtKB/TrEMBL
      Q66X48
    19. XM_054380337.1XP_054236312.1  MHC class II transactivator isoform X3

      UniProtKB/TrEMBL
      Q66X48
    20. XM_054380338.1XP_054236313.1  MHC class II transactivator isoform X3

      UniProtKB/TrEMBL
      Q66X48

    RNA

    1. XR_008489092.1 RNA Sequence

    2. XR_008489093.1 RNA Sequence

    3. XR_008489091.1 RNA Sequence

    4. XR_008489090.1 RNA Sequence