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

Gene ID: 85483, updated on 18-Aug-2021

Summary

Official Symbol
Ciitaprovided by RGD
Official Full Name
class II, major histocompatibility complex, transactivatorprovided by RGD
Primary source
RGD:619813
See related
Ensembl:ENSRNOG00000002659
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
C2ta; Mhc2ta
Summary
may play a role in transcriptional activation of MHC class II genes [RGD, Feb 2006]
Expression
Biased expression in Spleen (RPKM 130.5), Thymus (RPKM 59.8) and 6 other tissues See more
Orthologs
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Genomic context

See Ciita in Genome Data Viewer
Location:
10q11
Exon count:
21
Annotation release Status Assembly Chr Location
108 current mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (5139947..5187493, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (5212621..5260641, complement)

Chromosome 10 - NC_051345.1Genomic Context describing neighboring genes Neighboring gene C-type lectin domain containing 16A Neighboring gene uncharacterized LOC120095021 Neighboring gene Dexi homolog Neighboring gene 14-3-3 protein zeta/delta-like Neighboring gene hypothetical LOC100361397

Genomic regions, transcripts, and products

Expression

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

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
 
enables DNA-binding transcription factor binding ISO
Inferred from Sequence Orthology
more info
 
enables molecular_function ND
No biological Data available
more info
 
enables protein C-terminus binding ISO
Inferred from Sequence Orthology
more info
 
enables protein-containing complex binding ISO
Inferred from Sequence Orthology
more info
 
enables transcription cis-regulatory region binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
involved_in aging IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in cellular response to electrical stimulus IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in cellular response to exogenous dsRNA IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in cellular response to interferon-gamma IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in inflammatory response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in inflammatory response IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of viral entry into host cell ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of MHC class I biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
involved_in positive regulation of MHC class II biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of MHC class II biosynthetic process IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 positive regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within response to antibiotic ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within response to interferon-gamma ISO
Inferred from Sequence Orthology
more info
 
involved_in response to interferon-gamma ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
located_in PML body ISO
Inferred from Sequence Orthology
more info
 
located_in cell surface IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol IEA
Inferred from Electronic Annotation
more info
 
located_in cytosol ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
MHC class II transactivator
Names
MHC class II transactivator type IV
class II transactivator
NP_001257732.1
NP_001257733.1
NP_445981.2
XP_006245800.1
XP_038942928.1

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

    See identical proteins and their annotated locations for NP_001257732.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has an alternate first exon compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    JACYVU010000217
    UniProtKB/TrEMBL
    A0A0G2K9Q5
    Related
    ENSRNOP00000075087.1, ENSRNOT00000085310.1
    Conserved Domains (4) summary
    cd00116
    Location:7321057
    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:932959
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:900917
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:361530
    NACHT; NACHT domain
  2. NM_001270804.1NP_001257733.1  MHC class II transactivator isoform 3

    See identical proteins and their annotated locations for NP_001257733.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) has an alternate first exon compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    JACYVU010000217
    UniProtKB/TrEMBL
    A0A0G2JVN3
    Related
    ENSRNOP00000069553.1, ENSRNOT00000085479.1
    Conserved Domains (4) summary
    cd00116
    Location:7111036
    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:911938
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:879896
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:340509
    NACHT; NACHT domain
  3. NM_053529.2NP_445981.2  MHC class II transactivator isoform 1

    See identical proteins and their annotated locations for NP_445981.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    JACYVU010000217
    UniProtKB/TrEMBL
    G3V6C0
    Related
    ENSRNOP00000003572.2, ENSRNOT00000003572.3
    Conserved Domains (5) summary
    cd00116
    Location:8121137
    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:10121039
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:980997
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:441610
    NACHT; NACHT domain
    pfam17776
    Location:736841
    NLRC4_HD2; NLRC4 helical domain HD2

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 108 details...Open this link in a new tab

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

Reference mRatBN7.2 Primary Assembly

Genomic

  1. NC_051345.1 Reference mRatBN7.2 Primary Assembly

    Range
    5139947..5187493 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006245738.4XP_006245800.1  MHC class II transactivator isoform X1

    See identical proteins and their annotated locations for XP_006245800.1

    UniProtKB/TrEMBL
    G3V6C0
    Conserved Domains (5) summary
    cd00116
    Location:8121137
    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:10121039
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:980997
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:441610
    NACHT; NACHT domain
    pfam17776
    Location:736841
    NLRC4_HD2; NLRC4 helical domain HD2
  2. XM_039087000.1XP_038942928.1  MHC class II transactivator isoform X2

    Conserved Domains (5) summary
    cd00116
    Location:582907
    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:782809
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:750767
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam05729
    Location:211380
    NACHT; NACHT domain
    pfam17776
    Location:506611
    NLRC4_HD2; NLRC4 helical domain HD2

RNA

  1. XR_005489960.1 RNA Sequence

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