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    IK IK cytokine [ Homo sapiens (human) ]

    Gene ID: 3550, updated on 5-May-2024

    Summary

    Official Symbol
    IKprovided by HGNC
    Official Full Name
    IK cytokineprovided by HGNC
    Primary source
    HGNC:HGNC:5958
    See related
    Ensembl:ENSG00000113141 MIM:600549; AllianceGenome:HGNC:5958
    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
    RED; RER; CSA2
    Summary
    The protein encoded by this gene was identified by its RED repeat, a stretch of repeated arginine, glutamic acid and aspartic acid residues. The protein localizes to discrete dots within the nucleus, excluding the nucleolus. Its function is unknown. This gene maps to chromosome 5; however, a pseudogene may exist on chromosome 2. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in testis (RPKM 59.6), bone marrow (RPKM 39.1) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    Location:
    5q31.3
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (140647829..140662480)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (141173235..141187876)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (140027414..140042065)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene transmembrane and coiled-coil domains 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140011403-140011904 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140011905-140012404 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16452 Neighboring gene CD14 molecule Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:140026953-140027488 Neighboring gene NADH:ubiquinone oxidoreductase subunit A2 Neighboring gene microRNA 3655 Neighboring gene uncharacterized LOC124901088 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140043900-140044566 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140052035-140052830 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140052831-140053626 Neighboring gene WD repeat domain 55 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23284 Neighboring gene DND microRNA-mediated repression inhibitor 1 Neighboring gene histidyl-tRNA synthetase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23285 Neighboring gene HARS1 and HARS2 bidirectional promoter region

    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?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev HIV-1 Rev is identified to have a physical interaction with IK cytokine, down-regulator of HLA II (IK; RED) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC59741

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in mRNA splicing, via spliceosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in mitotic cell cycle IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in mitotic spindle assembly checkpoint signaling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein localization to kinetochore IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of U2-type precatalytic spliceosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    colocalizes_with mitotic spindle pole IDA
    Inferred from Direct Assay
    more info
    PubMed 
    colocalizes_with nuclear chromosome IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    protein Red
    Names
    IK cytokine, down-regulator of HLA II
    IK factor
    RD element
    chondrosarcoma-associated protein 2
    cytokine IK
    prer protein

    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.

    mRNA and Protein(s)

    1. NM_006083.4NP_006074.2  protein Red

      See identical proteins and their annotated locations for NP_006074.2

      Status: REVIEWED

      Source sequence(s)
      AF182645, BC013005, BC071964
      Consensus CDS
      CCDS47280.1
      UniProtKB/Swiss-Prot
      Q13123, Q6IPD8
      UniProtKB/TrEMBL
      B2R5Y4, Q95HA6, Q9UK43
      Related
      ENSP00000396301.2, ENST00000417647.7
      Conserved Domains (2) summary
      pfam07807
      Location:445549
      RED_C; RED-like protein C-terminal region
      pfam07808
      Location:84295
      RED_N; RED-like protein N-terminal region

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      140647829..140662480
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      141173235..141187876
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)