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    AFF4 AF4/FMR2 family member 4 [ Homo sapiens (human) ]

    Gene ID: 27125, updated on 17-Jun-2019

    Summary

    Official Symbol
    AFF4provided by HGNC
    Official Full Name
    AF4/FMR2 family member 4provided by HGNC
    Primary source
    HGNC:HGNC:17869
    See related
    Ensembl:ENSG00000072364 MIM:604417
    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
    MCEF; CHOPS; AF5Q31
    Summary
    The protein encoded by this gene belongs to the AF4 family of transcription factors involved in leukemia. It is a component of the positive transcription elongation factor b (P-TEFb) complex. A chromosomal translocation involving this gene and MLL gene on chromosome 11 is found in infant acute lymphoblastic leukemia with ins(5;11)(q31;q31q23). [provided by RefSeq, Oct 2011]
    Expression
    Ubiquitous expression in thyroid (RPKM 21.2), adrenal (RPKM 17.6) and 25 other tissues See more
    Orthologs

    Genomic context

    See AFF4 in Genome Data Viewer
    Location:
    5q31.1
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (132875381..132963655, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (132211071..132299354, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene growth differentiation factor 9 Neighboring gene ubiquinol-cytochrome c reductase complex III subunit VII Neighboring gene liver enriched antimicrobial peptide 2 Neighboring gene eukaryotic translation elongation factor 1 alpha 2 pseudogene Neighboring gene ATPase H+ transporting V0 subunit e1 pseudogene 1 Neighboring gene small nuclear ribonucleoprotein U4/U6.U5 subunit 27 pseudogene Neighboring gene cytochrome c oxidase subunit NDUFA4 pseudogene Neighboring gene zinc finger CCHC-type containing 10

    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 FunctionsWhat's a GeneRIF?

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    HIV-1 replication requires ELL2, AFF4 and AFF1 for transcriptional elongation as shown through CRISPR/Cas genome editing PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat HIV-1 Tat transactivation is mediated by the AFF4- super elongation complex but does so less than the AFF4-super elongation complex due to a single amino acid that causes a change in affinity of Tat for cyclin T1 PubMed
    tat HIV-1 Tat binds adjacent to AFF4, increases the affinity of AFF4 for P-TEFb, and rescues P-TEFb binding to AFF4 interface mutants. The AFF4 G61A/M62A mutant abolishes this rescue PubMed
    tat The crystal structure demonstrates that Met55Thr substitution in AFF4 forms a hydrogen bond with Glu246 of Cyclin T1, which is not as favorable for HIV-1 Tat docking PubMed
    tat The Tat-AFF4-P-TEFb complex containing HIV-1 Tat (residues 1-48), human Cyclin T1 (residues 1-266), human Cdk9 (residues 7-332), and human AFF4 (residues 27-69) is determined by the crystal structure analysis PubMed
    tat Binding of isolated AFF1(1-308) CBS to CDK9/CycT1 prevents HIV-1 Tat from activating HIV transcription and assembling complete SECs (AFF1, AFF4, ELL2, and ENL). The AFF1(1-308) M60A/L61A mutant shows no suppression of Tat transactivation PubMed
    tat HIV-1 Tat forms at least two distinct P-TEFb-containing complexes. Tatcom1 is composed of P-TEFb, AF9, ENL, ELL, AFF1, AFF4, and PAF1, presenting strong CTD-kinase activity, while Tatcom2 consists of 7SK, LARP7, and MEPCE with two molecules of Tat/P-TEFb PubMed
    tat HIV-1 Tat increases the amount of ELL2 bound to P-TEFb without affecting the AFF4-P-TEFb binding. CDK9 is required for the Tat-induced ELL2 accumulation and Tat interaction with ELL2 PubMed
    tat Brd4 inhibits HIV-1 Tat-human super elongation complex (components AFF4, ELL2, CycT1, and CDK9) by competing with HIV-1 Tat for binding to P-TEFb on HIV-1 promoter PubMed
    tat HIV-1 Tat is identified to have a physical interaction with AF4/FMR2 family, member 4 (AFF4) 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

    Pathways from BioSystems

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • MGC75036

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    DNA-binding transcription factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    double-stranded DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    regulation of transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    spermatid development IEA
    Inferred from Electronic Annotation
    more info
     
    transcription by RNA polymerase II TAS
    Traceable Author Statement
    more info
     
    transcription elongation from RNA polymerase II promoter TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    ELL-EAF complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    fibrillar center IDA
    Inferred from Direct Assay
    more info
     
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    nucleus IDA
    Inferred from Direct Assay
    more info
     
    transcription elongation factor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    transcription elongation factor complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcriptionally active chromatin ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    AF4/FMR2 family member 4
    Names
    ALL1-fused gene from chromosome 5q31 protein
    major CDK9 elongation factor-associated protein

    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_030340.1 RefSeqGene

      Range
      5001..93284
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_014423.4NP_055238.1  AF4/FMR2 family member 4

      See identical proteins and their annotated locations for NP_055238.1

      Status: REVIEWED

      Source sequence(s)
      AC004500, AF197927, BC100287, DA934874
      Consensus CDS
      CCDS4164.1
      UniProtKB/Swiss-Prot
      Q9UHB7
      Related
      ENSP00000265343.5, ENST00000265343.10
      Conserved Domains (1) summary
      pfam05110
      Location:31159
      AF-4; AF-4 proto-oncoprotein

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

      Range
      132875381..132963655 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006714587.4XP_006714650.1  AF4/FMR2 family member 4 isoform X2

      Conserved Domains (1) summary
      pfam05110
      Location:31130
      AF-4; AF-4 proto-oncoprotein
    2. XM_005271964.4XP_005272021.1  AF4/FMR2 family member 4 isoform X3

      Conserved Domains (1) summary
      pfam05110
      Location:1781
      AF-4; AF-4 proto-oncoprotein
    3. XM_005271963.5XP_005272020.1  AF4/FMR2 family member 4 isoform X1

      See identical proteins and their annotated locations for XP_005272020.1

      UniProtKB/Swiss-Prot
      Q9UHB7
      Conserved Domains (1) summary
      pfam05110
      Location:31159
      AF-4; AF-4 proto-oncoprotein
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