U.S. flag

An official website of the United States government


Send to:

Choose Destination

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

Gene ID: 27125, updated on 13-May-2022


Official Symbol
AFF4provided by HGNC
Official Full Name
AF4/FMR2 family member 4provided by HGNC
Primary source
See related
Ensembl:ENSG00000072364 MIM:604417; AllianceGenome:HGNC:17869
Gene type
protein coding
RefSeq status
Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
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]
Ubiquitous expression in thyroid (RPKM 21.2), adrenal (RPKM 17.6) and 25 other tissues See more
Try the new Gene table
Try the new Transcript table

Genomic context

See AFF4 in Genome Data Viewer
Exon count:
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (132875395..132963634, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (133395153..133483382, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (132211087..132299326, 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 1 pseudogene 50 Neighboring gene ATPase H+ transporting V0 subunit e1 pseudogene 1 Neighboring gene uncharacterized LOC124901065 Neighboring gene small nuclear ribonucleoprotein U4/U6.U5 subunit 27 pseudogene

Genomic regions, transcripts, and products


  • 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


GeneRIFs: Gene References Into Functions

What'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 PubChem


Products Interactant Other Gene Complex Source Pubs Description

General gene information



Clone Names

  • MGC75036

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
Process Evidence Code Pubs
involved_in regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
involved_in spermatid development IEA
Inferred from Electronic Annotation
more info
Component Evidence Code Pubs
located_in euchromatin ISS
Inferred from Sequence or Structural Similarity
more info
located_in fibrillar center 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
part_of super elongation complex IBA
Inferred from Biological aspect of Ancestor
more info
part_of transcription elongation factor complex IDA
Inferred from Direct Assay
more info

General protein information

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


  1. NG_030340.1 RefSeqGene

    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
    ENSP00000265343.5, ENST00000265343.10
    Conserved Domains (1) summary
    AF-4; AF-4 proto-oncoprotein

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly


  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    132875395..132963634 complement
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006714587.5XP_006714650.1  AF4/FMR2 family member 4 isoform X2

    Conserved Domains (1) summary
    AF-4; AF-4 proto-oncoprotein
  2. XM_047417103.1XP_047273059.1  AF4/FMR2 family member 4 isoform X2

  3. XM_005271963.6XP_005272020.1  AF4/FMR2 family member 4 isoform X1

    See identical proteins and their annotated locations for XP_005272020.1

    Conserved Domains (1) summary
    AF-4; AF-4 proto-oncoprotein
  4. XM_005271964.5XP_005272021.1  AF4/FMR2 family member 4 isoform X3

    Conserved Domains (1) summary
    AF-4; AF-4 proto-oncoprotein

Alternate T2T-CHM13v2.0


  1. NC_060929.1 Alternate T2T-CHM13v2.0

    133395153..133483382 complement
    GenBank, FASTA, Sequence Viewer (Graphics)