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Aliases for AFF1 Gene

Aliases for AFF1 Gene

  • AF4/FMR2 Family Member 1 2 3 3 5
  • ALL1-Fused Gene From Chromosome 4 Protein 3 4
  • Pre-B-Cell Monocytic Leukemia Partner 1 2 3
  • Proto-Oncogene AF4 3 4
  • MLLT2 3 4
  • PBM1 3 4
  • AF4 3 4
  • Myeloid/Lymphoid Or Mixed-Lineage Leukemia (Trithorax (Drosophila) Homolog); Translocated To, 2 2
  • Myeloid/Lymphoid Or Mixed-Lineage Leukemia (Trithorax Homolog, Drosophila); Translocated To, 2 3
  • AF4/FMR2 Family, Member 1 2
  • Protein AF-4 4
  • Protein FEL 4
  • FEL 4

External Ids for AFF1 Gene

Previous HGNC Symbols for AFF1 Gene

  • PBM1
  • MLLT2

Previous GeneCards Identifiers for AFF1 Gene

  • GC04P088214
  • GC04P088075
  • GC04P087856
  • GC04P083600

Summaries for AFF1 Gene

Entrez Gene Summary for AFF1 Gene

  • This gene encodes a member of the AF4/ lymphoid nuclear protein related to the Fragile X E syndrome (FRAXE) family of proteins, which have been implicated in human childhood lymphoblastic leukemia, fragile chromosome X intellectual disability, and ataxia. It is the prevalent mixed-lineage leukemia fusion gene associated with spontaneous acute lymphoblastic leukemia. Members of this family have three conserved domains: an N-terminal homology domain, an AF4/ lymphoid nuclear protein domain, and a C-terminal homology domain. The protein functions as a regulator of RNA polymerase II-mediated transcription through elongation and chromatin remodeling functions. Through RNA interference screens, this gene has been shown to promote the expression of CD133, a plasma membrane glycoprotein required for leukemia cell survival. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2017]

GeneCards Summary for AFF1 Gene

AFF1 (AF4/FMR2 Family Member 1) is a Protein Coding gene. Diseases associated with AFF1 include Leukemia, Acute Lymphoblastic 3 and Acute Leukemia. Among its related pathways are Transcriptional misregulation in cancer. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity. An important paralog of this gene is AFF4.

Gene Wiki entry for AFF1 Gene

Additional gene information for AFF1 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for AFF1 Gene

Genomics for AFF1 Gene

GeneHancer (GH) Regulatory Elements for AFF1 Gene

Promoters and enhancers for AFF1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04J087004 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 680.5 +75.9 75942 11.9 CLOCK MLX ZFP64 IRF4 YY1 ZNF213 E2F8 ZNF143 NFYC ZNF610 AFF1 RPL6P13 C4orf36 LOC100419572 LOC260422 MAPK10 HSD17B13 SLC10A6 GC04P087042 PIR55151
GH04J086933 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 655.6 +3.0 2996 7.8 HDGF PKNOX1 SMAD1 FOXA2 ARNT ARID4B SIN3A FEZF1 DMAP1 YY1 AFF1 C4orf36 ENSG00000284968 ENSG00000285458 RPL6P13 LOC100419572 LOC260422 MAPK10 SLC10A6 AFF1-AS1
GH04J086890 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 650.3 -42.2 -42208 3 ZFP64 SIN3A ZNF2 ZNF48 YY1 GLIS2 ZNF213 KLF7 SP3 REST C4orf36 AFF1 RPL6P13 MAPK10 LOC100419572 LOC260422 SLC10A6 GC04P086879 ENSG00000285458
GH04J086957 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 22.4 +25.8 25845 6.3 PKNOX1 FOXA2 ARNT SIN3A FEZF1 IRF4 YY1 ZNF766 ZNF213 JUNB AFF1 C4orf36 LOC260422 MAPK10 NUDT9 KLHL8 GC04P086967 PIR55151 TECRP1
GH04J087101 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 20.3 +171.1 171122 7.7 PKNOX1 CLOCK FOXA2 SCRT2 FOS CREM MIXL1 PPARG KAT8 ZNF217 AFF1 C4orf36 MAPK10 ENSG00000250572 HSD17B13 GC04P087116 LOC105377320
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around AFF1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the AFF1 gene promoter:
  • AML1a

Genomic Locations for AFF1 Gene

Genomic Locations for AFF1 Gene
206,544 bases
Plus strand
206,053 bases
Plus strand

Genomic View for AFF1 Gene

Genes around AFF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
AFF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for AFF1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for AFF1 Gene

Proteins for AFF1 Gene

  • Protein details for AFF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    AF4/FMR2 family member 1
    Protein Accession:
    Secondary Accessions:
    • B4DTU1
    • E9PBM3

    Protein attributes for AFF1 Gene

    1210 amino acids
    Molecular mass:
    131422 Da
    Quaternary structure:
    • Component of the super elongation complex (SEC), at least composed of EAF1, EAF2, CDK9, MLLT3/AF9, AFF (AFF1 or AFF4), the P-TEFb complex and ELL (ELL, ELL2 or ELL3).
    • Sequence=AAA36642.1; Type=Frameshift; Positions=897, 905, 1178; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for AFF1 Gene

    Alternative splice isoforms for AFF1 Gene


neXtProt entry for AFF1 Gene

Post-translational modifications for AFF1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for AFF1 Gene

Domains & Families for AFF1 Gene

Gene Families for AFF1 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for AFF1 Gene


Suggested Antigen Peptide Sequences for AFF1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the AF4 family.
  • Belongs to the AF4 family.
genes like me logo Genes that share domains with AFF1: view

Function for AFF1 Gene

Phenotypes From GWAS Catalog for AFF1 Gene

Gene Ontology (GO) - Molecular Function for AFF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003690 double-stranded DNA binding IBA --
GO:0003700 DNA binding transcription factor activity TAS 7689231
GO:0005515 protein binding IPI 21729782
genes like me logo Genes that share ontologies with AFF1: view
genes like me logo Genes that share phenotypes with AFF1: view

Animal Models for AFF1 Gene

MGI Knock Outs for AFF1:

Animal Model Products

miRNA for AFF1 Gene

miRTarBase miRNAs that target AFF1

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for AFF1 Gene

Localization for AFF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for AFF1 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for AFF1 gene
Compartment Confidence
nucleus 5
plasma membrane 2
cytosol 2
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for AFF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IBA --
GO:0008023 transcription elongation factor complex IDA 22195968
GO:0032783 ELL-EAF complex IBA --
genes like me logo Genes that share ontologies with AFF1: view

Pathways & Interactions for AFF1 Gene

genes like me logo Genes that share pathways with AFF1: view

Pathways by source for AFF1 Gene

1 KEGG pathway for AFF1 Gene

Gene Ontology (GO) - Biological Process for AFF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with AFF1: view

No data available for SIGNOR curated interactions for AFF1 Gene

Drugs & Compounds for AFF1 Gene

(1) Drugs for AFF1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for AFF1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with AFF1: view

Transcripts for AFF1 Gene

Unigene Clusters for AFF1 Gene

AF4/FMR2 family, member 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for AFF1 Gene

No ASD Table

Relevant External Links for AFF1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for AFF1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for AFF1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for AFF1 Gene

This gene is overexpressed in Cerebrospinal fluid (59.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for AFF1 Gene

Protein tissue co-expression partners for AFF1 Gene

NURSA nuclear receptor signaling pathways regulating expression of AFF1 Gene:


SOURCE GeneReport for Unigene cluster for AFF1 Gene:


Evidence on tissue expression from TISSUES for AFF1 Gene

  • Nervous system(2.8)
  • Blood(2.6)
  • Bone marrow(2.6)
  • Kidney(2.6)
genes like me logo Genes that share expression patterns with AFF1: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for AFF1 Gene

Orthologs for AFF1 Gene

This gene was present in the common ancestor of animals.

Orthologs for AFF1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia AFF1 34 33
  • 98.28 (n)
(Canis familiaris)
Mammalia AFF1 34 33
  • 86.13 (n)
(Bos Taurus)
Mammalia AFF1 34 33
  • 84.39 (n)
(Mus musculus)
Mammalia Aff1 16 34 33
  • 76.56 (n)
(Rattus norvegicus)
Mammalia Aff1 33
  • 75.49 (n)
(Ornithorhynchus anatinus)
Mammalia AFF1 34
  • 61 (a)
(Monodelphis domestica)
Mammalia AFF1 34
  • 57 (a)
(Gallus gallus)
Aves AFF1 34 33
  • 61.93 (n)
(Anolis carolinensis)
Reptilia AFF1 34
  • 53 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.32672 33
(Danio rerio)
Actinopterygii CABZ01072037.1 34
  • 36 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1795 33
fruit fly
(Drosophila melanogaster)
Insecta lilli 34
  • 15 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4989 34
  • 16 (a)
Species where no ortholog for AFF1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for AFF1 Gene

Gene Tree for AFF1 (if available)
Gene Tree for AFF1 (if available)
Evolutionary constrained regions (ECRs) for AFF1: view image

Paralogs for AFF1 Gene

Paralogs for AFF1 Gene

(4) SIMAP similar genes for AFF1 Gene using alignment to 9 proteins:

  • H0Y9S4_HUMAN
  • Q05D98_HUMAN
  • Q14C88_HUMAN
genes like me logo Genes that share paralogs with AFF1: view

Variants for AFF1 Gene

Sequence variations from dbSNP and Humsavar for AFF1 Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
VAR_036130 A breast cancer sample p.Gln1204Lys
rs1000027316 -- 87,098,196(+) G/T intron_variant
rs1000028612 -- 87,052,166(+) G/C genic_upstream_transcript_variant, intron_variant
rs1000029595 -- 87,138,146(+) C/T 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1000043124 -- 87,131,604(+) A/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for AFF1 Gene

Variant ID Type Subtype PubMed ID
nsv956402 CNV deletion 24416366
nsv594787 CNV gain 21841781
nsv508297 CNV deletion 20534489
nsv507181 OTHER sequence alteration 20534489
nsv477979 CNV novel sequence insertion 20440878
nsv472716 CNV novel sequence insertion 20440878
nsv291773 CNV deletion 16902084
nsv1136885 CNV deletion 24896259
nsv1013308 CNV gain 25217958
esv3564196 CNV deletion 23714750
esv3328451 CNV insertion 20981092
esv2727935 CNV deletion 23290073
esv2663810 CNV deletion 23128226
esv1030392 CNV deletion 17803354
esv1008659 CNV deletion 20482838
dgv5335n100 CNV gain 25217958
dgv2846n106 CNV deletion 24896259
dgv2845n106 CNV deletion 24896259

Variation tolerance for AFF1 Gene

Residual Variation Intolerance Score: 18.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.99; 49.81% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for AFF1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for AFF1 Gene

Disorders for AFF1 Gene

MalaCards: The human disease database

(8) MalaCards diseases for AFF1 Gene - From: Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
leukemia, acute lymphoblastic 3
  • leukemia, acute lymphoblastic, susceptibility to, 3
acute leukemia
  • stem cell leukaemia
lymphoblastic leukemia
  • acute lymphocytic leukemia
  • eosinophilic angiocentric fibrosis
chronic neutrophilic leukemia
  • cnl
- elite association - COSMIC cancer census association via MalaCards
Search AFF1 in MalaCards View complete list of genes associated with diseases


  • Note=A chromosomal aberration involving AFF1 is associated with acute leukemias. Translocation t(4;11)(q21;q23) with KMT2A/MLL1. The result is a rogue activator protein.

Additional Disease Information for AFF1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with AFF1: view

No data available for Genatlas for AFF1 Gene

Publications for AFF1 Gene

  1. The t(4;11) chromosome translocation of human acute leukemias fuses the ALL-1 gene, related to Drosophila trithorax, to the AF-4 gene. (PMID: 1423625) Gu Y … Canaani E (Cell 1992) 2 3 4 22 58
  2. The chromosome 4q21 gene (AF-4/FEL) is widely expressed in normal tissues and shows breakpoint diversity in t(4;11)(q21;q23) acute leukemia. (PMID: 8353274) Chen CS … Kersey JH (Blood 1993) 2 3 22 58
  3. Genes on chromosomes 4, 9, and 19 involved in 11q23 abnormalities in acute leukemia share sequence homology and/or common motifs. (PMID: 8506309) Nakamura T … Nowell PC (Proceedings of the National Academy of Sciences of the United States of America 1993) 3 4 22 58
  4. Leukemia fusion target AF9 is an intrinsically disordered transcriptional regulator that recruits multiple partners via coupled folding and binding. (PMID: 23260655) Leach BI … Bushweller JH (Structure (London, England : 1993) 2013) 3 4 58
  5. A genome-wide association study identified AFF1 as a susceptibility locus for systemic lupus eyrthematosus in Japanese. (PMID: 22291604) Okada Y … Yamamoto K (PLoS genetics 2012) 3 44 58

Products for AFF1 Gene

Sources for AFF1 Gene

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