AFF1 Gene (Protein Coding)

AF4/FMR2 Family Member 1

GC04P086934
GIFtS:
39
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 ... See more...

Aliases for AFF1 Gene

Aliases for AFF1 Gene

  • AF4/FMR2 Family Member 1 2 3 4 5
  • AF4 2 3 4
  • 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
  • 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
  • AFF1 5
  • AF-4 2
  • 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 Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for AFF1 Gene

Genomics for AFF1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for AFF1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around AFF1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for AFF1

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

Genomic Locations for AFF1 Gene

Latest Assembly
chr4:86,934,606-87,141,054
(GRCh38/hg38)
Size:
206,449 bases
Orientation:
Plus strand

Previous Assembly
chr4:87,856,154-88,062,206
(GRCh37/hg19 by Entrez Gene)
Size:
206,053 bases
Orientation:
Plus strand

chr4:87,856,154-88,062,206
(GRCh37/hg19 by Ensembl)
Size:
206,053 bases
Orientation:
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 Structure • Gene Density

RefSeq DNA sequence for AFF1 Gene

Proteins for AFF1 Gene

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  3. Assay products for research

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

    Protein Symbol:
    P51825-AFF1_HUMAN
    Recommended name:
    AF4/FMR2 family member 1
    Protein Accession:
    P51825
    Secondary Accessions:
    • B4DTU1
    • E9PBM3

    Protein attributes for AFF1 Gene

    Size:
    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).
    SequenceCaution:
    • Sequence=AAA36642.1; Type=Frameshift; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for AFF1 Gene

    Alternative splice isoforms for AFF1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for AFF1 Gene

Protein Expression for AFF1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for AFF1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for AFF1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for AFF1 Gene

Domains & Families for AFF1 Gene

Gene Families for AFF1 Gene

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

Protein Domains for AFF1 Gene

InterPro:
Blocks:
  • AF-4 proto-oncoprotein
ProtoNet:

Suggested Antigen Peptide Sequences for AFF1 Gene

GenScript: Design optimal peptide antigens:
  • Proto-oncogene AF4 (AFF1_HUMAN)
  • AFF1 protein (Q05D98_HUMAN)
  • AF4/FMR2 family, member 1, isoform CRA_b (Q14C88_HUMAN)
  • AF-4 protein (Q6LA76_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P51825

UniProtKB/Swiss-Prot:

AFF1_HUMAN :
  • Belongs to the AF4 family.
Family:
  • Belongs to the AF4 family.
genes like me logo Genes that share domains with AFF1: view

Function for AFF1 Gene

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  1. Animal Models for research
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  4. Inhibitory RNAs for research
  5. Clone products for research
  6. Cell Lines for research

Phenotypes From GWAS Catalog for AFF1 Gene

Gene Ontology (GO) - Molecular Function for AFF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
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 Models for research

miRNA for AFF1 Gene

miRTarBase miRNAs that target AFF1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for AFF1

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

Nucleus.

Subcellular locations from

COMPARTMENTS
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
cytosol 3
plasma membrane 2
extracellular 2
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 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 --
GO:0008023 transcription elongation factor complex IDA 22195968
GO:0032783 ELL-EAF complex IBA 21873635
genes like me logo Genes that share ontologies with AFF1: view

Pathways & Interactions for AFF1 Gene

PathCards logo

SuperPathways 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:0010468 regulation of gene expression IEA,IBA 21873635
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

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  1. Drug products for research

(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

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mRNA/cDNA for AFF1 Gene

4 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for AFF1

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

No ASD Table

Relevant External Links for AFF1 Gene

GeneLoc Exon Structure for
AFF1

Expression for AFF1 Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

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

mRNA expression in normal human tissues for AFF1 Gene
mRNA expression by GTEx for AFF1 GenemRNA expression by BioGPS 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for AFF1

SOURCE GeneReport for Unigene cluster for AFF1 Gene:

Hs.480190

Evidence on tissue expression from TISSUES for AFF1 Gene

  • Nervous system(3.3)
  • Kidney(3.1)
  • Muscle(2.9)
  • Skin(2.8)
  • Bone marrow(2.8)
  • Blood(2.7)
  • Liver(2.6)
  • Spleen(2.5)
  • Heart(2.4)
  • Intestine(2.4)
  • Thyroid gland(2.1)
  • Lung(2)
genes like me logo Genes that share expression patterns with AFF1: view

Primer products for research

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
Chimpanzee
(Pan troglodytes)
 Mammalia AFF1 30 31
  • 98.28 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia AFF1 30 31
  • 86.13 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia AFF1 30 31
  • 84.39 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Aff1 30 17 31
  • 76.56 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Aff1 30
  • 75.49 (n)
Platypus
(Ornithorhynchus anatinus)
 Mammalia AFF1 31
  • 61 (a)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia AFF1 31
  • 57 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves AFF1 30 31
  • 61.93 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia AFF1 31
  • 53 (a)
 OneToOne
African clawed frog
(Xenopus laevis)
 Amphibia Xl.32672 30
Zebrafish
(Danio rerio)
 Actinopterygii CABZ01072037.1 31
  • 36 (a)
 OneToOne
Rainbow Trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.1795 30
Fruit Fly
(Drosophila melanogaster)
 Insecta lilli 31
  • 15 (a)
 OneToMany
Sea Squirt
(Ciona savignyi)
 Ascidiacea CSA.4989 31
  • 16 (a)
 OneToMany
Species where no ortholog for AFF1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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

ENSEMBL:
Gene Tree for AFF1 (if available)
TreeFam:
Gene Tree for AFF1 (if available)
Aminode:
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:

  • AFF1_HUMAN
  • D6RAU0_HUMAN
  • D6RIZ5_HUMAN
  • E7EMC5_HUMAN
  • E7ETI4_HUMAN
  • F5GXF9_HUMAN
  • H0Y9S4_HUMAN
  • Q05D98_HUMAN
  • Q14C88_HUMAN
genes like me logo Genes that share paralogs with AFF1: view

Variants for AFF1 Gene

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  1. SNP Genotyping and Copy Number Assays for research

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for AFF1 Gene

SNP ID Clinical significance and condition Chr 04 pos Variation AA Info Type
rs113026065 Likely Benign: not provided 87,114,712(+) A/T
NM_001166693.2(AFF1):c.1879A>T (p.Ser627Cys) 		MISSENSE
rs113502077 Benign: not provided 87,090,058(+) T/C
NM_001166693.2(AFF1):c.1179T>C (p.Pro393=) 		SYNONYMOUS
rs1344808989 Likely Benign: not provided 87,115,041(+) G/A
NM_001166693.2(AFF1):c.2208G>A (p.Val736=) 		SYNONYMOUS
rs143673312 Likely Benign: not provided 87,047,102(+) C/T
NM_001166693.2(AFF1):c.567C>T (p.Asp189=) 		SYNONYMOUS_VARIANT,INTRON
rs145877283 Likely Benign: not provided 87,094,964(+) G/A
NM_001166693.2(AFF1):c.1278G>A (p.Thr426=) 		SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for AFF1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

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

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
AFF1

SNP Genotyping and Copy Number Assays for research

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

Disorders for AFF1 Gene

MalaCards: The human disease database

(12) MalaCards diseases for AFF1 Gene - From: ORP, COP, and GCD

Disorder Aliases PubMed IDs
leukemia, acute lymphoblastic 3
  • leukemia, acute lymphoblastic, susceptibility to, 3
acute leukemia
  • stem cell leukaemia
leukemia
  • leukemias
central nervous system leukemia
  • leukemia of the cns
amyotrophic lateral sclerosis, juvenile, with dementia
  • als-dementia complex
- elite association - COSMIC cancer census association via MalaCards
Search AFF1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

AFF1_HUMAN
  • 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
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
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 23
  2. 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 23
  3. 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 23
  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
  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 41

ExternalLinks

View latest publications for AFF1 gene in Mastermind

Products for AFF1 Gene

Sources for AFF1 Gene