AFF3 Gene (Protein Coding)

AF4/FMR2 Family Member 3

GC02M099545
GIFtS:
36
This gene encodes a tissue-restricted nuclear transcriptional activator that is preferentially expressed in lymphoid tissue. Isolation of this protein initially defined a highly conserved LAF4/MLLT2 gene family of nuclear transcription factors that may function in lymphoid development and oncogenesis. In some ALL patients, this gene has been found fused to the gene for MLL. Mul... See more...

Aliases for AFF3 Gene

Aliases for AFF3 Gene

  • AF4/FMR2 Family Member 3 2 3 4 5
  • Lymphoid Nuclear Protein Related To AF4 2 3 4
  • Protein LAF-4 3 4
  • MLLT2-Like 2 3
  • LAF4 3 4
  • Lymphoid Nuclear Protein 4 3
  • AF4/FMR2 Family, Member 3 2
  • MLLT2-Related Protein 3
  • AFF3 5

External Ids for AFF3 Gene

Previous HGNC Symbols for AFF3 Gene

  • LAF4

Previous GeneCards Identifiers for AFF3 Gene

  • GC02M099627
  • GC02M100163
  • GC02M093928

Summaries for AFF3 Gene

Entrez Gene Summary for AFF3 Gene

  • This gene encodes a tissue-restricted nuclear transcriptional activator that is preferentially expressed in lymphoid tissue. Isolation of this protein initially defined a highly conserved LAF4/MLLT2 gene family of nuclear transcription factors that may function in lymphoid development and oncogenesis. In some ALL patients, this gene has been found fused to the gene for MLL. Multiple alternatively spliced transcript variants that encode different proteins have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for AFF3 Gene

AFF3 (AF4/FMR2 Family Member 3) is a Protein Coding gene. Diseases associated with AFF3 include Childhood T-Cell Acute Lymphoblastic Leukemia and Leukemia, Acute Lymphoblastic. Gene Ontology (GO) annotations related to this gene include double-stranded DNA binding. An important paralog of this gene is AFF2.

UniProtKB/Swiss-Prot Summary for AFF3 Gene

  • Putative transcription activator that may function in lymphoid development and oncogenesis. Binds, in vitro, to double-stranded DNA.

Gene Wiki entry for AFF3 Gene

Additional gene information for AFF3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for AFF3 Gene

Genomics for AFF3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for AFF3 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH02J100192 Enhancer 0.8 Ensembl ENCODE 261.1 -1.4 -1366 4 ZNF395 GTF2E2 RXRA HNF4A ZNF589 CEBPG RAD21 ZNF584 SP1 HLF AFF3 piR-31199-171 RF00017-3277 LONRF2
GH02J100191 Enhancer 0.2 Ensembl 261.1 +1.1 1127 0.2 AFF3 piR-48222-181 RF00017-3277 REV1
GH02J100393 Enhancer 1.1 FANTOM5 Ensembl ENCODE 28 -202.5 -202473 2.6 SP1 BCL11A POLR2A IRF4 EBF1 MAX TAF1 BHLHE40 ELF1 IKZF1 AFF3 CHST10 LONRF2 ENSG00000270699 lnc-LONRF2-1
GH02J100113 Enhancer 0.7 Ensembl ENCODE dbSUPER 19 +77.9 77927 3 EBF1 SPI1 TCF12 AFF3 HSALNG0017286 MK280144-361 lnc-AFF3-1 RF00017-3277 REV1
GH02J100196 Enhancer 1.2 FANTOM5 Ensembl ENCODE CraniofacialAtlas 10.9 -5.3 -5273 3.8 TBP IKZF1 VEZF1 TAL1 RARA NRF1 ZNF148 RCOR1 MEIS2 HLF AFF3 piR-31199-171 RF00017-3277 LONRF2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around AFF3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for AFF3

Top Transcription factor binding sites by QIAGEN in the AFF3 gene promoter:
  • AML1a

Genomic Locations for AFF3 Gene

Latest Assembly
chr2:99,545,419-100,192,428
(GRCh38/hg38)
Size:
647,010 bases
Orientation:
Minus strand

Previous Assembly
chr2:100,161,881-100,759,052
(GRCh37/hg19 by Entrez Gene)
Size:
597,172 bases
Orientation:
Minus strand

chr2:100,162,323-100,759,201
(GRCh37/hg19 by Ensembl)
Size:
596,879 bases
Orientation:
Minus strand

Genomic View for AFF3 Gene

Genes around AFF3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
AFF3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for AFF3 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for AFF3 Gene

Proteins for AFF3 Gene

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  • Protein details for AFF3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P51826-AFF3_HUMAN
    Recommended name:
    AF4/FMR2 family member 3
    Protein Accession:
    P51826
    Secondary Accessions:
    • B7ZM46
    • B9EGL9
    • D3DVI6
    • Q53RD6
    • Q53S47
    • Q53SI6
    • Q53TB9
    • Q59F27
    • Q8IWJ5

    Protein attributes for AFF3 Gene

    Size:
    1226 amino acids
    Molecular mass:
    133503 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for AFF3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for AFF3 Gene

Protein Expression for AFF3 Gene

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

Post-translational modifications for AFF3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for AFF3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for AFF3 Gene

Domains & Families for AFF3 Gene

Gene Families for AFF3 Gene

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

Protein Domains for AFF3 Gene

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

Suggested Antigen Peptide Sequences for AFF3 Gene

GenScript: Design optimal peptide antigens:
  • Lymphoid nuclear protein related to AF4 (AFF3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P51826

UniProtKB/Swiss-Prot:

AFF3_HUMAN :
  • Belongs to the AF4 family.
Family:
  • Belongs to the AF4 family.
genes like me logo Genes that share domains with AFF3: view

Function for AFF3 Gene

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  1. Animal Models for research
  2. CRISPR products for research
  3. miRNA products for research
  4. Inhibitory RNAs for research
  5. Clone products for research
  6. Cell Lines for research

Molecular function for AFF3 Gene

UniProtKB/Swiss-Prot Function:
Putative transcription activator that may function in lymphoid development and oncogenesis. Binds, in vitro, to double-stranded DNA.

Phenotypes From GWAS Catalog for AFF3 Gene

Gene Ontology (GO) - Molecular Function for AFF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003690 double-stranded DNA binding IEA --
GO:0003700 DNA-binding transcription factor activity IEA --
genes like me logo Genes that share ontologies with AFF3: view
genes like me logo Genes that share phenotypes with AFF3: view

Animal Models for AFF3 Gene

MGI Knock Outs for AFF3:
  • Aff3 Aff3<tm1a(EUCOMM)Wtsi>

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for AFF3

Clone products for research

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for AFF3 Gene

Localization for AFF3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for AFF3 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 AFF3 gene
Compartment Confidence
nucleus 5
cytosol 4
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Cytosol (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for AFF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 8555498
GO:0005654 nucleoplasm IDA --
GO:0005829 cytosol IDA --
GO:0016604 nuclear body IDA --
GO:0032783 ELL-EAF complex IBA 21873635
genes like me logo Genes that share ontologies with AFF3: view

Pathways & Interactions for AFF3 Gene

PathCards logo

SuperPathways for AFF3 Gene

No Data Available

SIGNOR curated interactions for AFF3 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for AFF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0010468 regulation of gene expression IEA,IBA 21873635
GO:0034612 response to tumor necrosis factor IMP 20444755
GO:0035116 embryonic hindlimb morphogenesis IEA,IMP 18616733
genes like me logo Genes that share ontologies with AFF3: view

No data available for Pathways by source for AFF3 Gene

Drugs & Compounds for AFF3 Gene

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  1. Drug products for research
No Compound Related Data Available

Transcripts for AFF3 Gene

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mRNA/cDNA for AFF3 Gene

3 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
27 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 AFF3

Clone products for research

Alternative Splicing Database (ASD) splice patterns (SP) for AFF3 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^
SP1: -
SP2: -
SP3:
SP4:
SP5:

ExUns: 23 ^ 24 ^ 25
SP1:
SP2:
SP3:
SP4:
SP5:

Relevant External Links for AFF3 Gene

GeneLoc Exon Structure for
AFF3

Expression for AFF3 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 AFF3 Gene

mRNA expression in normal human tissues for AFF3 Gene
mRNA expression by BioGPS for AFF3 GenemRNA expression by GTEx for AFF3 Gene

Protein differential expression in normal tissues from HIPED for AFF3 Gene

This gene is overexpressed in Heart (30.4), Adipocyte (18.0), and Peripheral blood mononuclear cells (15.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for AFF3 Gene



Protein tissue co-expression partners for AFF3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for AFF3

SOURCE GeneReport for Unigene cluster for AFF3 Gene:

Hs.444414

mRNA Expression by UniProt/SwissProt for AFF3 Gene:

P51826-AFF3_HUMAN
Tissue specificity: Preferentially expressed in lymphoid tissues, highest levels being found in the thymus.

Evidence on tissue expression from TISSUES for AFF3 Gene

  • Nervous system(4.4)
  • Spleen(4.4)
  • Skin(2.2)
  • Blood(2.2)
  • Kidney(2.1)
genes like me logo Genes that share expression patterns with AFF3: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for AFF3 Gene

Orthologs for AFF3 Gene

This gene was present in the common ancestor of animals.

Orthologs for AFF3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia AFF3 30 31
  • 99.39 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia AFF3 30 31
  • 90.11 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia AFF3 30 31
  • 87.56 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Aff3 30 17 31
  • 85.63 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Aff3 30
  • 85.33 (n)
Oppossum
(Monodelphis domestica)
 Mammalia -- 31
  • 77 (a)
 OneToMany
-- 31
  • 73 (a)
 OneToMany
Platypus
(Ornithorhynchus anatinus)
 Mammalia -- 31
  • 68 (a)
 OneToMany
-- 31
  • 57 (a)
 OneToMany
Chicken
(Gallus gallus)
 Aves AFF3 30 31
  • 72.49 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia AFF3 31
  • 64 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia aff3 30
  • 60.51 (n)
Zebrafish
(Danio rerio)
 Actinopterygii aff3 31
  • 29 (a)
 OneToOne
Fruit Fly
(Drosophila melanogaster)
 Insecta lilli 31
  • 15 (a)
 OneToMany
Sea Squirt
(Ciona savignyi)
 Ascidiacea CSA.4989 31
  • 17 (a)
 OneToMany
Species where no ortholog for AFF3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • Rainbow Trout (Oncorhynchus mykiss)
  • 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)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for AFF3 Gene

ENSEMBL:
Gene Tree for AFF3 (if available)
TreeFam:
Gene Tree for AFF3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for AFF3: view image

Paralogs for AFF3 Gene

Paralogs for AFF3 Gene

(3) SIMAP similar genes for AFF3 Gene using alignment to 12 proteins:

  • AFF3_HUMAN
  • C9J622_HUMAN
  • C9J847_HUMAN
  • C9JC67_HUMAN
  • C9JIB1_HUMAN
  • C9JMS1_HUMAN
  • C9JUC4_HUMAN
  • C9JUY1_HUMAN
  • C9JZ66_HUMAN
  • H7C3W3_HUMAN
  • H7C4C2_HUMAN
  • L8E9Z7_HUMAN
genes like me logo Genes that share paralogs with AFF3: view

Variants for AFF3 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for AFF3 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
976685 Likely Pathogenic: AFF3-associated disorder 100,006,792(-) A/C
NM_002285.3(AFF3):c.713T>G (p.Met238Arg) 		MISSENSE
rs1131692272 Pathogenic: not provided 100,006,808(-) C/T
NM_002285.3(AFF3):c.697G>A (p.Ala233Thr) 		MISSENSE
rs34170229 Benign: not provided 100,006,824(-) G/A
NM_002285.3(AFF3):c.681C>T (p.Val227=) 		SYNONYMOUS
rs1047265 - p.Asn494Ser
rs4851223 - p.Asn358Ser

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for AFF3 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 AFF3 Gene

Variant ID Type Subtype PubMed ID
dgv1156e212 CNV loss 25503493
esv2137645 CNV deletion 18987734
esv2662354 CNV deletion 23128226
esv2720433 CNV deletion 23290073
esv2720434 CNV deletion 23290073
esv2759078 CNV gain+loss 17122850
esv3423347 CNV duplication 20981092
esv3559843 CNV deletion 23714750
esv3583981 CNV loss 25503493
esv3591739 CNV gain 21293372
esv3591740 CNV loss 21293372
esv3591743 CNV loss 21293372
esv3591744 CNV loss 21293372
esv9519 CNV gain 19470904
nsv1003114 CNV loss 25217958
nsv1072010 CNV deletion 25765185
nsv1133479 CNV deletion 24896259
nsv1146874 CNV duplication 26484159
nsv1148652 CNV duplication 26484159
nsv2845 CNV deletion 18451855
nsv2846 CNV insertion 18451855
nsv2847 CNV deletion 18451855
nsv2848 CNV insertion 18451855
nsv458707 CNV gain 19166990
nsv473190 CNV novel sequence insertion 20440878
nsv527481 CNV loss 19592680
nsv582529 CNV gain 21841781
nsv582530 CNV loss 21841781
nsv963672 CNV duplication 23825009
nsv979074 CNV duplication 23825009

Variation tolerance for AFF3 Gene

Residual Variation Intolerance Score: 3.33% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.13; 51.36% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for AFF3 Gene

Human Gene Mutation Database (HGMD)
AFF3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
AFF3

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for AFF3 Gene

Disorders for AFF3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for AFF3 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
childhood t-cell acute lymphoblastic leukemia
  • childhood precursor t-lymphoblastic lymphoma/leukemia
leukemia, acute lymphoblastic
  • all
- elite association - COSMIC cancer census association via MalaCards
Search AFF3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for AFF3

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 AFF3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for AFF3 Gene

Publications for AFF3 Gene

  1. LAF-4 encodes a lymphoid nuclear protein with transactivation potential that is homologous to AF-4, the gene fused to MLL in t(4;11) leukemias. (PMID: 8555498) Ma C … Staudt LM (Blood 1996) 2 3 4 23
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  3. Investigation of potential non-HLA rheumatoid arthritis susceptibility loci in a European cohort increases the evidence for nine markers. (PMID: 20498205) Plant D … Worthington J (Annals of the rheumatic diseases 2010) 3 41
  4. Investigation of rheumatoid arthritis susceptibility genes identifies association of AFF3 and CD226 variants with response to anti-tumour necrosis factor treatment. (PMID: 20444755) Tan RJ … Barton A (Annals of the rheumatic diseases 2010) 3 41
  5. Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci. (PMID: 20453842) Stahl EA … Plenge RM (Nature genetics 2010) 3 41

ExternalLinks

View latest publications for AFF3 gene in Mastermind

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