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Aliases for AFF4 Gene

Aliases for AFF4 Gene

  • AF4/FMR2 Family Member 4 2 3 5
  • Major CDK9 Elongation Factor-Associated Protein 3 4
  • ALL1-Fused Gene From Chromosome 5q31 Protein 3 4
  • AF5Q31 3 4
  • MCEF 3 4
  • ALL1 Fused Gene From 5q31 2
  • AF4/FMR2 Family, Member 4 2
  • Protein AF-5q31 4
  • CHOPS 3

External Ids for AFF4 Gene

Previous GeneCards Identifiers for AFF4 Gene

  • GC05M132243
  • GC05M132211
  • GC05M127403

Summaries for AFF4 Gene

Entrez Gene Summary for AFF4 Gene

  • 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]

GeneCards Summary for AFF4 Gene

AFF4 (AF4/FMR2 Family Member 4) is a Protein Coding gene. Diseases associated with AFF4 include Chops Syndrome and Lymphoblastic Leukemia. Among its related pathways are Formation of HIV elongation complex in the absence of HIV Tat and Gene Expression. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding. An important paralog of this gene is AFF1.

UniProtKB/Swiss-Prot for AFF4 Gene

  • Key component of the super elongation complex (SEC), a complex required to increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by the polymerase at multiple sites along the DNA. In the SEC complex, AFF4 acts as a central scaffold that recruits other factors through direct interactions with ELL proteins (ELL, ELL2 or ELL3) and the P-TEFb complex. In case of infection by HIV-1 virus, the SEC complex is recruited by the viral Tat protein to stimulate viral gene expression.

Additional gene information for AFF4 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for AFF4 Gene

Genomics for AFF4 Gene

Regulatory Elements for AFF4 Gene

Enhancers for AFF4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05H132452 2 FANTOM5 Ensembl ENCODE dbSUPER 59.7 +496.4 496419 29 HDGF PKNOX1 FOXA2 ARNT ZFP64 ARID4B FEZF1 DMAP1 YY1 SLC30A9 AFF4 RAD50 ZCCHC10 IL4 IRF1 SLC22A5 ENSG00000224431 LOC102723741 MIR3936HG C5orf56
GH05H132292 1.8 FANTOM5 ENCODE dbSUPER 39.4 +668.6 668643 5 PKNOX1 MLX ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 RAD50 AFF4 MIR3936HG IL4 FNIP1 ENSG00000202533 MIR3936 SLC22A5 ENSG00000224431 ENSG00000248648
GH05H132362 1.2 Ensembl ENCODE 36.3 +598.9 598933 4 FOXA2 SIN3A FEZF1 BRCA1 ZNF2 YY1 FOS TSHZ1 REST ZNF491 RAD50 MIR3936HG AFF4 ENSG00000224431 ENSG00000248648 ZCCHC10 P4HA2 SLC22A4 IL4 ENSG00000202533
GH05H132493 2.1 FANTOM5 Ensembl ENCODE dbSUPER 18.6 +465.1 465145 10 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A YBX1 ZNF2 ZBTB7B YY1 IRF1 AFF4 RAD50 SLC22A5 LOC105379175 SLC22A4 IL4 ENSG00000202533 MIR3936HG GC05P132531
GH05H132555 1.2 ENCODE 25.9 +406.1 406055 3 MLX FEZF1 DMAP1 YY1 ZNF143 SP3 NFYC ZC3H11A ZNF610 GLIS1 ENSG00000231585 RAD50 AFF4 IL4 P4HA2-AS1 LOC107987500 CTB-3M24.3 ENSG00000224431 ZCCHC10 ENSG00000202533
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around AFF4 on UCSC Golden Path with GeneCards custom track

Promoters for AFF4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000186917 762 2601 HDGF PKNOX1 MLX ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2

Genomic Location for AFF4 Gene

Chromosome:
5
Start:
132,875,379 bp from pter
End:
132,963,662 bp from pter
Size:
88,284 bases
Orientation:
Minus strand

Genomic View for AFF4 Gene

Genes around AFF4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
AFF4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for AFF4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for AFF4 Gene

Proteins for AFF4 Gene

  • Protein details for AFF4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UHB7-AFF4_HUMAN
    Recommended name:
    AF4/FMR2 family member 4
    Protein Accession:
    Q9UHB7
    Secondary Accessions:
    • B2RP19
    • B7WPD2
    • Q498B2
    • Q59FB3
    • Q6P592
    • Q8TDR1
    • Q9P0E4

    Protein attributes for AFF4 Gene

    Size:
    1163 amino acids
    Molecular mass:
    127459 Da
    Quaternary structure:
    • Interacts with ELL3; the interaction is direct (By similarity). Interacts with ELL2; the interaction is direct and leads to stabilize ELL2 and prevent ELL2 ubiquitination and degradation. 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). Interacts with ELL.
    SequenceCaution:
    • Sequence=AAI00288.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=BAD92784.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for AFF4 Gene

    Alternative splice isoforms for AFF4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for AFF4 Gene

Post-translational modifications for AFF4 Gene

  • Ubiquitination at Lys288
  • Modification sites at PhosphoSitePlus

Other Protein References for AFF4 Gene

No data available for DME Specific Peptides for AFF4 Gene

Domains & Families for AFF4 Gene

Gene Families for AFF4 Gene

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

Protein Domains for AFF4 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for AFF4 Gene

Graphical View of Domain Structure for InterPro Entry

Q9UHB7

UniProtKB/Swiss-Prot:

AFF4_HUMAN :
  • Belongs to the AF4 family.
Family:
  • Belongs to the AF4 family.
genes like me logo Genes that share domains with AFF4: view

Function for AFF4 Gene

Molecular function for AFF4 Gene

UniProtKB/Swiss-Prot Function:
Key component of the super elongation complex (SEC), a complex required to increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by the polymerase at multiple sites along the DNA. In the SEC complex, AFF4 acts as a central scaffold that recruits other factors through direct interactions with ELL proteins (ELL, ELL2 or ELL3) and the P-TEFb complex. In case of infection by HIV-1 virus, the SEC complex is recruited by the viral Tat protein to stimulate viral gene expression.

Phenotypes From GWAS Catalog for AFF4 Gene

Gene Ontology (GO) - Molecular Function for AFF4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003700 transcription factor activity, sequence-specific DNA binding TAS 10588740
GO:0005515 protein binding IPI 20153263
genes like me logo Genes that share ontologies with AFF4: view
genes like me logo Genes that share phenotypes with AFF4: view

Human Phenotype Ontology for AFF4 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for AFF4 Gene

MGI Knock Outs for AFF4:

Animal Model Products

CRISPR Products

miRNA for AFF4 Gene

miRTarBase miRNAs that target AFF4

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for AFF4
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for AFF4 Gene

Localization for AFF4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for AFF4 Gene

Nucleus. Note=Associates to transcriptionally active chromatin but not at snRNA genes. {ECO:0000250}.

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 AFF4 gene
Compartment Confidence
nucleus 5
mitochondrion 2
cytosol 2
cytoskeleton 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli fibrillar center (3)
  • Nucleus (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for AFF4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001650 fibrillar center IDA --
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm TAS --
GO:0008023 transcription elongation factor complex IDA 22195968
GO:0035327 transcriptionally active chromatin ISS --
genes like me logo Genes that share ontologies with AFF4: view

Pathways & Interactions for AFF4 Gene

genes like me logo Genes that share pathways with AFF4: view

Gene Ontology (GO) - Biological Process for AFF4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription from RNA polymerase II promoter TAS --
GO:0006368 transcription elongation from RNA polymerase II promoter TAS --
GO:0007286 spermatid development IEA --
genes like me logo Genes that share ontologies with AFF4: view

No data available for SIGNOR curated interactions for AFF4 Gene

Drugs & Compounds for AFF4 Gene

No Compound Related Data Available

Transcripts for AFF4 Gene

Unigene Clusters for AFF4 Gene

AF4/FMR2 family, member 4:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for AFF4
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for AFF4 Gene

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

ExUns: 20 ^ 21 ^ 22 ^ 23
SP1:
SP2:
SP3:
SP4:
SP5:

Relevant External Links for AFF4 Gene

GeneLoc Exon Structure for
AFF4
ECgene alternative splicing isoforms for
AFF4

Expression for AFF4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for AFF4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for AFF4 Gene

This gene is overexpressed in Plasma (31.0), Pancreatic juice (9.0), and Platelet (7.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for AFF4 Gene



NURSA nuclear receptor signaling pathways regulating expression of AFF4 Gene:

AFF4

SOURCE GeneReport for Unigene cluster for AFF4 Gene:

Hs.519313

mRNA Expression by UniProt/SwissProt for AFF4 Gene:

Q9UHB7-AFF4_HUMAN
Tissue specificity: Ubiquitously expressed. Strongly expressed in heart, placenta, skeletal muscle, pancreas and to a lower extent in brain.

Evidence on tissue expression from TISSUES for AFF4 Gene

  • Nervous system(4.7)
  • Liver(4.4)
  • Skin(4.4)
  • Blood(4.3)
  • Muscle(3.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for AFF4 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • cheek
  • chin
  • ear
  • epiglottis
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • larynx
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • pharynx
  • skull
  • vocal cord
Thorax:
  • bronchus
  • esophagus
  • heart
  • heart valve
  • lung
  • trachea
Abdomen:
  • kidney
  • stomach
Pelvis:
  • testicle
  • ureter
  • urinary bladder
Limb:
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • toe
  • upper limb
General:
  • blood
  • blood vessel
  • hair
  • skin
genes like me logo Genes that share expression patterns with AFF4: view

Primer Products

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for AFF4 Gene

Orthologs for AFF4 Gene

This gene was present in the common ancestor of animals.

Orthologs for AFF4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia AFF4 33 34
  • 99.86 (n)
cow
(Bos Taurus)
Mammalia AFF4 33 34
  • 94.81 (n)
dog
(Canis familiaris)
Mammalia AFF4 33 34
  • 94.58 (n)
rat
(Rattus norvegicus)
Mammalia Aff4 33
  • 90.54 (n)
mouse
(Mus musculus)
Mammalia Aff4 33 16 34
  • 89.41 (n)
oppossum
(Monodelphis domestica)
Mammalia AFF4 34
  • 89 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia AFF4 34
  • 84 (a)
OneToOne
chicken
(Gallus gallus)
Aves AFF4 33 34
  • 81.93 (n)
lizard
(Anolis carolinensis)
Reptilia AFF4 34
  • 83 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia aff4 33
  • 74.99 (n)
zebrafish
(Danio rerio)
Actinopterygii aff4 33 34
  • 61.06 (n)
fruit fly
(Drosophila melanogaster)
Insecta lilli 34
  • 15 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4989 34
  • 18 (a)
OneToMany
Species where no ortholog for AFF4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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 AFF4 Gene

ENSEMBL:
Gene Tree for AFF4 (if available)
TreeFam:
Gene Tree for AFF4 (if available)

Paralogs for AFF4 Gene

Paralogs for AFF4 Gene

(4) SIMAP similar genes for AFF4 Gene using alignment to 5 proteins:

Pseudogenes.org Pseudogenes for AFF4 Gene

genes like me logo Genes that share paralogs with AFF4: view

Variants for AFF4 Gene

Sequence variations from dbSNP and Humsavar for AFF4 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs786205233 Pathogenic, CHOPS syndrome (CHOPS) [MIM:616368] 132,934,305(-) AACCC(A/G)CTGCC reference, missense
rs786205679 Pathogenic, CHOPS syndrome (CHOPS) [MIM:616368] 132,934,304(-) ACCCA(C/G)TGCCT reference, missense
rs786205680 Pathogenic, CHOPS syndrome (CHOPS) [MIM:616368] 132,934,293(-) ATGTG(C/T)GGCCC reference, missense
rs1000076965 -- 132,883,955(+) CCTAA(A/G)AAACT intron-variant
rs1000089191 -- 132,932,026(+) GAAGA(A/G)AGTAA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for AFF4 Gene

Variant ID Type Subtype PubMed ID
esv2730796 CNV deletion 23290073
esv3606811 CNV gain 21293372
esv3606812 CNV loss 21293372
nsv1022039 CNV gain 25217958
nsv1137531 CNV deletion 24896259
nsv475496 CNV novel sequence insertion 20440878
nsv5003 CNV deletion 18451855
nsv830489 CNV loss 17160897
nsv830490 CNV gain 17160897
nsv968987 CNV duplication 23825009

Variation tolerance for AFF4 Gene

Residual Variation Intolerance Score: 5.24% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.62; 45.31% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for AFF4 Gene

Human Gene Mutation Database (HGMD)
AFF4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
AFF4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for AFF4 Gene

Disorders for AFF4 Gene

MalaCards: The human disease database

(2) MalaCards diseases for AFF4 Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
chops syndrome
  • cognitive impairment, coarse facies, heart defects, obesity, pulmonary involvement, short stature and skeletal dysplasia
lymphoblastic leukemia
  • leukemia, lymphoid
- elite association - COSMIC cancer census association via MalaCards
Search AFF4 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

AFF4_HUMAN
  • CHOPS syndrome (CHOPS) [MIM:616368]: A syndrome characterized by cognitive impairment, coarse facies, heart defects, obesity, pulmonary involvement, short stature, and skeletal dysplasia. {ECO:0000269 PubMed:25730767}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Note=A chromosomal aberration involving AFF4 is found in acute lymphoblastic leukemia (ALL). Insertion ins(5;11)(q31;q13q23) that forms a KMT2A/MLL1-AFF4 fusion protein.

Relevant External Links for AFF4

Genetic Association Database (GAD)
AFF4
Human Genome Epidemiology (HuGE) Navigator
AFF4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
AFF4
genes like me logo Genes that share disorders with AFF4: view

No data available for Genatlas for AFF4 Gene

Publications for AFF4 Gene

  1. AF5q31, a newly identified AF4-related gene, is fused to MLL in infant acute lymphoblastic leukemia with ins(5;11)(q31;q13q23). (PMID: 10588740) Taki T … Hayashi Y (Proceedings of the National Academy of Sciences of the United States of America 1999) 2 3 4 22 60
  2. Germline gain-of-function mutations in AFF4 cause a developmental syndrome functionally linking the super elongation complex and cohesin. (PMID: 25730767) Izumi K … Krantz ID (Nature genetics 2015) 3 4 60
  3. HIV-1 Tat recruits transcription elongation factors dispersed along a flexible AFF4 scaffold. (PMID: 23251033) Chou S … Alber T (Proceedings of the National Academy of Sciences of the United States of America 2013) 3 4 60
  4. The ubiquitin ligase Siah1 controls ELL2 stability and formation of super elongation complexes to modulate gene transcription. (PMID: 22483617) Liu M … Zhou Q (Molecular cell 2012) 3 4 60
  5. The little elongation complex regulates small nuclear RNA transcription. (PMID: 22195968) Smith ER … Shilatifard A (Molecular cell 2011) 3 4 60

Products for AFF4 Gene

Sources for AFF4 Gene

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