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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 Gene Expression and Formation of HIV elongation complex in the absence of HIV Tat. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity. 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

GeneHancer (GH) Regulatory Elements for AFF4 Gene

Promoters and enhancers for AFF4 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
GH05I132961 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 575.6 +0.7 694 3.6 CLOCK MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF213 SP3 ZNF610 AFF4 ENSG00000272023 GC05M132963 LOC105379177 IL4 RAD50 ENSG00000224431 ZCCHC10 HSPA4 GDF9
GH05I132292 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 39.4 +668.6 668642 5.2 PKNOX1 SMAD1 MLX ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 SLC22A4 P4HA2 RAD50 AFF4 MIR3936HG IL4 FNIP1 ENSG00000202533 MIR3936 SLC22A5
GH05I132452 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 32.8 +496.4 496418 29.7 HDGF PKNOX1 FOXA2 ARNT ZFP64 ARID4B FEZF1 DMAP1 IRF4 YY1 ENSG00000202533 GC05P132469 AFF4 RAD50 IRF1 SLC22A5 IL4 LOC102723741 MIR3936HG ENSG00000224431
GH05I132865 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 27.7 +96.5 96483 3.5 HDGF FOXA2 PKNOX1 SMAD1 ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B GDF9 PIR40966 UQCRQ AFF4 RAD50 IL4 ENSG00000202533 LOC105379175 KIF3A ZCCHC10
GH05I133048 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 24.5 -87.4 -87439 5.5 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 E2F8 ZNF143 SP3 HSPA4 GC05M133049 GC05M133050 ENSG00000279691 AFF4 IL4 ENSG00000202533 LOC105379175 RAD50 ENSG00000224431
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around AFF4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the AFF4 gene promoter:

Genomic Locations for AFF4 Gene

Genomic Locations for AFF4 Gene
chr5:132,875,379-132,963,662
(GRCh38/hg38)
Size:
88,284 bases
Orientation:
Minus strand
chr5:132,211,071-132,299,354
(GRCh37/hg19)

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

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 DNA binding transcription factor activity 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:

miRNA for AFF4 Gene

miRTarBase miRNAs that target AFF4

Clone Products

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 by RNA polymerase II 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:

Clone Products

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)
  • Blood(4.3)
  • Skin(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

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 Variation AA Info Type
rs786205233 pathogenic, Chops syndrome, CHOPS syndrome (CHOPS) [MIM:616368] 132,934,305(-) T/C coding_sequence_variant, genic_upstream_transcript_variant, missense_variant
rs786205679 pathogenic, Chops syndrome, CHOPS syndrome (CHOPS) [MIM:616368] 132,934,304(-) G/C coding_sequence_variant, genic_upstream_transcript_variant, missense_variant
rs786205680 pathogenic, Chops syndrome, not provided, CHOPS syndrome (CHOPS) [MIM:616368] 132,934,293(-) G/A coding_sequence_variant, genic_upstream_transcript_variant, missense_variant
rs138116584 likely-benign, not specified 132,892,356(-) G/A coding_sequence_variant, synonymous_variant
rs188073736 likely-benign, not specified 132,897,044(-) G/A coding_sequence_variant, missense_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)

Additional Variant Information 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, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
chops syndrome
  • chops
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.

Additional Disease Information for AFF4

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 58
  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 58
  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 58
  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 58
  5. The little elongation complex regulates small nuclear RNA transcription. (PMID: 22195968) Smith ER … Shilatifard A (Molecular cell 2011) 3 4 58

Products for AFF4 Gene

Sources for AFF4 Gene

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