Human Gene AFF4 (ENST00000265343.10) from GENCODE V41
  Description: Homo sapiens AF4/FMR2 family member 4 (AFF4), mRNA. (from RefSeq NM_014423)
RefSeq Summary (NM_014423): 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].
Gencode Transcript: ENST00000265343.10
Gencode Gene: ENSG00000072364.13
Transcript (Including UTRs)
   Position: hg38 chr5:132,875,395-132,963,634 Size: 88,240 Total Exon Count: 21 Strand: -
Coding Region
   Position: hg38 chr5:132,881,059-132,937,189 Size: 56,131 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2022-05-14 09:57:26

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr5:132,875,395-132,963,634)mRNA (may differ from genome)Protein (1163 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSCGAPEnsemblEntrez GeneExonPrimer

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=AF4/FMR2 family member 4; AltName: Full=ALL1-fused gene from chromosome 5q31 protein; Short=Protein AF-5q31; AltName: Full=Major CDK9 elongation factor-associated protein;
FUNCTION: May play a role in transcriptional regulation (By similarity).
SUBUNIT: Component of the cyclin-dependent kinase pair (CDK9/cyclin-T1) complex, also called positive transcription elongation factor b (P-TEFb).
INTERACTION: O60563:CCNT1; NbExp=5; IntAct=EBI-395282, EBI-2479671; Q03111:MLLT1; NbExp=8; IntAct=EBI-395282, EBI-1384215; P42568:MLLT3; NbExp=4; IntAct=EBI-395282, EBI-716132; P04608:tat (xeno); NbExp=4; IntAct=EBI-395282, EBI-6164389;
TISSUE SPECIFICITY: Ubiquitously expressed. Strongly expressed in heart, placenta, skeletal muscle, pancreas and to a lower extent in brain.
DEVELOPMENTAL STAGE: Expressed in fetal heart, lung, brain and to a lower extent liver.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
DISEASE: Note=A chromosomal aberration involving AFF4 is found in acute lymphoblastic leukemia (ALL). Insertion ins(5;11)(q31;q13q23) that forms a MLL-AFF4 fusion protein.
SIMILARITY: Belongs to the AF4 family.
SEQUENCE CAUTION: Sequence=AAI00288.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=BAD92784.1; Type=Erroneous initiation;
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="";

-  MalaCards Disease Associations
  MalaCards Gene Search: AFF4
Diseases sorted by gene-association score: chops syndrome* (1678), lymphoblastic leukemia (16)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 17.57 RPKM in Ovary
Total median expression: 602.97 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -183.50380-0.483 Picture PostScript Text
3' UTR -1458.705664-0.258 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR007797 - TF_AF4/FMR2

Pfam Domains:
PF05110 - AF-4 proto-oncoprotein

ModBase Predicted Comparative 3D Structure on Q9UHB7
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein SequenceProtein Sequence   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0006368 transcription elongation from RNA polymerase II promoter
GO:0007286 spermatid development

Cellular Component:
GO:0001650 fibrillar center
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0008023 transcription elongation factor complex
GO:0035327 transcriptionally active chromatin

-  Descriptions from all associated GenBank mRNAs
  LF384726 - JP 2014500723-A/192229: Polycomb-Associated Non-Coding RNAs.
MA620303 - JP 2018138019-A/192229: Polycomb-Associated Non-Coding RNAs.
BC137226 - Homo sapiens AF4/FMR2 family, member 4, mRNA (cDNA clone MGC:168846 IMAGE:9021223), complete cds.
BC144538 - Homo sapiens cDNA clone IMAGE:9053065.
AF213987 - Homo sapiens MCEF protein (MCEF) mRNA, complete cds.
AF197927 - Homo sapiens AF5q31 protein (AF5q31) mRNA, complete cds.
AB209547 - Homo sapiens mRNA for ALL1 fused gene from 5q31 variant protein.
AK024831 - Homo sapiens cDNA: FLJ21178 fis, clone CAS11144, highly similar to AF197927 Homo sapiens AF5q31 protein (AF5q31) mRNA.
AK055638 - Homo sapiens cDNA FLJ31076 fis, clone HSYRA2001567, highly similar to Homo sapiens AF5q31 protein (AF5q31) mRNA.
AK307407 - Homo sapiens cDNA, FLJ97355.
BC025700 - Homo sapiens AF4/FMR2 family, member 4, mRNA (cDNA clone IMAGE:5221893), complete cds.
KJ904724 - Synthetic construct Homo sapiens clone ccsbBroadEn_14118 AFF4 gene, encodes complete protein.
BC100287 - Homo sapiens AF4/FMR2 family, member 4, mRNA (cDNA clone IMAGE:6167752), partial cds.
AF173886 - Homo sapiens MSTP111 (MST111) mRNA, complete cds.
AK126818 - Homo sapiens cDNA FLJ44868 fis, clone BRALZ2018834.
LF325777 - JP 2014500723-A/133280: Polycomb-Associated Non-Coding RNAs.
MA561354 - JP 2018138019-A/133280: Polycomb-Associated Non-Coding RNAs.
LF325776 - JP 2014500723-A/133279: Polycomb-Associated Non-Coding RNAs.
MA561353 - JP 2018138019-A/133279: Polycomb-Associated Non-Coding RNAs.
LF325775 - JP 2014500723-A/133278: Polycomb-Associated Non-Coding RNAs.
MA561352 - JP 2018138019-A/133278: Polycomb-Associated Non-Coding RNAs.
LF325774 - JP 2014500723-A/133277: Polycomb-Associated Non-Coding RNAs.
MA561351 - JP 2018138019-A/133277: Polycomb-Associated Non-Coding RNAs.
LF325773 - JP 2014500723-A/133276: Polycomb-Associated Non-Coding RNAs.
MA561350 - JP 2018138019-A/133276: Polycomb-Associated Non-Coding RNAs.
LF325772 - JP 2014500723-A/133275: Polycomb-Associated Non-Coding RNAs.
MA561349 - JP 2018138019-A/133275: Polycomb-Associated Non-Coding RNAs.
LF325771 - JP 2014500723-A/133274: Polycomb-Associated Non-Coding RNAs.
MA561348 - JP 2018138019-A/133274: Polycomb-Associated Non-Coding RNAs.
LF325770 - JP 2014500723-A/133273: Polycomb-Associated Non-Coding RNAs.
MA561347 - JP 2018138019-A/133273: Polycomb-Associated Non-Coding RNAs.
LF325769 - JP 2014500723-A/133272: Polycomb-Associated Non-Coding RNAs.
MA561346 - JP 2018138019-A/133272: Polycomb-Associated Non-Coding RNAs.
LF325768 - JP 2014500723-A/133271: Polycomb-Associated Non-Coding RNAs.
MA561345 - JP 2018138019-A/133271: Polycomb-Associated Non-Coding RNAs.
LF325767 - JP 2014500723-A/133270: Polycomb-Associated Non-Coding RNAs.
MA561344 - JP 2018138019-A/133270: Polycomb-Associated Non-Coding RNAs.
LF325766 - JP 2014500723-A/133269: Polycomb-Associated Non-Coding RNAs.
MA561343 - JP 2018138019-A/133269: Polycomb-Associated Non-Coding RNAs.
LF325765 - JP 2014500723-A/133268: Polycomb-Associated Non-Coding RNAs.
MA561342 - JP 2018138019-A/133268: Polycomb-Associated Non-Coding RNAs.
LF325764 - JP 2014500723-A/133267: Polycomb-Associated Non-Coding RNAs.
MA561341 - JP 2018138019-A/133267: Polycomb-Associated Non-Coding RNAs.
LF325763 - JP 2014500723-A/133266: Polycomb-Associated Non-Coding RNAs.
MA561340 - JP 2018138019-A/133266: Polycomb-Associated Non-Coding RNAs.
JD082493 - Sequence 63517 from Patent EP1572962.
JD469427 - Sequence 450451 from Patent EP1572962.
LF325762 - JP 2014500723-A/133265: Polycomb-Associated Non-Coding RNAs.
MA561339 - JP 2018138019-A/133265: Polycomb-Associated Non-Coding RNAs.
LF325761 - JP 2014500723-A/133264: Polycomb-Associated Non-Coding RNAs.
MA561338 - JP 2018138019-A/133264: Polycomb-Associated Non-Coding RNAs.
LF325759 - JP 2014500723-A/133262: Polycomb-Associated Non-Coding RNAs.
MA561336 - JP 2018138019-A/133262: Polycomb-Associated Non-Coding RNAs.
AF161355 - Homo sapiens HSPC092 mRNA, partial cds.
LF325758 - JP 2014500723-A/133261: Polycomb-Associated Non-Coding RNAs.
MA561335 - JP 2018138019-A/133261: Polycomb-Associated Non-Coding RNAs.
LF325757 - JP 2014500723-A/133260: Polycomb-Associated Non-Coding RNAs.
MA561334 - JP 2018138019-A/133260: Polycomb-Associated Non-Coding RNAs.
LF325755 - JP 2014500723-A/133258: Polycomb-Associated Non-Coding RNAs.
MA561332 - JP 2018138019-A/133258: Polycomb-Associated Non-Coding RNAs.
LF325754 - JP 2014500723-A/133257: Polycomb-Associated Non-Coding RNAs.
MA561331 - JP 2018138019-A/133257: Polycomb-Associated Non-Coding RNAs.
LF325753 - JP 2014500723-A/133256: Polycomb-Associated Non-Coding RNAs.
MA561330 - JP 2018138019-A/133256: Polycomb-Associated Non-Coding RNAs.
BX537585 - Homo sapiens mRNA; cDNA DKFZp686E17119 (from clone DKFZp686E17119).
BC063007 - Homo sapiens AF4/FMR2 family, member 4, mRNA (cDNA clone IMAGE:5213733), complete cds.
KJ902450 - Synthetic construct Homo sapiens clone ccsbBroadEn_11844 AFF4 gene, encodes complete protein.
LF325745 - JP 2014500723-A/133248: Polycomb-Associated Non-Coding RNAs.
MA561322 - JP 2018138019-A/133248: Polycomb-Associated Non-Coding RNAs.
CU687624 - Synthetic construct Homo sapiens gateway clone IMAGE:100021675 5' read AFF4 mRNA.
CU693016 - Synthetic construct Homo sapiens gateway clone IMAGE:100018177 5' read AFF4 mRNA.
LF325741 - JP 2014500723-A/133244: Polycomb-Associated Non-Coding RNAs.
MA561318 - JP 2018138019-A/133244: Polycomb-Associated Non-Coding RNAs.
LF325740 - JP 2014500723-A/133243: Polycomb-Associated Non-Coding RNAs.
MA561317 - JP 2018138019-A/133243: Polycomb-Associated Non-Coding RNAs.
BC040454 - Homo sapiens AF4/FMR2 family, member 4, mRNA (cDNA clone IMAGE:4689215), with apparent retained intron.
JD461595 - Sequence 442619 from Patent EP1572962.
JD403262 - Sequence 384286 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9UHB7 (Reactome details) participates in the following event(s):

R-HSA-112381 Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex
R-HSA-113429 Elongating transcript encounters a lesion in the template
R-HSA-112379 Recruitment of elongation factors to form elongation complex
R-HSA-113411 2-4 nt.backtracking of Pol II complex on the template leading to elongation pausing
R-HSA-113412 Pol II elongation complex moves on the template as transcript elongates
R-HSA-113414 7-14 nt. Backtracking of Pol II complex on the template leading to elongation arrest
R-HSA-112385 Addition of nucleotides leads to transcript elongation
R-HSA-112392 Resumption of elongation after recovery from pausing
R-HSA-113413 TFIIS-mediated recovery of elongation from arrest
R-HSA-112395 Abortive termination of elongation after arrest
R-HSA-112396 Separation of elongating transcript from template
R-HSA-112382 Formation of RNA Pol II elongation complex
R-HSA-674695 RNA Polymerase II Pre-transcription Events
R-HSA-75955 RNA Polymerase II Transcription Elongation
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: AF5Q31, AFF4_HUMAN, B2RP19, B7WPD2, ENST00000265343.1, ENST00000265343.2, ENST00000265343.3, ENST00000265343.4, ENST00000265343.5, ENST00000265343.6, ENST00000265343.7, ENST00000265343.8, ENST00000265343.9, HSPC092, MCEF, NM_014423, Q498B2, Q59FB3, Q6P592, Q8TDR1, Q9P0E4, Q9UHB7, uc003kyd.1, uc003kyd.2, uc003kyd.3, uc003kyd.4, uc003kyd.5
UCSC ID: ENST00000265343.10
RefSeq Accession: NM_014423
Protein: Q9UHB7 (aka AFF4_HUMAN)
CCDS: CCDS4164.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.