Human Gene AFF1 (uc003hqj.4) Description and Page Index
  Description: Homo sapiens AF4/FMR2 family, member 1 (AFF1), transcript variant 2, mRNA.
RefSeq Summary (NM_005935): 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].
Transcript (Including UTRs)
   Position: hg19 chr4:87,928,153-88,062,206 Size: 134,054 Total Exon Count: 20 Strand: +
Coding Region
   Position: hg19 chr4:87,928,560-88,056,853 Size: 128,294 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr4:87,928,153-88,062,206)mRNA (may differ from genome)Protein (1210 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
OMIMPubMedStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=AF4/FMR2 family member 1; AltName: Full=ALL1-fused gene from chromosome 4 protein; Short=Protein AF-4; AltName: Full=Protein FEL; AltName: Full=Proto-oncogene AF4;
INTERACTION: P04608:tat (xeno); NbExp=3; IntAct=EBI-2610180, EBI-6164389;
SUBCELLULAR LOCATION: Nucleus (Potential).
DISEASE: Note=A chromosomal aberration involving AFF1 is associated with acute leukemias. Translocation t(4;11)(q21;q23) with MLL/HRX. The result is a rogue activator protein.
SIMILARITY: Belongs to the AF4 family.
SEQUENCE CAUTION: Sequence=AAA36642.1; Type=Frameshift; Positions=897, 905, 1178;
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): AFF1
CDC HuGE Published Literature: AFF1
Positive Disease Associations: Lupus Erythematosus, Systemic , Triglycerides
Related Studies:
  1. Lupus Erythematosus, Systemic
    Yukinori Okada et al. PLoS genetics 2012, A genome-wide association study identified AFF1 as a susceptibility locus for systemic lupus eyrthematosus in Japanese., PLoS genetics. [PubMed 22291604]
  2. Triglycerides
    Sekar Kathiresan et al. BMC medical genetics 2007, A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903299]
    Using a 100K genome-wide scan, we have generated a set of putative associations for common sequence variants and lipid phenotypes. Validation of selected hypotheses in additional samples did not identify any new loci underlying variability in blood lipids. Lack of replication may be due to inadequate statistical power to detect modest quantitative trait locus effects (i.e., <1% of trait variance explained) or reduced genomic coverage of the 100K array. GWAS in FHS using a denser genome-wide genotyping platform and a better-powered replication strategy may identify novel loci underlying blood lipids.
  3. Triglycerides
    Tanya M Teslovich et al. Nature 2010, Biological, clinical and population relevance of 95 loci for blood lipids., Nature. [PubMed 20686565]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: AFF1
Diseases sorted by gene-association score: leukemia, acute lymphoblastic 3* (88), lymphoblastic leukemia (6), acute leukemia (6), leukemia, acute lymphoblastic (3), myeloid/lymphoid or mixed lineage leukemia (2), chronic neutrophilic leukemia (2), neonatal leukemia (2), intellectual disability (1), leukemia, acute myeloid (1)
* = Manually curated disease association

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 37.90 RPKM in Thyroid
Total median expression: 644.91 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 -209.92407-0.516 Picture PostScript Text
3' UTR -1507.015353-0.282 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 P51825
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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     

-  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:0006355 regulation of transcription, DNA-templated

Cellular Component:
GO:0005634 nucleus
GO:0008023 transcription elongation factor complex

-  Descriptions from all associated GenBank mRNAs
  AK296149 - Homo sapiens cDNA FLJ55277 complete cds, highly similar to AF4/FMR2 family member 1.
LF383988 - JP 2014500723-A/191491: Polycomb-Associated Non-Coding RNAs.
BC017432 - Homo sapiens AF4/FMR2 family, member 1, mRNA (cDNA clone IMAGE:4720485), partial cds.
AK300364 - Homo sapiens cDNA FLJ61397 complete cds, highly similar to AF4/FMR2 family member 1.
AK302199 - Homo sapiens cDNA FLJ61458 complete cds, highly similar to AF4/FMR2 family member 1.
L13773 - Human AF-4 mRNA, complete cds.
BC114930 - Homo sapiens AF4/FMR2 family, member 1, mRNA (cDNA clone MGC:134969 IMAGE:40074243), complete cds.
LF213723 - JP 2014500723-A/21226: Polycomb-Associated Non-Coding RNAs.
AK296243 - Homo sapiens cDNA FLJ55278 complete cds, highly similar to AF4/FMR2 family member 1.
L25050 - Human serine/proline-rich protein mRNA, complete cds.
AB385236 - Synthetic construct DNA, clone: pF1KB9478, Homo sapiens AFF1 gene for AF4/FMR2 family member 1, complete cds, without stop codon, in Flexi system.
MA619565 - JP 2018138019-A/191491: Polycomb-Associated Non-Coding RNAs.
MA449300 - JP 2018138019-A/21226: Polycomb-Associated Non-Coding RNAs.
JD190803 - Sequence 171827 from Patent EP1572962.
JD460737 - Sequence 441761 from Patent EP1572962.
JD407270 - Sequence 388294 from Patent EP1572962.
JD211004 - Sequence 192028 from Patent EP1572962.
JD141269 - Sequence 122293 from Patent EP1572962.
LF359127 - JP 2014500723-A/166630: Polycomb-Associated Non-Coding RNAs.
LF359128 - JP 2014500723-A/166631: Polycomb-Associated Non-Coding RNAs.
AF177238 - Homo sapiens patient A1 AF4-MLL fusion protein (AF4-MLL) mRNA, partial cds.
AF177239 - Homo sapiens cell-line MV4-11 AF4-MLL fusion protein (AF4-MLL) mRNA, partial cds.
KT444632 - Homo sapiens AFF1/KMT2A fusion variant 2, mRNA, breakpoint junction region, partial sequence.
AF487906 - Homo sapiens AF4/MLL fusion protein mRNA, partial cds.
AF492831 - Homo sapiens AF4/MLL fusion protein mRNA, partial cds.
MH401087 - Homo sapiens KMT2A/AFF1 fusion protein mRNA, partial cds.
AF024541 - Homo sapiens MLL-AF4 fusion protein mRNA, partial cds.
AF031404 - Homo sapiens MLL-AF4 fusion protein mRNA, partial cds.
AF492832 - Homo sapiens MLL/AF4 fusion protein mRNA, partial cds.
KT444630 - Homo sapiens KMT2A/AFF1 fusion mRNA, breakpoint junction region, partial sequence.
AF487905 - Homo sapiens MLL/AF4 fusion protein mRNA, partial cds.
AF177236 - Homo sapiens patient A1 MLL/AF4 fusion protein (MLL/AF4) mRNA, partial cds.
AF177237 - Homo sapiens cell-line MV4-11 MLL/AF4 fusion protein (MLL/AF4) mRNA, partial cds.
KT444629 - Homo sapiens KMT2A/AFF1 fusion variant 2, mRNA, breakpoint junction region, partial sequence.
KT444628 - Homo sapiens KMT2A/AFF1 fusion variant 1, mRNA, breakpoint junction region, partial sequence.
LF359137 - JP 2014500723-A/166640: Polycomb-Associated Non-Coding RNAs.
LF359140 - JP 2014500723-A/166643: Polycomb-Associated Non-Coding RNAs.
LF359141 - JP 2014500723-A/166644: Polycomb-Associated Non-Coding RNAs.
LF359142 - JP 2014500723-A/166645: Polycomb-Associated Non-Coding RNAs.
LF359143 - JP 2014500723-A/166646: Polycomb-Associated Non-Coding RNAs.
LF359144 - JP 2014500723-A/166647: Polycomb-Associated Non-Coding RNAs.
LF359145 - JP 2014500723-A/166648: Polycomb-Associated Non-Coding RNAs.
LF359147 - JP 2014500723-A/166650: Polycomb-Associated Non-Coding RNAs.
LF359148 - JP 2014500723-A/166651: Polycomb-Associated Non-Coding RNAs.
JD281618 - Sequence 262642 from Patent EP1572962.
JD499476 - Sequence 480500 from Patent EP1572962.
JD449152 - Sequence 430176 from Patent EP1572962.
JD168298 - Sequence 149322 from Patent EP1572962.
JD550776 - Sequence 531800 from Patent EP1572962.
JD345143 - Sequence 326167 from Patent EP1572962.
JD048480 - Sequence 29504 from Patent EP1572962.
JD465370 - Sequence 446394 from Patent EP1572962.
JD496016 - Sequence 477040 from Patent EP1572962.
JD373146 - Sequence 354170 from Patent EP1572962.
JD462056 - Sequence 443080 from Patent EP1572962.
JD247705 - Sequence 228729 from Patent EP1572962.
JD550128 - Sequence 531152 from Patent EP1572962.
JD358426 - Sequence 339450 from Patent EP1572962.
JD303639 - Sequence 284663 from Patent EP1572962.
JD359042 - Sequence 340066 from Patent EP1572962.
JD433643 - Sequence 414667 from Patent EP1572962.
JD351165 - Sequence 332189 from Patent EP1572962.
LF359149 - JP 2014500723-A/166652: Polycomb-Associated Non-Coding RNAs.
JD490792 - Sequence 471816 from Patent EP1572962.
JD482355 - Sequence 463379 from Patent EP1572962.
JD207336 - Sequence 188360 from Patent EP1572962.
JD445292 - Sequence 426316 from Patent EP1572962.
JD164620 - Sequence 145644 from Patent EP1572962.
JD440827 - Sequence 421851 from Patent EP1572962.
JD358086 - Sequence 339110 from Patent EP1572962.
JD155215 - Sequence 136239 from Patent EP1572962.
JD135438 - Sequence 116462 from Patent EP1572962.
JD427043 - Sequence 408067 from Patent EP1572962.
JD545945 - Sequence 526969 from Patent EP1572962.
JD502486 - Sequence 483510 from Patent EP1572962.
JD233356 - Sequence 214380 from Patent EP1572962.
JD232450 - Sequence 213474 from Patent EP1572962.
JD495088 - Sequence 476112 from Patent EP1572962.
JD243802 - Sequence 224826 from Patent EP1572962.
LF359150 - JP 2014500723-A/166653: Polycomb-Associated Non-Coding RNAs.
JD327736 - Sequence 308760 from Patent EP1572962.
JD092902 - Sequence 73926 from Patent EP1572962.
JD299146 - Sequence 280170 from Patent EP1572962.
JD102207 - Sequence 83231 from Patent EP1572962.
JD048303 - Sequence 29327 from Patent EP1572962.
JD263612 - Sequence 244636 from Patent EP1572962.
JD086763 - Sequence 67787 from Patent EP1572962.
LF359151 - JP 2014500723-A/166654: Polycomb-Associated Non-Coding RNAs.
JD285067 - Sequence 266091 from Patent EP1572962.
JD087346 - Sequence 68370 from Patent EP1572962.
LF359152 - JP 2014500723-A/166655: Polycomb-Associated Non-Coding RNAs.
JD116174 - Sequence 97198 from Patent EP1572962.
JD546169 - Sequence 527193 from Patent EP1572962.
JD178579 - Sequence 159603 from Patent EP1572962.
JD092611 - Sequence 73635 from Patent EP1572962.
JD056160 - Sequence 37184 from Patent EP1572962.
JD093755 - Sequence 74779 from Patent EP1572962.
JD053080 - Sequence 34104 from Patent EP1572962.
JD284074 - Sequence 265098 from Patent EP1572962.
JD299130 - Sequence 280154 from Patent EP1572962.
JD503095 - Sequence 484119 from Patent EP1572962.
JD533949 - Sequence 514973 from Patent EP1572962.
JD535365 - Sequence 516389 from Patent EP1572962.
JD399010 - Sequence 380034 from Patent EP1572962.
JD136768 - Sequence 117792 from Patent EP1572962.
JD524244 - Sequence 505268 from Patent EP1572962.
JD385470 - Sequence 366494 from Patent EP1572962.
JD248212 - Sequence 229236 from Patent EP1572962.
JD185698 - Sequence 166722 from Patent EP1572962.
JD142523 - Sequence 123547 from Patent EP1572962.
JD349498 - Sequence 330522 from Patent EP1572962.
LF359154 - JP 2014500723-A/166657: Polycomb-Associated Non-Coding RNAs.
JD242042 - Sequence 223066 from Patent EP1572962.
JD068908 - Sequence 49932 from Patent EP1572962.
JD229931 - Sequence 210955 from Patent EP1572962.
LF359155 - JP 2014500723-A/166658: Polycomb-Associated Non-Coding RNAs.
MA594704 - JP 2018138019-A/166630: Polycomb-Associated Non-Coding RNAs.
MA594705 - JP 2018138019-A/166631: Polycomb-Associated Non-Coding RNAs.
MA594714 - JP 2018138019-A/166640: Polycomb-Associated Non-Coding RNAs.
MA594717 - JP 2018138019-A/166643: Polycomb-Associated Non-Coding RNAs.
MA594718 - JP 2018138019-A/166644: Polycomb-Associated Non-Coding RNAs.
MA594719 - JP 2018138019-A/166645: Polycomb-Associated Non-Coding RNAs.
MA594720 - JP 2018138019-A/166646: Polycomb-Associated Non-Coding RNAs.
MA594721 - JP 2018138019-A/166647: Polycomb-Associated Non-Coding RNAs.
MA594722 - JP 2018138019-A/166648: Polycomb-Associated Non-Coding RNAs.
MA594724 - JP 2018138019-A/166650: Polycomb-Associated Non-Coding RNAs.
MA594725 - JP 2018138019-A/166651: Polycomb-Associated Non-Coding RNAs.
MA594726 - JP 2018138019-A/166652: Polycomb-Associated Non-Coding RNAs.
MA594727 - JP 2018138019-A/166653: Polycomb-Associated Non-Coding RNAs.
MA594728 - JP 2018138019-A/166654: Polycomb-Associated Non-Coding RNAs.
MA594729 - JP 2018138019-A/166655: Polycomb-Associated Non-Coding RNAs.
MA594731 - JP 2018138019-A/166657: Polycomb-Associated Non-Coding RNAs.
MA594732 - JP 2018138019-A/166658: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: AF4, AFF1_HUMAN, FEL, MLLT2, NM_005935, NP_005926, P51825, PBM1
UCSC ID: uc003hqj.4
RefSeq Accession: NM_005935
Protein: P51825 (aka AFF1_HUMAN)
CCDS: CCDS3616.1, CCDS54775.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_005935.2
exon count: 20CDS single in 3' UTR: no RNA size: 9378
ORF size: 3633CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 7359.50frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

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