Human Gene AFF1 (uc011ccx.2) Description and Page Index
  Description: Homo sapiens AF4/FMR2 family, member 1 (AFF1), transcript variant 1, mRNA.
RefSeq Summary (NM_001166693): 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 chr4:87,856,154-87,969,201 Size: 113,048 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr4:87,967,886-87,968,839 Size: 954 Coding Exon Count: 1 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr4:87,856,154-87,969,201)mRNA (may differ from genome)Protein (317 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
MGIPubMedStanford SOURCEUniProtKBWikipedia

-  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 -157.00352-0.446 Picture PostScript Text
3' UTR -87.54362-0.242 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 Q13718
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     

-  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.
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.
L13743 - Human 5' altered transcript of AF-4 mRNA.
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.
MA594705 - JP 2018138019-A/166631: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: AK296149, Q13718, Q13718_HUMAN
UCSC ID: uc011ccx.2
RefSeq Accession: NM_001166693
Protein: Q13718

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: AK296149.1
exon count: 3CDS single in 3' UTR: no RNA size: 1668
ORF size: 954CDS single in intron: no Alignment % ID: 99.94
txCdsPredict score: 1944.00frame 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: 455# 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.