Human Gene AFDN (uc003qwf.3)
  Description: Homo sapiens myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AFDN), transcript variant 1, mRNA.
RefSeq Summary (NM_001207008): This gene encodes a multi-domain protein involved in signaling and organization of cell junctions during embryogenesis. It has also been identified as the fusion partner of acute lymphoblastic leukemia (ALL-1) gene, involved in acute myeloid leukemias with t(6;11)(q27;q23) translocation. Alternatively spliced transcript variants encoding different isoforms have been described for this gene, however, not all have been fully characterized.[provided by RefSeq, May 2011].
Transcript (Including UTRs)
   Position: hg19 chr6:168,281,040-168,312,844 Size: 31,805 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr6:168,289,898-168,312,205 Size: 22,308 Coding Exon Count: 8 

Page IndexSequence and LinksPrimersMalaCardsGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:168,281,040-168,312,844)mRNA (may differ from genome)Protein (375 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGeneCardsH-INVLynx
MalacardsMGIPubMedUniProtKBWikipedia

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: AFDN
Diseases sorted by gene-association score: central nervous system leukemia (16), cleft lip/palate-ectodermal dysplasia syndrome (7), acute monocytic leukemia (7), acrodermatitis chronica atrophicans (7), myeloid/lymphoid or mixed lineage leukemia (6), leukemia, acute myeloid (1)

+  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: 29.20 RPKM in Esophagus - Mucosa
Total median expression: 575.37 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 -30.00161-0.186 Picture PostScript Text
3' UTR -138.86639-0.217 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
IPR000253 - FHA_dom
IPR000159 - Ras-assoc
IPR008984 - SMAD_FHA_domain

Pfam Domains:
PF00498 - FHA domain
PF00788 - Ras association (RalGDS/AF-6) domain

SCOP Domains:
49879 - SMAD/FHA domain

ModBase Predicted Comparative 3D Structure on Q96C95
FrontTopSide
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
  Biological Process:
GO:0007165 signal transduction

Cellular Component:
GO:0005911 cell-cell junction


-  Descriptions from all associated GenBank mRNAs
  LF210696 - JP 2014500723-A/18199: Polycomb-Associated Non-Coding RNAs.
BC156048 - Synthetic construct Homo sapiens clone IMAGE:100062353, MGC:190478 myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (MLLT4) mRNA, encodes complete protein.
BC156934 - Synthetic construct Homo sapiens clone IMAGE:100063579, MGC:190804 myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (MLLT4) mRNA, encodes complete protein.
U02478 - Human AF-6 mRNA, complete cds.
KT258903 - Homo sapiens l-afadin mRNA, complete cds.
AB209420 - Homo sapiens mRNA for Afadin variant protein.
AB621809 - Homo sapiens MLLT4 mRNA for afadin, complete cds, clone: HP06858-RBd05D03.
BC014505 - Homo sapiens myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4, mRNA (cDNA clone IMAGE:4861456), partial cds.
AL161973 - Homo sapiens mRNA; cDNA DKFZp761K2213 (from clone DKFZp761K2213); partial cds.
MA446273 - JP 2018138019-A/18199: Polycomb-Associated Non-Coding RNAs.
LF340327 - JP 2014500723-A/147830: Polycomb-Associated Non-Coding RNAs.
LF340328 - JP 2014500723-A/147831: Polycomb-Associated Non-Coding RNAs.
MA575904 - JP 2018138019-A/147830: Polycomb-Associated Non-Coding RNAs.
MA575905 - JP 2018138019-A/147831: Polycomb-Associated Non-Coding RNAs.
LF340333 - JP 2014500723-A/147836: Polycomb-Associated Non-Coding RNAs.
LF340335 - JP 2014500723-A/147838: Polycomb-Associated Non-Coding RNAs.
DQ578645 - Homo sapiens piRNA piR-46757, complete sequence.
LF340336 - JP 2014500723-A/147839: Polycomb-Associated Non-Coding RNAs.
LF340337 - JP 2014500723-A/147840: Polycomb-Associated Non-Coding RNAs.
LF340339 - JP 2014500723-A/147842: Polycomb-Associated Non-Coding RNAs.
LF340341 - JP 2014500723-A/147844: Polycomb-Associated Non-Coding RNAs.
LF340342 - JP 2014500723-A/147845: Polycomb-Associated Non-Coding RNAs.
MA575910 - JP 2018138019-A/147836: Polycomb-Associated Non-Coding RNAs.
MA575912 - JP 2018138019-A/147838: Polycomb-Associated Non-Coding RNAs.
MA575913 - JP 2018138019-A/147839: Polycomb-Associated Non-Coding RNAs.
MA575914 - JP 2018138019-A/147840: Polycomb-Associated Non-Coding RNAs.
MA575916 - JP 2018138019-A/147842: Polycomb-Associated Non-Coding RNAs.
MA575918 - JP 2018138019-A/147844: Polycomb-Associated Non-Coding RNAs.
MA575919 - JP 2018138019-A/147845: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04520 - Adherens junction
hsa04530 - Tight junction
hsa04670 - Leukocyte transendothelial migration

-  Other Names for This Gene
  Alternate Gene Symbols: BC014505, MLLT4, Q96C95, Q96C95_HUMAN, RP3-470B24.4-005
UCSC ID: uc003qwf.3
RefSeq Accession: NM_001207008
Protein: Q96C95

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: BC014505.1
exon count: 9CDS single in 3' UTR: no RNA size: 1832
ORF size: 1128CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2401.50frame shift in genome: no % Coverage: 98.64
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: 675# 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.