Human Gene AFF3 (ENST00000672756.2_10) from GENCODE V47lift37
  Description: AF4/FMR2 family member 3, transcript variant 3 (from RefSeq NM_001386135.1)
Gencode Transcript: ENST00000672756.2_10
Gencode Gene: ENSG00000144218.21_18
Transcript (Including UTRs)
   Position: hg19 chr2:100,161,881-100,759,052 Size: 597,172 Total Exon Count: 25 Strand: -
Coding Region
   Position: hg19 chr2:100,167,936-100,720,916 Size: 552,981 Coding Exon Count: 22 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:100,161,881-100,759,052)mRNA (may differ from genome)Protein (1226 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblExonPrimerGeneCardsHGNC
MalacardsMGIPubMedReactomeUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: AFF3_HUMAN
DESCRIPTION: RecName: Full=AF4/FMR2 family member 3; AltName: Full=Lymphoid nuclear protein related to AF4; Short=Protein LAF-4;
FUNCTION: Putative transcription activator that may function in lymphoid development and oncogenesis. Binds, in vitro, to double- stranded DNA.
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Preferentially expressed in lymphoid tissues, highest levels being found in the thymus.
SIMILARITY: Belongs to the AF4 family.
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/LAF4ID315.html";

-  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: AFF3
Diseases sorted by gene-association score: fibular aplasia (18)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -103.20334-0.309 Picture PostScript Text
3' UTR -1652.196055-0.273 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 N-terminal region
PF18875 - AF4 interaction motif
PF18876 - AF-4 proto-oncoprotein C-terminal region

ModBase Predicted Comparative 3D Structure on P51826
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 DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003690 double-stranded DNA binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0034612 response to tumor necrosis factor
GO:0035116 embryonic hindlimb morphogenesis

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005829 cytosol
GO:0016604 nuclear body


-  Descriptions from all associated GenBank mRNAs
  U34360 - Human lymphoid nuclear protein (LAF-4) mRNA, complete cds.
BC136579 - Homo sapiens AF4/FMR2 family, member 3, mRNA (cDNA clone MGC:168192 IMAGE:9020569), complete cds.
BC144266 - Homo sapiens AF4/FMR2 family, member 3, mRNA (cDNA clone MGC:177803 IMAGE:9052786), complete cds.
AK290468 - Homo sapiens cDNA FLJ77059 partial cds, highly similar to Homo sapiens AF4/FMR2 family, member 3 (AFF3), transcript variant 1, mRNA.
AK297407 - Homo sapiens cDNA FLJ55581 partial cds, highly similar to AF4/FMR2 family member 3.
AK092327 - Homo sapiens cDNA FLJ35008 fis, clone OCBBF2012191, highly similar to LAF-4 PROTEIN.
AX747484 - Sequence 1009 from Patent EP1308459.
BC036895 - Homo sapiens AF4/FMR2 family, member 3, mRNA (cDNA clone IMAGE:5498133), partial cds.
AK308645 - Homo sapiens cDNA, FLJ98686.
BC021283 - Homo sapiens cDNA clone IMAGE:5017375, partial cds.
AK055117 - Homo sapiens cDNA FLJ30555 fis, clone BRAWH2003818.
AK091320 - Homo sapiens cDNA FLJ34001 fis, clone FCBBF1000139.
JD233604 - Sequence 214628 from Patent EP1572962.
JD346290 - Sequence 327314 from Patent EP1572962.
JD333711 - Sequence 314735 from Patent EP1572962.
JD114670 - Sequence 95694 from Patent EP1572962.
JD417477 - Sequence 398501 from Patent EP1572962.
JD243106 - Sequence 224130 from Patent EP1572962.
JD348981 - Sequence 330005 from Patent EP1572962.
JD393575 - Sequence 374599 from Patent EP1572962.
JD280510 - Sequence 261534 from Patent EP1572962.
JD167199 - Sequence 148223 from Patent EP1572962.
JD081205 - Sequence 62229 from Patent EP1572962.
JD304104 - Sequence 285128 from Patent EP1572962.
JD255785 - Sequence 236809 from Patent EP1572962.
JD071853 - Sequence 52877 from Patent EP1572962.
JD397185 - Sequence 378209 from Patent EP1572962.
JD069831 - Sequence 50855 from Patent EP1572962.
JD542021 - Sequence 523045 from Patent EP1572962.
JD234838 - Sequence 215862 from Patent EP1572962.
JD235765 - Sequence 216789 from Patent EP1572962.
JD557626 - Sequence 538650 from Patent EP1572962.
JD211661 - Sequence 192685 from Patent EP1572962.
JD076647 - Sequence 57671 from Patent EP1572962.
JD347773 - Sequence 328797 from Patent EP1572962.
JD312558 - Sequence 293582 from Patent EP1572962.
JD415067 - Sequence 396091 from Patent EP1572962.
JD099500 - Sequence 80524 from Patent EP1572962.
JD516466 - Sequence 497490 from Patent EP1572962.
JD239822 - Sequence 220846 from Patent EP1572962.
JD078981 - Sequence 60005 from Patent EP1572962.
JD325190 - Sequence 306214 from Patent EP1572962.
JD242791 - Sequence 223815 from Patent EP1572962.
JD238965 - Sequence 219989 from Patent EP1572962.
JD345731 - Sequence 326755 from Patent EP1572962.
JD255988 - Sequence 237012 from Patent EP1572962.
JD413833 - Sequence 394857 from Patent EP1572962.
JD463304 - Sequence 444328 from Patent EP1572962.
JD413832 - Sequence 394856 from Patent EP1572962.
JD463303 - Sequence 444327 from Patent EP1572962.
JD213396 - Sequence 194420 from Patent EP1572962.
JD407681 - Sequence 388705 from Patent EP1572962.
JD152361 - Sequence 133385 from Patent EP1572962.
JD399338 - Sequence 380362 from Patent EP1572962.
JD258837 - Sequence 239861 from Patent EP1572962.
JD322129 - Sequence 303153 from Patent EP1572962.
JD353114 - Sequence 334138 from Patent EP1572962.
JD213395 - Sequence 194419 from Patent EP1572962.
JD463302 - Sequence 444326 from Patent EP1572962.
JD213393 - Sequence 194417 from Patent EP1572962.
JD100290 - Sequence 81314 from Patent EP1572962.
JD152359 - Sequence 133383 from Patent EP1572962.
JD353112 - Sequence 334136 from Patent EP1572962.
JD564526 - Sequence 545550 from Patent EP1572962.
JD082683 - Sequence 63707 from Patent EP1572962.
JD285609 - Sequence 266633 from Patent EP1572962.
JD182358 - Sequence 163382 from Patent EP1572962.
JD473379 - Sequence 454403 from Patent EP1572962.
JD512004 - Sequence 493028 from Patent EP1572962.
JD232574 - Sequence 213598 from Patent EP1572962.
JD453158 - Sequence 434182 from Patent EP1572962.
JD354672 - Sequence 335696 from Patent EP1572962.
JD353939 - Sequence 334963 from Patent EP1572962.
JD508109 - Sequence 489133 from Patent EP1572962.
JD486492 - Sequence 467516 from Patent EP1572962.
JD410765 - Sequence 391789 from Patent EP1572962.
JD407063 - Sequence 388087 from Patent EP1572962.
JD552714 - Sequence 533738 from Patent EP1572962.
JD080702 - Sequence 61726 from Patent EP1572962.
JD174510 - Sequence 155534 from Patent EP1572962.
JD430796 - Sequence 411820 from Patent EP1572962.
JD360253 - Sequence 341277 from Patent EP1572962.
JD047134 - Sequence 28158 from Patent EP1572962.
AB209634 - Homo sapiens mRNA for AF4 homolog protein.
JD218159 - Sequence 199183 from Patent EP1572962.
JD135138 - Sequence 116162 from Patent EP1572962.
DL491771 - Novel nucleic acids.

-  Other Names for This Gene
  Alternate Gene Symbols: AFF3 , AFF3_HUMAN, B7ZM46, B9EGL9, D3DVI6, ENST00000672756.1, LAF4, NM_001386135, P51826, Q53RD6, Q53S47, Q53SI6, Q53TB9, Q59F27, Q8IWJ5, uc329wsp.1, uc329wsp.2
UCSC ID: ENST00000672756.2_10
RefSeq Accession: NM_001386135.1
Protein: P51826 (aka AFF3_HUMAN)

-  Gene Model Information
  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.