Human Gene BANF2 (uc002wpz.2)
  Description: Homo sapiens barrier to autointegration factor 2 (BANF2), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr20:17,680,593-17,716,517 Size: 35,925 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr20:17,705,671-17,716,456 Size: 10,786 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:17,680,593-17,716,517)mRNA (may differ from genome)Protein (90 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtPubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: BAFL_HUMAN
DESCRIPTION: RecName: Full=Barrier-to-autointegration factor-like protein; Short=BAF-L; AltName: Full=Barrier-to-autointegration factor 2;
FUNCTION: May play a role in BANF1 regulation and influence tissue-specific roles of BANF1.
SUBUNIT: Homodimer. Heterodimerizes with BANF1.
SUBCELLULAR LOCATION: Nucleus. Cytoplasm.
TISSUE SPECIFICITY: Expressed strongly in testis and pancreas. Also detected in brain, colon, liver, lung, ovary, placenta, prostate, small intestine, spleen and thymus. Not detected in heart, kidney and skeletal muscle.
SIMILARITY: Belongs to the BAF family.
CAUTION: In contrast to BANF1, it does not seems to bind DNA.

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): BANF2
CDC HuGE Published Literature: BANF2
Positive Disease Associations: Magnesium , Tunica Media
Related Studies:
  1. Magnesium
    , , . [PubMed 0]
  2. Tunica Media
    , , . [PubMed 0]

-  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.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 40.23 RPKM in Testis
Total median expression: 40.81 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 -80.80274-0.295 Picture PostScript Text
3' UTR -9.3061-0.152 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
IPR004122 - BAF_prot

Pfam Domains:
PF02961 - Barrier to autointegration factor

SCOP Domains:
47798 - Barrier-to-autointegration factor, BAF

ModBase Predicted Comparative 3D Structure on Q9H503
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
  Molecular Function:
GO:0003677 DNA binding

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  BC054871 - Homo sapiens barrier to autointegration factor 2, mRNA (cDNA clone MGC:62093 IMAGE:6592641), complete cds.
HM005625 - Homo sapiens clone HTL-S-212a testis secretory sperm-binding protein Li 212a mRNA, complete cds.
BC062735 - Homo sapiens barrier to autointegration factor 2, mRNA (cDNA clone MGC:72082 IMAGE:6591888), complete cds.
JD170051 - Sequence 151075 from Patent EP1572962.
JD221486 - Sequence 202510 from Patent EP1572962.
JD360683 - Sequence 341707 from Patent EP1572962.
JD200132 - Sequence 181156 from Patent EP1572962.
JD335781 - Sequence 316805 from Patent EP1572962.
JD133976 - Sequence 115000 from Patent EP1572962.
JD064758 - Sequence 45782 from Patent EP1572962.
KJ900204 - Synthetic construct Homo sapiens clone ccsbBroadEn_09598 BANF2 gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: BAFL, BAFL_HUMAN, C20orf179, D3DW25, NM_178477, NP_848572, Q7Z4M6, Q9H503
UCSC ID: uc002wpz.2
RefSeq Accession: NM_178477
Protein: Q9H503 (aka BAFL_HUMAN)
CCDS: CCDS13129.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_178477.4
exon count: 4CDS single in 3' UTR: no RNA size: 629
ORF size: 273CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 593.00frame shift in genome: no % Coverage: 96.66
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.