Human Gene BANF1 (uc001ogp.3) Description and Page Index
  Description: Homo sapiens barrier to autointegration factor 1 (BANF1), transcript variant 2, mRNA.
RefSeq Summary (NM_001143985): The protein encoded by this gene was first identified by its ability to protect retroviruses from intramolecular integration and therefore promote intermolecular integration into the host cell genome. The protein forms a homodimer which localizes to both the nucleus and cytoplasm and is specifically associated with chromosomes during mitosis. This protein binds to double stranded DNA in a non-specific manner and also binds to LEM-domain containing proteins of the nuclear envelope. This protein is thought to facilitate nuclear reassembly by binding with both DNA and inner nuclear membrane proteins and thereby recruit chromatin to the nuclear periphery. Alternative splicing results in multiple transcript variants encoding the same protein.[provided by RefSeq, Jan 2009].
Transcript (Including UTRs)
   Position: hg19 chr11:65,769,550-65,771,617 Size: 2,068 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr11:65,770,722-65,771,243 Size: 522 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:65,769,550-65,771,617)mRNA (may differ from genome)Protein (89 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: BAF_HUMAN
DESCRIPTION: RecName: Full=Barrier-to-autointegration factor; AltName: Full=Breakpoint cluster region protein 1;
FUNCTION: Plays fundamental roles in nuclear assembly, chromatin organization, gene expression and gonad development. May potently compress chromatin structure and be involved in membrane recruitment and chromatin decondensation during nuclear assembly. Contains 2 non-specific dsDNA-binding sites which may promote DNA cross-bridging. Exploited by retroviruses for inhibiting self- destructing autointegration of retroviral DNA, thereby promoting integration of viral DNA into the host chromosome. EMD and BAF are cooperative cofactors of HIV-1 infection. Association of EMD with the viral DNA requires the presence of BAF and viral integrase. The association of viral DNA with chromatin requires the presence of BAF and EMD.
SUBUNIT: Homodimer. Heterodimerizes with BAFL. Interacts with ANKLE2/LEM4, leading to decreased phosphorylation by VRK1 and promoting dephosphorylation by protein phosphatase 2A (PP2A). Binds non-specifically to double-stranded DNA, and is found as a hexamer or dodecamer upon DNA binding. Binds to LEM domain- containing nuclear proteins such as LEMD3/MAN1, TMPO/LAP2 and EMD (emerin). Interacts with CRX and LMNA (lamin-A). Binds linker histone H1.1 and core histones H3 with in vitro affinities of 500- 900 and 100-200 nM. Interacts with HIV-1 pre-integration complex in cytoplasm by binding to viral matrix protein and Gag polyprotein.
SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Chromosome. Note=Significantly enriched at the nuclear inner membrane, diffusely throughout the nucleus during interphase and concentrated at the chromosomes during the M-phase. May be included in HIV-1 virions via its interaction with viral GAG polyprotein. The phosphorylated form (by VRK1) shows a cytoplasmic localization.
TISSUE SPECIFICITY: Widely expressed. Expressed in colon, brain, heart, kidney, liver, lung, ovary, pancreas, placenta, prostate, skeletal muscle, small intestine, spleen and testis. Not detected in thymus and peripheral blood leukocytes.
DOMAIN: Has a helix-hairpin-helix (HhH) structural motif conserved among proteins that bind non-specifically to DNA.
DOMAIN: LEM domain proteins bind centrally on the BAF dimer, whereas DNA binds to the left and right sides.
PTM: Ser-4 is the major site of phosphorylation as compared to Thr-2 and Thr-3. Phosphorylation on Thr-2; Thr-3 and Ser-4 disrupts its ability to bind DNA and reduces its ability to bind LEM domain-containing proteins. Non phosphorylated BAF seems to enhance binding between EMD and LMNA. Dephosphorylated by protein phosphatase 2A (PP2A) following interaction with ANKLE2/LEM4 during mitotic exit, leading to mitotic nuclear envelope reassembly.
DISEASE: Defects in BANF1 are the cause of Nestor-Guillermo progeria syndrome (NGPS) [MIM:614008]. NGPS is an atypical progeroid syndrome characterized by normal development in the first years of life, later followed by the emergence of generalized lipoatrophy, severe osteoporosis, and marked osteolysis. The atrophic facial subcutaneous fat pad and the marked osteolysis of the maxilla and mandible result in a typical pseudosenile facial appearance with micrognatia, prominent subcutaneous venous patterning, a convex nasal ridge, and proptosis. Cognitive development is completely normal. Patients do not have cardiovascular dysfunction, atherosclerosis, or metabolic anomalies.
SIMILARITY: Belongs to the BAF family.
SEQUENCE CAUTION: Sequence=AAC08964.1; Type=Frameshift; Positions=87;

-  MalaCards Disease Associations
  MalaCards Gene Search: BANF1
Diseases sorted by gene-association score: nestor-guillermo progeria syndrome* (1680), hiv-1 (11), anthracosis (11), vaccinia (9), mandibuloacral dysplasia (9), emery-dreifuss muscular dystrophy (8), middle lobe syndrome (8), lymphoproliferative syndrome 2 (7), chromosome 2p16.1-p15 deletion syndrome (6), coffin-siris syndrome 1 (6), borjeson-forssman-lehmann syndrome (4)
* = 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: 86.70 RPKM in Artery - Aorta
Total median expression: 2931.01 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 -150.21451-0.333 Picture PostScript Text
3' UTR -91.30374-0.244 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

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1CI4
- X-ray MuPIT

1QCK
- NMR MuPIT

2BZF
- X-ray MuPIT
To conserve bandwidth, only the images from the first 3 structures are shown.
2EZX - NMR MuPIT 2EZY - NMR MuPIT 2EZZ - NMR MuPIT
2ODG - NMR MuPIT


ModBase Predicted Comparative 3D Structure on O75531
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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
 Gene Details Gene DetailsGene Details 
 Gene Sorter Gene SorterGene Sorter 
 RGDEnsemblFlyBaseWormBase 
 Protein SequenceProtein SequenceProtein SequenceProtein Sequence 
 AlignmentAlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0008022 protein C-terminus binding
GO:0019899 enzyme binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0047485 protein N-terminus binding
GO:0097726 LEM domain binding

Biological Process:
GO:0007084 mitotic nuclear envelope reassembly
GO:0009615 response to virus
GO:0016032 viral process
GO:0045071 negative regulation of viral genome replication
GO:0051169 nuclear transport
GO:0075713 establishment of integrated proviral latency

Cellular Component:
GO:0005634 nucleus
GO:0005635 nuclear envelope
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  JD385347 - Sequence 366371 from Patent EP1572962.
AF068235 - Homo sapiens barrier-to-autointegration factor mRNA, complete cds.
JD537744 - Sequence 518768 from Patent EP1572962.
JD483200 - Sequence 464224 from Patent EP1572962.
JD186213 - Sequence 167237 from Patent EP1572962.
JD540874 - Sequence 521898 from Patent EP1572962.
BC107702 - Homo sapiens barrier to autointegration factor 1, mRNA (cDNA clone MGC:111161 IMAGE:6495215), complete cds.
AF044773 - Homo sapiens breakpoint cluster region protein 1 (BCRG1) mRNA, complete cds.
JD557672 - Sequence 538696 from Patent EP1572962.
BC005942 - Homo sapiens barrier to autointegration factor 1, mRNA (cDNA clone MGC:14564 IMAGE:4074168), complete cds.
AK311961 - Homo sapiens cDNA, FLJ92232, highly similar to Homo sapiens barrier to autointegration factor 1 (BANF1), mRNA.
BC008705 - Homo sapiens cDNA clone IMAGE:3027737, containing frame-shift errors.
CR542140 - Homo sapiens full open reading frame cDNA clone RZPDo834H0223D for gene BANF1, barrier to autointegration factor 1; complete cds, without stopcodon.
KJ892628 - Synthetic construct Homo sapiens clone ccsbBroadEn_02022 BANF1 gene, encodes complete protein.
AF070447 - Homo sapiens barrier-to-autointegration factor (BAF) mRNA, complete cds.
JD160078 - Sequence 141102 from Patent EP1572962.
JD465161 - Sequence 446185 from Patent EP1572962.
JD383587 - Sequence 364611 from Patent EP1572962.
JD382711 - Sequence 363735 from Patent EP1572962.
JD433527 - Sequence 414551 from Patent EP1572962.
JD297741 - Sequence 278765 from Patent EP1572962.
JD142234 - Sequence 123258 from Patent EP1572962.
JD385971 - Sequence 366995 from Patent EP1572962.
JD565514 - Sequence 546538 from Patent EP1572962.
JD275005 - Sequence 256029 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O75531 (Reactome details) participates in the following event(s):

R-HSA-8951690 Formation of RTC with integration competent viral DNA:BANF1:HMGA1:PSIP1
R-HSA-164845 Suicidal integration leading to inverted circle formation
R-HSA-175108 Target DNA binding
R-HSA-175117 1-LTR circle formation
R-HSA-175174 Association of Ku heterodimer with viral DNA ends
R-HSA-175250 Suicidal integration leading to smaller circles of viral DNA
R-HSA-162590 Import of PIC to the Host Nucleus
R-HSA-164514 Integrase binds viral DNA ends
R-HSA-173115 Formation of Pre-Integration Complex (PIC)
R-HSA-180622 Vpr binds nucleoporins
R-HSA-180627 Interaction of Vpr with importin alpha
R-HSA-180630 Association of APOBEC3G with Gag
R-HSA-164522 Terminal (3' end) cleavage of viral DNA
R-HSA-2995376 BANF1 binds chromatin, EMD/TMPO/LEMD3/LEMD2 and lamins
R-HSA-2995388 PP2A dephosphorylates BANF1
R-HSA-2993898 VRK1/VRK2 phosphorylate BANF1
R-HSA-162592 Integration of provirus
R-HSA-177539 Autointegration results in viral DNA circles
R-HSA-175567 Integration of viral DNA into host genomic DNA
R-HSA-164843 2-LTR circle formation
R-HSA-180910 Vpr-mediated nuclear import of PICs
R-HSA-180689 APOBEC3G mediated resistance to HIV-1 infection
R-HSA-2995383 Initiation of Nuclear Envelope Reformation
R-HSA-162594 Early Phase of HIV Life Cycle
R-HSA-2993913 Clearance of Nuclear Envelope Membranes from Chromatin
R-HSA-176033 Interactions of Vpr with host cellular proteins
R-HSA-162909 Host Interactions of HIV factors
R-HSA-2995410 Nuclear Envelope Reassembly
R-HSA-162587 HIV Life Cycle
R-HSA-2980766 Nuclear Envelope Breakdown
R-HSA-162906 HIV Infection
R-HSA-68882 Mitotic Anaphase
R-HSA-68875 Mitotic Prophase
R-HSA-5663205 Infectious disease
R-HSA-2555396 Mitotic Metaphase and Anaphase
R-HSA-68886 M Phase
R-HSA-1643685 Disease
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-1640170 Cell Cycle

-  Other Names for This Gene
  Alternate Gene Symbols: BAF, BAF_HUMAN, BCRG1, NM_001143985, NP_003851, O60558, O75531, Q6FGG7
UCSC ID: uc001ogp.3
RefSeq Accession: NM_001143985
Protein: O75531 (aka BAF_HUMAN)
CCDS: CCDS8125.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001143985.1
exon count: 3CDS single in 3' UTR: no RNA size: 1122
ORF size: 270CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 725.00frame shift in genome: no % Coverage: 97.59
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.