Human Gene RSF1 (uc001oyn.3) Description and Page Index
  Description: Homo sapiens remodeling and spacing factor 1 (RSF1), mRNA.
RefSeq Summary (NM_016578): This gene encodes a nuclear protein that interacts with hepatitis B virus X protein (HBX) and facilitates transcription of hepatitis B virus genes by the HBX transcription activator, suggesting a role for this interaction in the virus life cycle. This protein also interacts with SNF2H protein to form the RSF chromatin-remodeling complex, where the SNF2H subunit functions as the nucleosome-dependent ATPase, and this protein as the histone chaperone. [provided by RefSeq, Sep 2011]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: AF380176.1, SRR1660803.138265.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr11:77,377,274-77,531,880 Size: 154,607 Total Exon Count: 16 Strand: -
Coding Region
   Position: hg19 chr11:77,377,962-77,531,760 Size: 153,799 Coding Exon Count: 16 

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 (chr11:77,377,274-77,531,880)mRNA (may differ from genome)Protein (1441 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: RSF1_HUMAN
DESCRIPTION: RecName: Full=Remodeling and spacing factor 1; Short=Rsf-1; AltName: Full=HBV pX-associated protein 8; AltName: Full=Hepatitis B virus X-associated protein; AltName: Full=p325 subunit of RSF chromatin-remodeling complex;
FUNCTION: Required for assembly of regular nucleosome arrays by the RSF chromatin-remodeling complex. Facilitates transcription of hepatitis B virus (HBV) genes by the pX transcription activator. In case of infection by HBV, together with pX, it represses TNF- alpha induced NF-kappa-B transcription activation. Represses transcription when artificially recruited to chromatin by fusion to a heterogeneous DNA binding domain.
SUBUNIT: Interacts with SMARCA5/SNF2H to form the RSF complex. Also binds the HBV pX/HBx protein, which is required to activate transcription of the viral genome.
INTERACTION: O60264:SMARCA5; NbExp=5; IntAct=EBI-926768, EBI-352588;
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Ubiquitously expressed.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Contains 1 DDT domain.
SIMILARITY: Contains 1 PHD-type zinc finger.
SEQUENCE CAUTION: Sequence=AAG43114.1; Type=Frameshift; Positions=549; Sequence=AAH46124.2; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=AAK57515.1; Type=Erroneous initiation; Sequence=BAA91591.1; Type=Erroneous initiation;
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org//Genes/RSF1ID44107ch11q13.html";

-  MalaCards Disease Associations
  MalaCards Gene Search: RSF1
Diseases sorted by gene-association score: hepatitis b (42), hepatitis (11), malignant ovarian surface epithelial-stromal neoplasm (1), ovary epithelial cancer (1)

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 6.33 RPKM in Artery - Tibial
Total median expression: 207.08 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -24.71120-0.206 Picture PostScript Text
3' UTR -144.42688-0.210 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
IPR019786 - Zinc_finger_PHD-type_CS
IPR011011 - Znf_FYVE_PHD
IPR001965 - Znf_PHD
IPR019787 - Znf_PHD-finger
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF00628 - PHD-finger
PF15612 - WSTF, HB1, Itc1p, MBD9 motif 1

SCOP Domains:
57903 - FYVE/PHD zinc finger

ModBase Predicted Comparative 3D Structure on Q96T23
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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 orthologGenome BrowserGenome BrowserNo orthologNo ortholog
Gene Details  Gene Details  
Gene Sorter  Gene Sorter  
  EnsemblFlyBase  
  Protein SequenceProtein Sequence  
  AlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0042393 histone binding
GO:0046872 metal ion binding
GO:0016887 ATPase activity

Biological Process:
GO:0006325 chromatin organization
GO:0006334 nucleosome assembly
GO:0006338 chromatin remodeling
GO:0006351 transcription, DNA-templated
GO:0006352 DNA-templated transcription, initiation
GO:0006355 regulation of transcription, DNA-templated
GO:0016584 nucleosome positioning
GO:0034080 CENP-A containing nucleosome assembly
GO:0043392 negative regulation of DNA binding
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045893 positive regulation of transcription, DNA-templated
GO:0050434 positive regulation of viral transcription

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0031213 RSF complex


-  Descriptions from all associated GenBank mRNAs
  AF380176 - Homo sapiens HBV pX associated protein 8 large isoform (XAP8alpha) mRNA, complete cds.
BC153210 - Synthetic construct Homo sapiens clone IMAGE:100016320, MGC:184229 remodeling and spacing factor 1 (RSF1) mRNA, encodes complete protein.
BC148326 - Synthetic construct Homo sapiens clone IMAGE:100015312, MGC:182982 remodeling and spacing factor 1 (RSF1) mRNA, encodes complete protein.
AB527448 - Synthetic construct DNA, clone: pF1KB7334, Homo sapiens RSF1 gene for remodeling and spacing factor 1, without stop codon, in Flexi system.
BC015360 - Homo sapiens remodeling and spacing factor 1, mRNA (cDNA clone IMAGE:3854916), partial cds.
AF227948 - Homo sapiens HBV pX associated protein-8 mRNA, complete cds.
JD288516 - Sequence 269540 from Patent EP1572962.
JD090230 - Sequence 71254 from Patent EP1572962.
BC000774 - Homo sapiens hepatitis B virus x associated protein, mRNA (cDNA clone IMAGE:3508250), partial cds.
AK001268 - Homo sapiens cDNA FLJ10406 fis, clone NT2RM4000515.
BC046124 - Homo sapiens remodeling and spacing factor 1, mRNA (cDNA clone IMAGE:4384806), partial cds.
AF059317 - Homo sapiens My001 protein mRNA, complete cds.
BC046347 - Homo sapiens, clone IMAGE:4388477, mRNA.
JD359677 - Sequence 340701 from Patent EP1572962.
AK098130 - Homo sapiens cDNA FLJ40811 fis, clone TRACH2009934.

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

Protein Q96T23 (Reactome details) participates in the following event(s):

R-HSA-606279 Deposition of new CENPA-containing nucleosomes at the centromere
R-HSA-774815 Nucleosome assembly
R-HSA-73886 Chromosome Maintenance
R-HSA-1640170 Cell Cycle

-  Other Names for This Gene
  Alternate Gene Symbols: HBXAP, NM_016578, NP_057662, Q86X86, Q96T23, Q9H3L8, Q9NVZ8, Q9NYU0, RSF1_HUMAN, XAP8
UCSC ID: uc001oyn.3
RefSeq Accession: NM_016578
Protein: Q96T23 (aka RSF1_HUMAN)
CCDS: CCDS8253.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_016578.3
exon count: 16CDS single in 3' UTR: no RNA size: 5138
ORF size: 4326CDS single in intron: no Alignment % ID: 99.98
txCdsPredict score: 8797.00frame shift in genome: no % Coverage: 99.92
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
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-  Methods, Credits, and Use Restrictions
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