Human Gene SSBP1 (uc031szi.1) Description and Page Index
  Description: Homo sapiens single-stranded DNA binding protein 1, mitochondrial (SSBP1), nuclear gene encoding mitochondrial protein, transcript variant 3, mRNA.
RefSeq Summary (NM_001256512): SSBP1 is a housekeeping gene involved in mitochondrial biogenesis (Tiranti et al., 1995 [PubMed 7789991]). It is also a subunit of a single-stranded DNA (ssDNA)-binding complex involved in the maintenance of genome stability (Huang et al., 2009) [PubMed 19683501].[supplied by OMIM, Feb 2010].
Transcript (Including UTRs)
   Position: hg19 chr7:141,438,121-141,450,288 Size: 12,168 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr7:141,438,967-141,450,154 Size: 11,188 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:141,438,121-141,450,288)mRNA (may differ from genome)Protein (148 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMGIneXtProtOMIM
PubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: SSBP_HUMAN
DESCRIPTION: RecName: Full=Single-stranded DNA-binding protein, mitochondrial; Short=Mt-SSB; Short=MtSSB; AltName: Full=PWP1-interacting protein 17; Flags: Precursor;
FUNCTION: This protein binds preferentially and cooperatively to ss-DNA. Probably involved in mitochondrial DNA replication. Associates with mitochondrial DNA.
SUBUNIT: Homotetramer (By similarity).
INTERACTION: P04618:rev (xeno); NbExp=3; IntAct=EBI-353460, EBI-6164309;
SUBCELLULAR LOCATION: Mitochondrion. Mitochondrion matrix, mitochondrion nucleoid.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Contains 1 SSB domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SSBP1
CDC HuGE Published Literature: SSBP1
Positive Disease Associations: Hemoglobin A, Glycosylated
Related Studies:
  1. Hemoglobin A, Glycosylated
    James B Meigs et al. BMC medical genetics 2007, Genome-wide association with diabetes-related traits in the Framingham Heart Study., BMC medical genetics. [PubMed 17903298]
    Framingham 100K SNP data is a resource for association tests of known and novel genes with diabetes and related traits posted at http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000007 webcite. Framingham 100K data replicate the TCF7L2 association with diabetes.

-  MalaCards Disease Associations
  MalaCards Gene Search: SSBP1
Diseases sorted by gene-association score: autistic disorder (1)

-  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: 58.65 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1182.88 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 -100.30298-0.337 Picture PostScript Text
3' UTR -25.50134-0.190 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
IPR012340 - NA-bd_OB-fold
IPR016027 - NA-bd_OB-fold-like
IPR000424 - Primosome_PriB/ssb
IPR011344 - ssDNA-bd

Pfam Domains:
PF00436 - Single-strand binding protein family

SCOP Domains:
50249 - Nucleic acid-binding proteins

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

1S3O
- X-ray

2DUD
- X-ray MuPIT

3ULL
- X-ray


ModBase Predicted Comparative 3D Structure on Q04837
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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003697 single-stranded DNA binding
GO:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0006260 DNA replication
GO:0007005 mitochondrion organization
GO:0051096 positive regulation of helicase activity
GO:0070584 mitochondrion morphogenesis

Cellular Component:
GO:0005634 nucleus
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0042645 mitochondrial nucleoid
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  BC008402 - Homo sapiens single-stranded DNA binding protein 1, mRNA (cDNA clone IMAGE:4294746), partial cds.
BC093054 - Homo sapiens single-stranded DNA binding protein 1, mRNA (cDNA clone MGC:111135 IMAGE:30722138), complete cds.
AK294393 - Homo sapiens cDNA FLJ51825 complete cds, highly similar to Single-stranded DNA-binding protein, mitochondrial precursor.
AF277319 - Homo sapiens single-stranded DNA-binding protein mRNA, complete cds.
M94556 - Human mitochondrial specific single stranded DNA binding protein mRNA, complete cds.
AK311200 - Homo sapiens cDNA, FLJ18242.
AK313033 - Homo sapiens cDNA, FLJ93504, Homo sapiens single-stranded DNA binding protein 1 (SSBP1), mRNA.
BC000895 - Homo sapiens single-stranded DNA binding protein 1, mRNA (cDNA clone MGC:5185 IMAGE:3464282), complete cds.
DQ896693 - Synthetic construct Homo sapiens clone IMAGE:100011153; FLH196718.01L; RZPDo839H05155D single-stranded DNA binding protein 1 (SSBP1) gene, encodes complete protein.
DQ893371 - Synthetic construct clone IMAGE:100006001; FLH196722.01X; RZPDo839H05156D single-stranded DNA binding protein 1 (SSBP1) gene, encodes complete protein.
KJ892202 - Synthetic construct Homo sapiens clone ccsbBroadEn_01596 SSBP1 gene, encodes complete protein.
JD209668 - Sequence 190692 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03030 - DNA replication
hsa03430 - Mismatch repair
hsa03440 - Homologous recombination

Reactome (by CSHL, EBI, and GO)

Protein Q04837 (Reactome details) participates in the following event(s):

R-HSA-2151201 Transcriptional activation of mitochondrial biogenesis
R-HSA-1592230 Mitochondrial biogenesis
R-HSA-1852241 Organelle biogenesis and maintenance

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001256512, NP_003134, Q04837, SSBP, SSBP_HUMAN, uc010lnp.1
UCSC ID: uc031szi.1
RefSeq Accession: NM_001256512
Protein: Q04837 (aka SSBP_HUMAN)
CCDS: CCDS5866.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001256512.1
exon count: 7CDS single in 3' UTR: no RNA size: 879
ORF size: 447CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1094.00frame shift in genome: no % Coverage: 100.00
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.