Human Gene SSBP3 (ENST00000610401.6_7) from GENCODE V45lift37
  Description: Homo sapiens single stranded DNA binding protein 3 (SSBP3), transcript variant 1, mRNA. (from RefSeq NM_145716)
Gencode Transcript: ENST00000610401.6_7
Gencode Gene: ENSG00000157216.17_13
Transcript (Including UTRs)
   Position: hg19 chr1:54,691,105-54,872,067 Size: 180,963 Total Exon Count: 18 Strand: -
Coding Region
   Position: hg19 chr1:54,692,804-54,871,681 Size: 178,878 Coding Exon Count: 18 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesMicroarray ExpressionRNA StructureProtein StructureGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2024-04-24 11:59:55

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:54,691,105-54,872,067)mRNA (may differ from genome)Protein (388 aa)
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-  Comments and Description Text from UniProtKB
  ID: SSBP3_HUMAN
DESCRIPTION: RecName: Full=Single-stranded DNA-binding protein 3; AltName: Full=Sequence-specific single-stranded-DNA-binding protein;
FUNCTION: May be involved in transcription regulation of the alpha 2(I) collagen gene where it binds to the single-stranded polypyrimidine sequences in the promoter region.
INTERACTION: Q9BWW4; P51451: BLK; NbExp=3; IntAct=EBI-2902395, EBI-2105445; Q9BWW4; O60941-5: DTNB; NbExp=3; IntAct=EBI-2902395, EBI-11984733; Q9BWW4; Q01844: EWSR1; NbExp=3; IntAct=EBI-2902395, EBI-739737; Q9BWW4; Q9UBH0: IL36RN; NbExp=8; IntAct=EBI-2902395, EBI-465156; Q9BWW4; Q86U70: LDB1; NbExp=4; IntAct=EBI-2902395, EBI-677177; Q9BWW4; Q86U70-2: LDB1; NbExp=5; IntAct=EBI-2902395, EBI-11979761; Q9BWW4; O43679: LDB2; NbExp=4; IntAct=EBI-2902395, EBI-2865580; Q9BWW4; Q9NPJ8: NXT2; NbExp=3; IntAct=EBI-2902395, EBI-752122; Q9BWW4; Q9NPJ8-3: NXT2; NbExp=3; IntAct=EBI-2902395, EBI-10698339; Q9BWW4; Q13526: PIN1; NbExp=6; IntAct=EBI-2902395, EBI-714158; Q9BWW4; O75177-5: SS18L1; NbExp=3; IntAct=EBI-2902395, EBI-12035119; Q9BWW4; Q9NUY8: TBC1D23; NbExp=3; IntAct=EBI-2902395, EBI-2853126; Q9BWW4; Q9NUY8-2: TBC1D23; NbExp=3; IntAct=EBI-2902395, EBI-10314276; Q9BWW4; P07947: YES1; NbExp=6; IntAct=EBI-2902395, EBI-515331;
SUBCELLULAR LOCATION: Nucleus
TISSUE SPECIFICITY: Highly expressed in all hematopoietic tissues, including spleen, lymph node, peripheral blood, bone marrow, thymus, and fetal liver, with highest expression in thymus and fetal liver. Expression is also high in heart, brain, kidney, and skeletal muscle.

-  Primer design for this transcript
 

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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): SSBP3
CDC HuGE Published Literature: SSBP3
Positive Disease Associations: Stroke , Triglycerides
Related Studies:
  1. Stroke
    , , . [PubMed 0]
  2. Triglycerides
    Sekar Kathiresan et al. BMC medical genetics 2007, A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903299]
    Using a 100K genome-wide scan, we have generated a set of putative associations for common sequence variants and lipid phenotypes. Validation of selected hypotheses in additional samples did not identify any new loci underlying variability in blood lipids. Lack of replication may be due to inadequate statistical power to detect modest quantitative trait locus effects (i.e., <1% of trait variance explained) or reduced genomic coverage of the 100K array. GWAS in FHS using a denser genome-wide genotyping platform and a better-powered replication strategy may identify novel loci underlying blood lipids.

-  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.

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -197.00386-0.510 Picture PostScript Text
3' UTR -513.901699-0.302 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
IPR006594 - LisH
IPR008116 - SSDP_DNA-bd

Pfam Domains:
PF04503 - Single-stranded DNA binding protein, SSDP

ModBase Predicted Comparative 3D Structure on Q9BWW4
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003697 single-stranded DNA binding
GO:0005515 protein binding

Biological Process:
GO:0002244 hematopoietic progenitor cell differentiation
GO:0008284 positive regulation of cell proliferation
GO:0021501 prechordal plate formation
GO:0021547 midbrain-hindbrain boundary initiation
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048382 mesendoderm development
GO:0060322 head development
GO:0060323 head morphogenesis
GO:0065003 macromolecular complex assembly
GO:2000744 positive regulation of anterior head development

Cellular Component:
GO:0005634 nucleus
GO:0005667 transcription factor complex
GO:0032991 macromolecular complex


-  Descriptions from all associated GenBank mRNAs
  AK093975 - Homo sapiens cDNA FLJ36656 fis, clone UTERU2001747, highly similar to Rattus norvegicus sequence-specific single-stranded-DNA-binding protein mRNA.
AK289474 - Homo sapiens cDNA FLJ75947 complete cds, highly similar to Homo sapiens single stranded DNA binding protein 3 (SSBP3), transcript variant 3, mRNA.
BC066365 - Homo sapiens single stranded DNA binding protein 3, mRNA (cDNA clone MGC:74589 IMAGE:6169677), complete cds.
BC003605 - Homo sapiens single stranded DNA binding protein 3, mRNA (cDNA clone MGC:977 IMAGE:3546126), complete cds.
AF500116 - Homo sapiens single-stranded DNA-binding protein mRNA, complete cds.
KJ893430 - Synthetic construct Homo sapiens clone ccsbBroadEn_02824 SSBP3 gene, encodes complete protein.
HQ448133 - Synthetic construct Homo sapiens clone IMAGE:100071516; CCSB012334_02 single stranded DNA binding protein 3 (SSBP3) gene, encodes complete protein.
KJ893429 - Synthetic construct Homo sapiens clone ccsbBroadEn_02823 SSBP3 gene, encodes complete protein.
CU688156 - Synthetic construct Homo sapiens gateway clone IMAGE:100021699 5' read SSBP3 mRNA.
BC127866 - Homo sapiens cDNA clone IMAGE:40134424, partial cds.
JD193032 - Sequence 174056 from Patent EP1572962.
JD548473 - Sequence 529497 from Patent EP1572962.
JD102677 - Sequence 83701 from Patent EP1572962.
JD302284 - Sequence 283308 from Patent EP1572962.
BC004335 - Homo sapiens single stranded DNA binding protein 3, mRNA (cDNA clone IMAGE:3631555), partial cds.
AF086085 - Homo sapiens full length insert cDNA clone YZ84E01.
AK001217 - Homo sapiens cDNA FLJ10355 fis, clone NT2RM2001196.
JD121760 - Sequence 102784 from Patent EP1572962.
JD252084 - Sequence 233108 from Patent EP1572962.
JD315951 - Sequence 296975 from Patent EP1572962.
JD271643 - Sequence 252667 from Patent EP1572962.
JD352752 - Sequence 333776 from Patent EP1572962.
JD525612 - Sequence 506636 from Patent EP1572962.
KJ904698 - Synthetic construct Homo sapiens clone ccsbBroadEn_14092 SSBP3-like gene, encodes complete protein.
CU678672 - Synthetic construct Homo sapiens gateway clone IMAGE:100020254 5' read SSBP3 mRNA.
JD302308 - Sequence 283332 from Patent EP1572962.
JD320457 - Sequence 301481 from Patent EP1572962.
JD320456 - Sequence 301480 from Patent EP1572962.
JD153929 - Sequence 134953 from Patent EP1572962.
JD392332 - Sequence 373356 from Patent EP1572962.
JD407343 - Sequence 388367 from Patent EP1572962.
JD484444 - Sequence 465468 from Patent EP1572962.
JD484746 - Sequence 465770 from Patent EP1572962.
JD438175 - Sequence 419199 from Patent EP1572962.
JD263893 - Sequence 244917 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K0A9, ENST00000610401.1, ENST00000610401.2, ENST00000610401.3, ENST00000610401.4, ENST00000610401.5, NM_145716, Q5T860, Q5T861, Q9BTM0, Q9BWW3, Q9BWW4, SSBP3_HUMAN, SSDP, SSDP1, uc327mtd.1
UCSC ID: ENST00000610401.6_7
RefSeq Accession: NM_145716
Protein: Q9BWW4 (aka SSBP3_HUMAN or SSB3_HUMAN)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.