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SSBP3 single stranded DNA binding protein 3 [ Homo sapiens (human) ]

Gene ID: 23648, updated on 2-Nov-2024

Summary

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Official Symbol
SSBP3provided by HGNC
Official Full Name
single stranded DNA binding protein 3provided by HGNC
Primary source
HGNC:HGNC:15674
See related
Ensembl:ENSG00000157216 MIM:607390; AllianceGenome:HGNC:15674
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CSDP; SSDP; SSDP1
Summary
Predicted to enable single-stranded DNA binding activity and transcription coactivator activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within hematopoietic progenitor cell differentiation. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in ovary (RPKM 35.7), brain (RPKM 22.6) and 24 other tissues See more
Orthologs
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Genomic context

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See SSBP3 in Genome Data Viewer
Location:
1p32.3
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (54225432..54413490, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (54108317..54296354, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (54691105..54879163, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54603591-54604217 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54630713-54631214 Neighboring gene CUB domain containing protein 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:54646436-54646936 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:54652758-54652971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1056 Neighboring gene cytochrome b5 reductase like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:54689121-54689841 Neighboring gene mitochondrial ribosomal protein L37 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54704367-54704867 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:54712147-54712309 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54714101-54714600 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:54715268-54715931 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:54716595-54717257 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:54717258-54717919 Neighboring gene SSBP3 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:54728759-54729751 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:54738457-54739025 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:54740736-54741304 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:54746851-54747658 Neighboring gene Sharpr-MPRA regulatory region 4453 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54755897-54756569 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54763406-54763906 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54763907-54764407 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:54777293-54777798 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:54777799-54778302 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:54794077-54794739 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:54797494-54798031 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54802703-54803326 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:54808704-54809225 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:54816098-54816645 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54818040-54818718 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:54820753-54821430 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1058 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1057 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:54838933-54839482 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:54841683-54842232 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1061 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1062 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:54842784-54843333 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:54843885-54844433 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:54844434-54844984 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1063 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54857123-54857644 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54857645-54858164 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:54870662-54871573 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 917 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:54873396-54874305 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:54876715-54877490 Neighboring gene VISTA enhancer hs1487 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:54929901-54930736 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1064 Neighboring gene Sharpr-MPRA regulatory region 12771 Neighboring gene Sharpr-MPRA regulatory region 12692 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54933797-54934298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54937369-54937869 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54940477-54941110 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54941111-54941744 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54941745-54942377 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54945522-54946108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54953393-54953911 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 918 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:54954958-54955168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54965271-54965822 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54965823-54966374 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:54973259-54973431 Neighboring gene uncharacterized LOC105378735 Neighboring gene long intergenic non-protein coding RNA 2784 Neighboring gene transaldolase 1 pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Tyrosine phosphorylation controls nuclear localization and transcriptional activity of Ssdp1 in mammalian cells. Dey-Guha I, et al. J Cell Biochem, 2008 Apr 15. PMID 18080319
  2. [SIVA1 Regulates the Stability of Single-Stranded DNA-Binding Protein 3 Isoforms]. Yin Z, et al. Mol Biol (Mosk), 2018 Sep-Oct. PMID 30363057
  3. Structure and functional characterization of single-strand DNA binding protein SSDP1: carboxyl-terminal of SSDP1 has transcription activity. Wu L. Biochem Biophys Res Commun, 2006 Jan 20. PMID 16325762
  4. Cloning of a cDNA encoding a sequence-specific single-stranded-DNA-binding protein from Rattus norvegicus. Raval-Fernandes S, et al. Gene, 1999 Sep 3. PMID 10524251
  5. A novel, evolutionarily conserved gene family with putative sequence-specific single-stranded DNA-binding activity. Castro P, et al. Genomics, 2002 Jul. PMID 12079286

See all (43) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The SSBP3 co-regulator is required for glucose homeostasis, pancreatic islet architecture, and beta-cell identity.
    Title: The SSBP3 co-regulator is required for glucose homeostasis, pancreatic islet architecture, and beta-cell identity.
  2. SIVA1 enhances SSBP3 ubiquitination and promotes SSBP3 protein turnover
    Title: [SIVA1 Regulates the Stability of Single-Stranded DNA-Binding Protein 3 Isoforms].
  3. SSBP3 Interacts With Islet-1 and Ldb1 to Impact Pancreatic beta-Cell Target Genes
    Title: SSBP3 Interacts With Islet-1 and Ldb1 to Impact Pancreatic β-Cell Target Genes.
  4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  5. phosphorylation involving N-terminal tyrosine residues of Ssdp1 is a means of regulating its nuclear localization and subsequent transcriptional activation of LIM-HD complexes.
    Title: Tyrosine phosphorylation controls nuclear localization and transcriptional activity of Ssdp1 in mammalian cells.
  6. Ssdp proteins interact with the LIM-domain-binding protein Ldb1 to regulate development
    Title: Ssdp proteins interact with the LIM-domain-binding protein Ldb1 to regulate development.
  7. Thus, biochemical data of SSDP1 presented by this study provides biochemical evidence for a better understanding of transcriptional regulation.
    Title: Structure and functional characterization of single-strand DNA binding protein SSDP1: carboxyl-terminal of SSDP1 has transcription activity.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ10355

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables single-stranded DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables transcription coactivator activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in head morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in hematopoietic progenitor cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in mesendoderm development IEA
Inferred from Electronic Annotation
more info
  
involved_in midbrain-hindbrain boundary initiation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of anterior head development IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of cell population proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in prechordal plate formation IEA
Inferred from Electronic Annotation
more info
  
involved_in protein-containing complex assembly IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of transcription regulator complex IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
single-stranded DNA-binding protein 3
Names
sequence-specific single-stranded-DNA-binding protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001009955.4 → NP_001009955.1  single-stranded DNA-binding protein 3 isoform c

    See identical proteins and their annotated locations for NP_001009955.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon, compared to variant 1. The encoded isoform (c) is shorter than isoform a.
    Source sequence(s)
    AL035415, AL161644, BC066365, BF060746, BQ051652, DN602300
    Consensus CDS
    CCDS30726.1
    UniProtKB/TrEMBL
    A0A087WVT6
    Related
    ENSP00000360370.3, ENST00000371319.8
    Conserved Domains (2) summary
    smart00667
    Location:17 → 43
    LisH; Lissencephaly type-1-like homology motif
    pfam04503
    Location:81 → 338
    SSDP; Single-stranded DNA binding protein, SSDP

  2. NM_001394360.1 → NP_001381289.1  single-stranded DNA-binding protein 3 isoform d

    Status: VALIDATED

    Source sequence(s)
    AL035415, AL161644
    UniProtKB/TrEMBL
    A0A087WVT6
    Conserved Domains (2) summary
    smart00667
    Location:17 → 43
    LisH; Lissencephaly type-1-like homology motif
    pfam04503
    Location:81 → 346
    SSDP; Single-stranded DNA binding protein, SSDP

  3. NM_001394361.1 → NP_001381290.1  single-stranded DNA-binding protein 3 isoofrm e

    Status: VALIDATED

    Source sequence(s)
    AL035415, AL161644
    UniProtKB/TrEMBL
    A0A087WVT6
    Conserved Domains (1) summary
    TIGR01628
    Location:111 → 215
    PABP-1234; polyadenylate binding protein, human types 1, 2, 3, 4 family

  4. NM_001394362.1 → NP_001381291.1  single-stranded DNA-binding protein 3 isosform f

    Status: VALIDATED

    Source sequence(s)
    AL035415, AL161644
    UniProtKB/TrEMBL
    A0A087WVT6
    Conserved Domains (2) summary
    smart00667
    Location:17 → 43
    LisH; Lissencephaly type-1-like homology motif
    pfam04503
    Location:81 → 318
    SSDP; Single-stranded DNA binding protein, SSDP

  5. NM_001394363.1 → NP_001381292.1  single-stranded DNA-binding protein 3 isoform g

    Status: VALIDATED

    Source sequence(s)
    AL035415, AL161644
    UniProtKB/TrEMBL
    A0A087WVT6
    Conserved Domains (1) summary
    smart00667
    Location:17 → 43
    LisH; Lissencephaly type-1-like homology motif

  6. NM_001394364.1 → NP_001381293.1  single-stranded DNA-binding protein 3 isoform h

    Status: VALIDATED

    Source sequence(s)
    AL035415, AL161644
    Consensus CDS
    CCDS90961.1
    UniProtKB/TrEMBL
    Q9NW25
    Conserved Domains (1) summary
    pfam04503
    Location:1 → 255
    SSDP; Single-stranded DNA binding protein, SSDP

  7. NM_001394365.1 → NP_001381294.1  single-stranded DNA-binding protein 3 isoform i

    Status: VALIDATED

    Source sequence(s)
    AL035415, AL161644
    UniProtKB/TrEMBL
    Q9BT57
    Related
    ENST00000326956.12
    Conserved Domains (1) summary
    pfam04503
    Location:12 → 228
    SSDP; Single-stranded DNA binding protein, SSDP

  8. NM_001394366.1 → NP_001381295.1  single-stranded DNA-binding protein 3 isoform i

    Status: VALIDATED

    Source sequence(s)
    AL035415, AL161644
    UniProtKB/TrEMBL
    Q9BT57
    Conserved Domains (1) summary
    pfam04503
    Location:12 → 228
    SSDP; Single-stranded DNA binding protein, SSDP

  9. NM_001394367.1 → NP_001381296.1  single-stranded DNA-binding protein 3 isoform j

    Status: VALIDATED

    Source sequence(s)
    AL035415, AL161644
    UniProtKB/TrEMBL
    Q9BT57
    Conserved Domains (1) summary
    TIGR01628
    Location:14 → 154
    PABP-1234; polyadenylate binding protein, human types 1, 2, 3, 4 family

  10. NM_018070.5 → NP_060540.2  single-stranded DNA-binding protein 3 isoform b

    See identical proteins and their annotated locations for NP_060540.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1. The encoded isoform (b) is shorter than isoform a.
    Source sequence(s)
    AF500116, AL035415, AL161644, BC066365, BF060746, DN602300
    Consensus CDS
    CCDS590.1
    UniProtKB/TrEMBL
    A0A087WVT6
    Related
    ENSP00000350067.4, ENST00000357475.9
    Conserved Domains (2) summary
    smart00667
    Location:17 → 43
    LisH; Lissencephaly type-1-like homology motif
    pfam04503
    Location:81 → 345
    SSDP; Single-stranded DNA binding protein, SSDP

  11. NM_145716.4 → NP_663768.1  single-stranded DNA-binding protein 3 isoform a

    See identical proteins and their annotated locations for NP_663768.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AF500116, AL035415, AL161644, BC066365, BF060746, DN602300
    Consensus CDS
    CCDS591.1
    UniProtKB/Swiss-Prot
    A8K0A9, Q5T860, Q5T861, Q9BTM0, Q9BWW3, Q9BWW4
    UniProtKB/TrEMBL
    A0A087WVT6
    Related
    ENSP00000479674.2, ENST00000610401.6
    Conserved Domains (2) summary
    smart00667
    Location:17 → 43
    LisH; Lissencephaly type-1-like homology motif
    pfam04503
    Location:81 → 365
    SSDP; Single-stranded DNA binding protein, SSDP

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    54225432..54413490 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047416697.1 → XP_047272653.1  single-stranded DNA-binding protein 3 isoform X2

  2. XM_017000897.3 → XP_016856386.1  single-stranded DNA-binding protein 3 isoform X1

    UniProtKB/TrEMBL
    Q9NW25
    Related
    ENSP00000414361.2, ENST00000417664.7
    Conserved Domains (1) summary
    pfam04503
    Location:1 → 255
    SSDP; Single-stranded DNA binding protein, SSDP

  3. XM_047416695.1 → XP_047272651.1  single-stranded DNA-binding protein 3 isoform X3

  4. XM_047416693.1 → XP_047272649.1  single-stranded DNA-binding protein 3 isoform X2

  5. XM_047416692.1 → XP_047272648.1  single-stranded DNA-binding protein 3 isoform X1

    UniProtKB/TrEMBL
    Q9NW25

  6. XM_017000898.3 → XP_016856387.1  single-stranded DNA-binding protein 3 isoform X1

    UniProtKB/TrEMBL
    Q9NW25
    Conserved Domains (1) summary
    pfam04503
    Location:1 → 255
    SSDP; Single-stranded DNA binding protein, SSDP

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    54108317..54296354 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054335741.1 → XP_054191716.1  single-stranded DNA-binding protein 3 isoform X2

  2. XM_054335740.1 → XP_054191715.1  single-stranded DNA-binding protein 3 isoform X1

    UniProtKB/TrEMBL
    Q9NW25

  3. XM_054335742.1 → XP_054191717.1  single-stranded DNA-binding protein 3 isoform X1

    UniProtKB/TrEMBL
    Q9NW25
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BWW4.1 GenPept UniProtKB/Swiss-Prot:Q9BWW4

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