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

    Gene ID: 23648, updated on 27-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
    mouse all
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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
    • 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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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    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)

    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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