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SSBP4 single stranded DNA binding protein 4 [ Homo sapiens (human) ]

Gene ID: 170463, updated on 5-Mar-2024

Summary

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Official Symbol
SSBP4provided by HGNC
Official Full Name
single stranded DNA binding protein 4provided by HGNC
Primary source
HGNC:HGNC:15676
See related
Ensembl:ENSG00000130511 MIM:607391; AllianceGenome:HGNC:15676
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
Summary
Predicted to enable single-stranded DNA binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to be integral component of membrane. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in spleen (RPKM 6.5), fat (RPKM 4.8) and 25 other tissues See more
Orthologs
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Genomic context

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See SSBP4 in Genome Data Viewer
Location:
19p13.11
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (18402725..18434562)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (18536880..18568741)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (18530208..18545372)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene microRNA 3189 Neighboring gene growth differentiation factor 15 Neighboring gene leucine rich repeat containing 25 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18518971-18519471 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10391 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10392 Neighboring gene CRISPRi-validated cis-regulatory element chr19.2899 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18526865-18527500 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10393 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:18528379-18528618 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10395 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18534153-18534654 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18534655-18535154 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10396 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10397 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14318 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18541209-18541757 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18541758-18542305 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10398 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10399 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18546343-18547240 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18548168-18549155 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18549156-18550142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14319 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14320 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18557131-18557659 Neighboring gene inositol-3-phosphate synthase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18561006-18561812 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18561813-18562619 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:18566359-18566575 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14321 Neighboring gene elongation factor for RNA polymerase II Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18579531-18580168 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10403 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18587281-18588108 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18589364-18590266 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:18594428-18594928 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:18594929-18595429 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18596277-18596862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18605831-18606730 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14323 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18611236-18612222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18618231-18619072 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10405 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18631869-18632384 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18632385-18632900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14325 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18640318-18641203 Neighboring gene Sharpr-MPRA regulatory region 11651 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18652136-18652636 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10407 Neighboring gene FKBP prolyl isomerase 8

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. A novel, evolutionarily conserved gene family with putative sequence-specific single-stranded DNA-binding activity. Castro P, et al. Genomics, 2002 Jul. PMID 12079286
  2. Control of developmentally primed erythroid genes by combinatorial co-repressor actions. Stadhouders R, et al. Nat Commun, 2015 Nov 23. PMID 26593974, Free PMC Article
  3. TIF1gamma controls erythroid cell fate by regulating transcription elongation. Bai X, et al. Cell, 2010 Jul 9. PMID 20603019, Free PMC Article
  4. Large-scale genotyping identifies 41 new loci associated with breast cancer risk. Michailidou K, et al. Nat Genet, 2013 Apr. PMID 23535729, Free PMC Article
  5. Identification of proteins that interact with alpha A-crystallin using a human proteome microarray. Fan Q, et al. Mol Vis, 2014. PMID 24453475, Free PMC Article

See all (27) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  2. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
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

EBI GWAS Catalog

Description
Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
EBI GWAS Catalog

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

  • MGC3181

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
  
Process Evidence Code Pubs
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
single-stranded DNA-binding protein 4

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_001009998.4 → NP_001009998.1  single-stranded DNA-binding protein 4 isoform b

    See identical proteins and their annotated locations for NP_001009998.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (b) is shorter than isoform 1.
    Source sequence(s)
    BC000274, BU838485, CX873722
    Consensus CDS
    CCDS32960.1
    UniProtKB/Swiss-Prot
    Q9BWG4
    Related
    ENSP00000252807.7, ENST00000348495.10
    Conserved Domains (3) summary
    smart00667
    Location:18 → 44
    LisH; Lissencephaly type-1-like homology motif
    pfam04503
    Location:82 → 338
    SSDP; Single-stranded DNA binding protein, SSDP
    pfam04959
    Location:109 → 195
    ARS2; Arsenite-resistance protein 2

  2. NM_032627.5 → NP_116016.1  single-stranded DNA-binding protein 4 isoform a

    See identical proteins and their annotated locations for NP_116016.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    BC000274, CX873722
    Consensus CDS
    CCDS12378.1
    UniProtKB/Swiss-Prot
    Q9BWG4, Q9BWW5
    Related
    ENSP00000270061.5, ENST00000270061.12
    Conserved Domains (2) summary
    smart00667
    Location:18 → 44
    LisH; Lissencephaly type-1-like homology motif
    pfam04503
    Location:82 → 360
    SSDP; Single-stranded DNA binding protein, SSDP

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    18402725..18434562
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047438370.1 → XP_047294326.1  single-stranded DNA-binding protein 4 isoform X11

  2. XM_047438368.1 → XP_047294324.1  single-stranded DNA-binding protein 4 isoform X6

  3. XM_047438374.1 → XP_047294330.1  single-stranded DNA-binding protein 4 isoform X14

  4. XM_006722665.5 → XP_006722728.1  single-stranded DNA-binding protein 4 isoform X1

    Conserved Domains (1) summary
    pfam04503
    Location:104 → 382
    SSDP; Single-stranded DNA binding protein, SSDP

  5. XM_005259790.4 → XP_005259847.1  single-stranded DNA-binding protein 4 isoform X9

    Conserved Domains (1) summary
    pfam04503
    Location:104 → 382
    SSDP; Single-stranded DNA binding protein, SSDP

  6. XM_047438367.1 → XP_047294323.1  single-stranded DNA-binding protein 4 isoform X5

  7. XM_017026437.2 → XP_016881926.1  single-stranded DNA-binding protein 4 isoform X10

  8. XM_006722666.3 → XP_006722729.1  single-stranded DNA-binding protein 4 isoform X4

    Conserved Domains (2) summary
    smart00667
    Location:18 → 44
    LisH; Lissencephaly type-1-like homology motif
    pfam04503
    Location:82 → 360
    SSDP; Single-stranded DNA binding protein, SSDP

  9. XM_047438366.1 → XP_047294322.1  single-stranded DNA-binding protein 4 isoform X3

  10. XM_047438377.1 → XP_047294333.1  single-stranded DNA-binding protein 4 isoform X17

  11. XM_006722668.3 → XP_006722731.1  single-stranded DNA-binding protein 4 isoform X8

    Conserved Domains (3) summary
    smart00667
    Location:18 → 44
    LisH; Lissencephaly type-1-like homology motif
    pfam04503
    Location:82 → 338
    SSDP; Single-stranded DNA binding protein, SSDP
    pfam04959
    Location:109 → 195
    ARS2; Arsenite-resistance protein 2

  12. XM_047438371.1 → XP_047294327.1  single-stranded DNA-binding protein 4 isoform X12

  13. XM_047438372.1 → XP_047294328.1  single-stranded DNA-binding protein 4 isoform X13

  14. XM_047438375.1 → XP_047294331.1  single-stranded DNA-binding protein 4 isoform X15

  15. XM_047438376.1 → XP_047294332.1  single-stranded DNA-binding protein 4 isoform X16

  16. XM_047438373.1 → XP_047294329.1  single-stranded DNA-binding protein 4 isoform X14

  17. XM_047438365.1 → XP_047294321.1  single-stranded DNA-binding protein 4 isoform X2

  18. XM_047438369.1 → XP_047294325.1  single-stranded DNA-binding protein 4 isoform X7

RNA

  1. XR_936164.4 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    18536880..18568741
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054320115.1 → XP_054176090.1  single-stranded DNA-binding protein 4 isoform X23

  2. XM_054320119.1 → XP_054176094.1  single-stranded DNA-binding protein 4 isoform X11

  3. XM_054320109.1 → XP_054176084.1  single-stranded DNA-binding protein 4 isoform X18

  4. XM_054320114.1 → XP_054176089.1  single-stranded DNA-binding protein 4 isoform X9

  5. XM_054320113.1 → XP_054176088.1  single-stranded DNA-binding protein 4 isoform X22

  6. XM_054320118.1 → XP_054176093.1  single-stranded DNA-binding protein 4 isoform X10

  7. XM_054320121.1 → XP_054176096.1  single-stranded DNA-binding protein 4 isoform X13

  8. XM_054320120.1 → XP_054176095.1  single-stranded DNA-binding protein 4 isoform X12

  9. XM_054320124.1 → XP_054176099.1  single-stranded DNA-binding protein 4 isoform X17

  10. XM_054320112.1 → XP_054176087.1  single-stranded DNA-binding protein 4 isoform X21

  11. XM_054320111.1 → XP_054176086.1  single-stranded DNA-binding protein 4 isoform X20

  12. XM_054320117.1 → XP_054176092.1  single-stranded DNA-binding protein 4 isoform X25

  13. XM_054320122.1 → XP_054176097.1  single-stranded DNA-binding protein 4 isoform X15

  14. XM_054320123.1 → XP_054176098.1  single-stranded DNA-binding protein 4 isoform X16

  15. XM_054320110.1 → XP_054176085.1  single-stranded DNA-binding protein 4 isoform X19

  16. XM_054320116.1 → XP_054176091.1  single-stranded DNA-binding protein 4 isoform X24

RNA

  1. XR_008485113.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BWG4.1 GenPept UniProtKB/Swiss-Prot:Q9BWG4

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