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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
    mouse all
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    Genomic context

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    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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    NEW Try the new Transcript table

    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

    Gene LinkOut

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