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    Ssbp3 single stranded DNA binding protein 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 84354, updated on 2-Nov-2024

    Summary

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    Symbol
    Ssbp3provided by RGD
    Full Name
    single stranded DNA binding protein 3provided by RGD
    Primary source
    RGD:621502
    See related
    EnsemblRapid:ENSRNOG00000007920 AllianceGenome:RGD:621502
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Ssdp; Ssdp3
    Summary
    Predicted to enable transcription coactivator activity. Predicted to be involved in several processes, including head morphogenesis; nervous system development; and positive regulation of anterior head development. 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. Orthologous to human SSBP3 (single stranded DNA binding protein 3). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Thymus (RPKM 85.7), Spleen (RPKM 35.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Ssbp3 in Genome Data Viewer
    Location:
    5q34
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (126920145..127057968)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (121691370..121828035)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (126511339..126649830)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene TLC domain containing 3B, pseudogene 1 Neighboring gene uncharacterized LOC120102946 Neighboring gene uncharacterized LOC134479027 Neighboring gene mitochondrial ribosomal protein L37 Neighboring gene uncharacterized LOC120102947 Neighboring gene cytochrome b5 reductase-like Neighboring gene ribosomal protein L28, pseudogene 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. 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
    2. LMO4 controls the balance between excitatory and inhibitory spinal V2 interneurons. Joshi K, et al. Neuron, 2009 Mar 26. PMID 19323994, Free PMC Article
    3. Ssdp1 regulates head morphogenesis of mouse embryos by activating the Lim1-Ldb1 complex. Nishioka N, et al. Development, 2005 Jun. PMID 15857913
    4. Lhx1 functions together with Otx2, Foxa2, and Ldb1 to govern anterior mesendoderm, node, and midline development. Costello I, et al. Genes Dev, 2015 Oct 15. PMID 26494787, Free PMC Article
    5. Haploinsufficiency of SAMD9L, an endosome fusion facilitator, causes myeloid malignancies in mice mimicking human diseases with monosomy 7. Nagamachi A, et al. Cancer Cell, 2013 Sep 9. PMID 24029230

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC124589

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables single-stranded DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables single-stranded DNA binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables transcription coactivator activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transcription coactivator activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in head development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in head morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in head morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in hematopoietic progenitor cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within hematopoietic progenitor cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mesendoderm development IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of mesendoderm development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in midbrain-hindbrain boundary initiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in midbrain-hindbrain boundary initiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of anterior head development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of anterior head development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of cell population proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of cell population proliferation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in prechordal plate formation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in prechordal plate formation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein-containing complex assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein-containing complex assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of protein-containing complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of transcription regulator complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of transcription regulator complex ISO
    Inferred from Sequence Orthology
    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_053358.2 → NP_445810.2  single-stranded DNA-binding protein 3

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000005
      UniProtKB/Swiss-Prot
      Q9R050
      UniProtKB/TrEMBL
      Q3B7C9
      Related
      ENSRNOP00000089190.2, ENSRNOT00000101748.2
      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

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086023.1 Reference GRCr8

      Range
      126920145..127057968
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063288492.1 → XP_063144562.1  single-stranded DNA-binding protein 3 isoform X8

    2. XM_006238532.5 → XP_006238594.1  single-stranded DNA-binding protein 3 isoform X1

      See identical proteins and their annotated locations for XP_006238594.1

      UniProtKB/Swiss-Prot
      Q9R050
      Conserved Domains (2) summary
      smart00667
      Location:17 → 43
      LisH; Lissencephaly type-1-like homology motif
      pfam04503
      Location:81 → 387
      SSDP; Single-stranded DNA binding protein, SSDP

    3. XM_006238534.5 → XP_006238596.1  single-stranded DNA-binding protein 3 isoform X3

      See identical proteins and their annotated locations for XP_006238596.1

      UniProtKB/Swiss-Prot
      Q9R050
      UniProtKB/TrEMBL
      A0A8I5ZWL0
      Conserved Domains (2) summary
      smart00667
      Location:17 → 43
      LisH; Lissencephaly type-1-like homology motif
      pfam04503
      Location:81 → 373
      SSDP; Single-stranded DNA binding protein, SSDP

    4. XM_006238533.5 → XP_006238595.1  single-stranded DNA-binding protein 3 isoform X2

      See identical proteins and their annotated locations for XP_006238595.1

      UniProtKB/Swiss-Prot
      Q9R050
      Conserved Domains (2) summary
      smart00667
      Location:17 → 43
      LisH; Lissencephaly type-1-like homology motif
      pfam04503
      Location:81 → 379
      SSDP; Single-stranded DNA binding protein, SSDP

    5. XM_063288494.1 → XP_063144564.1  single-stranded DNA-binding protein 3 isoform X11

    6. XM_063288493.1 → XP_063144563.1  single-stranded DNA-binding protein 3 isoform X10

    7. XM_006238536.5 → XP_006238598.1  single-stranded DNA-binding protein 3 isoform X5

      See identical proteins and their annotated locations for XP_006238598.1

      UniProtKB/Swiss-Prot
      Q9R050
      Conserved Domains (2) summary
      smart00667
      Location:17 → 43
      LisH; Lissencephaly type-1-like homology motif
      pfam04503
      Location:81 → 360
      SSDP; Single-stranded DNA binding protein, SSDP

    8. XM_006238535.5 → XP_006238597.1  single-stranded DNA-binding protein 3 isoform X4

      See identical proteins and their annotated locations for XP_006238597.1

      UniProtKB/Swiss-Prot
      Q9R050
      UniProtKB/TrEMBL
      A6JYP3
      Related
      ENSRNOP00000082297.2, ENSRNOT00000096305.2
      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

    9. XM_006238537.5 → XP_006238599.1  single-stranded DNA-binding protein 3 isoform X6

      See identical proteins and their annotated locations for XP_006238599.1

      UniProtKB/Swiss-Prot
      Q9R050
      Conserved Domains (2) summary
      smart00667
      Location:17 → 43
      LisH; Lissencephaly type-1-like homology motif
      pfam04503
      Location:81 → 352
      SSDP; Single-stranded DNA binding protein, SSDP

    10. XM_063288495.1 → XP_063144565.1  single-stranded DNA-binding protein 3 isoform X12

    11. XM_006238538.5 → XP_006238600.1  single-stranded DNA-binding protein 3 isoform X7

      See identical proteins and their annotated locations for XP_006238600.1

      UniProtKB/Swiss-Prot
      Q9R050
      UniProtKB/TrEMBL
      F7FHV2
      Related
      ENSRNOP00000011408.6, ENSRNOT00000011408.9
      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

    12. XM_039110869.2 → XP_038966797.1  single-stranded DNA-binding protein 3 isoform X14

      UniProtKB/TrEMBL
      A6JYP5
      Conserved Domains (1) summary
      pfam04503
      Location:1 → 277
      SSDP; Single-stranded DNA binding protein, SSDP

    13. XM_039110871.2 → XP_038966799.1  single-stranded DNA-binding protein 3 isoform X16

      UniProtKB/TrEMBL
      A6JYP5
      Conserved Domains (1) summary
      pfam04503
      Location:12 → 250
      SSDP; Single-stranded DNA binding protein, SSDP

    14. XM_039110872.2 → XP_038966800.1  single-stranded DNA-binding protein 3 isoform X17

      UniProtKB/TrEMBL
      A6JYP5, A6JYP9
      Conserved Domains (1) summary
      pfam04503
      Location:12 → 228
      SSDP; Single-stranded DNA binding protein, SSDP

    15. XM_017593663.3 → XP_017449152.1  single-stranded DNA-binding protein 3 isoform X9

    16. XM_039110867.2 → XP_038966795.1  single-stranded DNA-binding protein 3 isoform X13

      UniProtKB/TrEMBL
      A6JYP5
      Conserved Domains (1) summary
      pfam04503
      Location:31 → 298
      SSDP; Single-stranded DNA binding protein, SSDP

    17. XM_063288496.1 → XP_063144566.1  single-stranded DNA-binding protein 3 isoform X15

    18. XM_039110873.2 → XP_038966801.1  single-stranded DNA-binding protein 3 isoform X18

      Conserved Domains (1) summary
      pfam04503
      Location:1 → 203
      SSDP; Single-stranded DNA binding protein, SSDP

    19. XM_063288497.1 → XP_063144567.1  single-stranded DNA-binding protein 3 isoform X19

    20. XM_063288498.1 → XP_063144568.1  single-stranded DNA-binding protein 3 isoform X20

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9R050.1 GenPept UniProtKB/Swiss-Prot:Q9R050

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