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    Safb scaffold attachment factor B [ Rattus norvegicus (Norway rat) ]

    Gene ID: 64196, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Safbprovided by RGD
    Official Full Name
    scaffold attachment factor Bprovided by RGD
    Primary source
    RGD:620613
    See related
    EnsemblRapid:ENSRNOG00000050543 AllianceGenome:RGD:620613
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Enables sequence-specific DNA binding activity. Involved in regulation of mRNA processing and regulation of transcription by RNA polymerase II. Predicted to be located in midbody and nucleoplasm. Predicted to be active in nucleus. Orthologous to human SAFB (scaffold attachment factor B). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Thymus (RPKM 146.4), Spleen (RPKM 128.5) and 9 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Safb in Genome Data Viewer
    Location:
    9q11
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (1504657..1525545)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (1417449..1438408)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (10450216..10471174, complement)

    Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene TINCR ubiquitin domain containing Neighboring gene scaffold attachment factor B2 Neighboring gene mitochondrial contact site and cristae organizing system subunit 13 Neighboring gene ribosomal protein L36

    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
    • 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. Scaffold attachment factor B: distribution and interaction with ERα in the rat brain. Hashimoto T, et al. Histochem Cell Biol, 2020 May. PMID 32086573
    2. Cloning and characterization of an alternatively spliced form of SR protein kinase 1 that interacts specifically with scaffold attachment factor-B. Nikolakaki E, et al. J Biol Chem, 2001 Oct 26. PMID 11509566
    3. The tight junction protein ZO-2 localizes to the nucleus and interacts with the heterogeneous nuclear ribonucleoprotein scaffold attachment factor-B. Traweger A, et al. J Biol Chem, 2003 Jan 24. PMID 12403786
    4. Scaffold attachment factor B1 functions in development, growth, and reproduction. Ivanova M, et al. Mol Cell Biol, 2005 Apr. PMID 15798188, Free PMC Article
    5. The interaction and colocalization of Sam68 with the splicing-associated factor YT521-B in nuclear dots is regulated by the Src family kinase p59(fyn). Hartmann AM, et al. Mol Biol Cell, 1999 Nov. PMID 10564280, Free PMC Article

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Scaffold attachment factor B: distribution and interaction with ERalpha in the rat brain.
      Title: Scaffold attachment factor B: distribution and interaction with ERα in the rat brain.
    2. nuclear tight junction protein ZO-2 directly interacts with the DNA-binding protein scaffold attachment factor-B
      Title: The tight junction protein ZO-2 localizes to the nucleus and interacts with the heterogeneous nuclear ribonucleoprotein scaffold attachment factor-B.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chromatin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in estrogen receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within estrogen receptor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within hormone metabolic process 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 regulation of androgen receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within regulation of growth ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of mRNA processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of mRNA processing IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in midbody ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    scaffold attachment factor B1
    Names
    SAF-B
    SAF-B1

    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_022394.2 → NP_071789.2  scaffold attachment factor B1

      See identical proteins and their annotated locations for NP_071789.2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/Swiss-Prot
      O88453
      UniProtKB/TrEMBL
      A6KQX0
      Related
      ENSRNOP00000106846.1, ENSRNOT00000151400.1
      Conserved Domains (2) summary
      cd12679
      Location:428 → 503
      RRM_SAFB1_SAFB2; RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins
      pfam02037
      Location:31 → 65
      SAP; SAP domain

    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_086027.1 Reference GRCr8

      Range
      1504657..1525545
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017596622.3 → XP_017452111.1  scaffold attachment factor B1 isoform X1

      UniProtKB/Swiss-Prot
      O88453
      UniProtKB/TrEMBL
      A0A0G2JZI0
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O88453.2 GenPept UniProtKB/Swiss-Prot:O88453

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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