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

Gene ID: 64196, updated on 30-Mar-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
Ensembl: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. Located in nucleus. Orthologous to human SAFB (scaffold attachment factor B). [provided by Alliance of Genome Resources, Apr 2022]
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. Scaffold attachment factor B1 functions in development, growth, and reproduction. Ivanova M, et al. Mol Cell Biol, 2005 Apr. PMID 15798188, Free PMC Article
  4. 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
  5. SAFB1, an RBMX-binding protein, is a newly identified regulator of hepatic SREBP-1c gene. Omura Y, et al. BMB Rep, 2009 Apr 30. PMID 19403048

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
acts_upstream_of_or_within hormone metabolic process ISO
Inferred from Sequence Orthology
more info
  
involved_in intracellular estrogen receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within intracellular estrogen receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
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
    ENSRNOP00000069796.2, ENSRNOT00000081770.2
    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
    Related
    ENSRNOP00000071054.2
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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