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    Sbf1 SET binding factor 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 300147, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Sbf1provided by RGD
    Official Full Name
    SET binding factor 1provided by RGD
    Primary source
    RGD:1307090
    See related
    EnsemblRapid:ENSRNOG00000008392 AllianceGenome:RGD:1307090
    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
    Predicted to enable guanyl-nucleotide exchange factor activity. Involved in spermatid development. Predicted to be located in nuclear body. Predicted to be active in cytoplasm and membrane. Human ortholog(s) of this gene implicated in Charcot-Marie-Tooth disease type 4B3. Orthologous to human SBF1 (SET binding factor 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 169.8), Brain (RPKM 168.9) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Sbf1 in Genome Data Viewer
    Location:
    7q34
    Exon count:
    42
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 7 NC_086025.1 (122237968..122264591, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 7 NC_051342.1 (120358338..120385022, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 7 NC_005106.4 (130261552..130288566, complement)

    Chromosome 7 - NC_086025.1Genomic Context describing neighboring genes Neighboring gene DENN domain containing 6B Neighboring gene protein phosphatase 6, regulatory subunit 2 Neighboring gene uncharacterized LOC102549998 Neighboring gene adrenomedullin 2 Neighboring gene myo-inositol oxygenase

    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. Splicing mutation in Sbf1 causes nonsyndromic male infertility in the rat. Liška F, et al. Reproduction, 2016 Sep. PMID 27335132
    2. Male infertility, impaired spermatogenesis, and azoospermia in mice deficient for the pseudophosphatase Sbf1. Firestein R, et al. J Clin Invest, 2002 May. PMID 11994405, Free PMC Article
    3. Systematic analysis of myotubularins: heteromeric interactions, subcellular localisation and endosome related functions. Lorenzo O, et al. J Cell Sci, 2006 Jul 15. PMID 16787938
    4. Family-wide characterization of the DENN domain Rab GDP-GTP exchange factors. Yoshimura S, et al. J Cell Biol, 2010 Oct 18. PMID 20937701, Free PMC Article
    5. Association of SET domain and myotubularin-related proteins modulates growth control. Cui X, et al. Nat Genet, 1998 Apr. PMID 9537414

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Splicing mutation in Sbf1 causes nonsyndromic male infertility.
      Title: Splicing mutation in Sbf1 causes nonsyndromic male infertility in the rat.
    Submit: New GeneRIF Correction

    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 guanyl-nucleotide exchange factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables guanyl-nucleotide exchange factor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    NOT enables phosphatase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in spermatid development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within spermatogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nuclear body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear body ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    myotubularin-related protein 5

    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_001271173.1 → NP_001258102.1  myotubularin-related protein 5

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000007
      UniProtKB/TrEMBL
      M0RAP5
      Related
      ENSRNOP00000066598.1, ENSRNOT00000072955.5
      Conserved Domains (8) summary
      smart00801
      Location:364 → 432
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00799
      Location:129 → 310
      DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
      smart00800
      Location:1 → 86
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      cd01235
      Location:1786 → 1891
      PH_Sbf1_hMTMR5; Set binding factor 1 (also called Human MTMR5) Pleckstrin Homology (PH) domain
      pfam00169
      Location:1790 → 1891
      PH; PH domain
      pfam06602
      Location:1128 → 1556
      Myotub-related; Myotubularin-like phosphatase domain
      pfam12335
      Location:543 → 764
      SBF2; Myotubularin protein
      cl17171
      Location:893 → 1011
      PH-like; Pleckstrin homology-like 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_086025.1 Reference GRCr8

      Range
      122237968..122264591 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039078878.2 → XP_038934806.1  myotubularin-related protein 5 isoform X3

      Conserved Domains (7) summary
      smart00801
      Location:364 → 432
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00799
      Location:129 → 310
      DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
      smart00800
      Location:1 → 86
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      cd01235
      Location:1760 → 1865
      PH_Sbf1_hMTMR5; Set binding factor 1 (also called Human MTMR5) Pleckstrin Homology (PH) domain
      pfam12335
      Location:543 → 764
      SBF2; Myotubularin protein
      cl17171
      Location:893 → 1011
      PH-like; Pleckstrin homology-like domain
      cl28904
      Location:1150 → 1496
      PTP_DSP_cys; cys-based protein tyrosine phosphatase and dual-specificity phosphatase superfamily

    2. XM_063263346.1 → XP_063119416.1  myotubularin-related protein 5 isoform X2

      UniProtKB/TrEMBL
      A0A8I6AD51
      Related
      ENSRNOP00000090211.1, ENSRNOT00000119425.2

    3. XM_039078877.2 → XP_038934805.1  myotubularin-related protein 5 isoform X1

      Conserved Domains (7) summary
      smart00801
      Location:372 → 440
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00799
      Location:129 → 318
      DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
      smart00800
      Location:1 → 86
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      cd01235
      Location:1794 → 1899
      PH_Sbf1_hMTMR5; Set binding factor 1 (also called Human MTMR5) Pleckstrin Homology (PH) domain
      pfam12335
      Location:551 → 772
      SBF2; Myotubularin protein
      cl17171
      Location:901 → 1019
      PH-like; Pleckstrin homology-like domain
      cl28904
      Location:1158 → 1530
      PTP_DSP_cys; cys-based protein tyrosine phosphatase and dual-specificity phosphatase superfamily

    4. XM_039078879.2 → XP_038934807.1  myotubularin-related protein 5 isoform X4

      Conserved Domains (6) summary
      smart00801
      Location:277 → 345
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00799
      Location:34 → 223
      DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
      cd01235
      Location:1699 → 1804
      PH_Sbf1_hMTMR5; Set binding factor 1 (also called Human MTMR5) Pleckstrin Homology (PH) domain
      pfam12335
      Location:456 → 677
      SBF2; Myotubularin protein
      cl17171
      Location:806 → 924
      PH-like; Pleckstrin homology-like domain
      cl28904
      Location:1063 → 1435
      PTP_DSP_cys; cys-based protein tyrosine phosphatase and dual-specificity phosphatase superfamily
    Nucleotide Protein Strain
    Heading Accession and Version

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