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    Pmfbp1 polyamine modulated factor 1 binding protein 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 171414, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Pmfbp1provided by RGD
    Official Full Name
    polyamine modulated factor 1 binding protein 1provided by RGD
    Primary source
    RGD:621677
    See related
    EnsemblRapid:ENSRNOG00000014505 AllianceGenome:RGD:621677
    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
    Also known as
    ODF3; Stap
    Summary
    Predicted to be involved in spermatogenesis. Predicted to act upstream of or within several processes, including protein-containing complex assembly; regulation of protein localization; and spermatid development. Predicted to be located in cytoplasm. Predicted to be active in sperm flagellum; sperm head; and sperm head-tail coupling apparatus. Human ortholog(s) of this gene implicated in spermatogenic failure 31. Orthologous to human PMFBP1 (polyamine modulated factor 1 binding protein 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Restricted expression toward (RPKM 225.5) See more
    Orthologs
    human mouse all
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    Genomic context

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    See Pmfbp1 in Genome Data Viewer
    Location:
    19q12
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 19 NC_086037.1 (54367562..54417405)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 19 NC_051354.1 (37458126..37507880)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 19 NC_005118.4 (42132551..42196990, complement)

    Chromosome 19 - NC_086037.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134483642 Neighboring gene uncharacterized LOC134483361 Neighboring gene uncharacterized LOC134483362 Neighboring gene uncharacterized LOC134483363 Neighboring gene DEAH-box helicase 38 Neighboring gene thioredoxin-like 4B Neighboring gene haptoglobin

    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. Molecular cloning of Odf3 encoding a novel coiled-coil protein of sperm tail outer dense fibers. Petersen C, et al. Mol Reprod Dev, 2002 Jan. PMID 11774381
    2. Mutations in PMFBP1 Cause Acephalic Spermatozoa Syndrome. Zhu F, et al. Am J Hum Genet, 2018 Aug 2. PMID 30032984, Free PMC Article
    3. Characterization of a novel gene, sperm-tail-associated protein (Stap), in mouse post-meiotic testicular germ cells. Ohuchi J, et al. Mol Reprod Dev, 2001 Aug. PMID 11468771
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in cytoskeleton organization NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in gene expression IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein localization IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within protein localization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein-containing complex assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within protein-containing complex assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of protein localization IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulation of protein localization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in spermatid development IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within spermatid development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in spermatogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within spermatogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in spermatogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in spermatogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in outer dense fiber TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in sperm flagellum IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in sperm flagellum ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in sperm head IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in sperm head ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in sperm head-tail coupling apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in sperm head-tail coupling apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in sperm head-tail coupling apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in sperm head-tail coupling apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in sperm head-tail coupling apparatus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    polyamine-modulated factor 1-binding protein 1
    Names
    PMF-1-binding protein
    outer dense fiber ODF3
    outer dense fiber protein 3
    sperm tail associated 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_134393.3 → NP_599220.2  polyamine-modulated factor 1-binding protein 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000019
      UniProtKB/Swiss-Prot
      Q9Z221
      UniProtKB/TrEMBL
      F1M8J2
      Related
      ENSRNOP00000096927.1, ENSRNOT00000112356.2
      Conserved Domains (1) summary
      TIGR02168
      Location:117 → 825
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    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_086037.1 Reference GRCr8

      Range
      54367562..54417405
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_008772468.4 → XP_008770690.3  polyamine-modulated factor 1-binding protein 1 isoform X8

    2. XM_006255570.5 → XP_006255632.4  polyamine-modulated factor 1-binding protein 1 isoform X3

    3. XM_017601167.3 → XP_017456656.2  polyamine-modulated factor 1-binding protein 1 isoform X5

      UniProtKB/TrEMBL
      A0A8I6AA55
      Conserved Domains (2) summary
      COG1196
      Location:490 → 842
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      TIGR02168
      Location:336 → 595
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    4. XM_006255571.5 → XP_006255633.3  polyamine-modulated factor 1-binding protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A8I6AA55
      Conserved Domains (1) summary
      TIGR02168
      Location:183 → 888
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    5. XM_063277749.1 → XP_063133819.1  polyamine-modulated factor 1-binding protein 1 isoform X9

    6. XM_006255576.5 → XP_006255638.3  polyamine-modulated factor 1-binding protein 1 isoform X7

      UniProtKB/TrEMBL
      A0A8I6AA55
      Related
      ENSRNOP00000111515.1, ENSRNOT00000144325.1
      Conserved Domains (2) summary
      COG1196
      Location:490 → 842
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      TIGR02168
      Location:124 → 792
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    7. XM_063277748.1 → XP_063133818.1  polyamine-modulated factor 1-binding protein 1 isoform X6

      Related
      ENSRNOP00000098832.1, ENSRNOT00000155394.1

    8. XM_063277751.1 → XP_063133821.1  polyamine-modulated factor 1-binding protein 1 isoform X11

    9. XM_006255574.5 → XP_006255636.3  polyamine-modulated factor 1-binding protein 1 isoform X2

      UniProtKB/TrEMBL
      A0A0G2JTR6, A0A8I6AA55
      Related
      ENSRNOP00000090483.2, ENSRNOT00000096710.2
      Conserved Domains (1) summary
      TIGR02168
      Location:171 → 891
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    10. XM_063277752.1 → XP_063133822.1  polyamine-modulated factor 1-binding protein 1 isoform X12

    11. XM_006255572.5 → XP_006255634.1  polyamine-modulated factor 1-binding protein 1 isoform X4

      See identical proteins and their annotated locations for XP_006255634.1

      UniProtKB/TrEMBL
      A0A8I6AA55
      Related
      ENSRNOP00000068814.3, ENSRNOT00000089515.3
      Conserved Domains (3) summary
      COG0419
      Location:70 → 600
      SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
      pfam15742
      Location:418 → 814
      DUF4686; Domain of unknown function (DUF4686)
      cl19219
      Location:613 → 715
      DUF342; Protein of unknown function (DUF342)

    12. XM_017601168.3 → XP_017456657.1  polyamine-modulated factor 1-binding protein 1 isoform X10

      UniProtKB/Swiss-Prot
      Q9Z221

    13. XM_017601169.3 → XP_017456658.1  polyamine-modulated factor 1-binding protein 1 isoform X10

      UniProtKB/Swiss-Prot
      Q9Z221

    RNA

    1. XR_001842203.3 RNA Sequence

    2. XR_361827.5 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Z221.2 GenPept UniProtKB/Swiss-Prot:Q9Z221

    Gene LinkOut

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