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    Prtg protogenin [ Rattus norvegicus (Norway rat) ]

    Gene ID: 315806, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Prtgprovided by RGD
    Official Full Name
    protogeninprovided by RGD
    Primary source
    RGD:1307157
    See related
    EnsemblRapid:ENSRNOG00000055251 AllianceGenome:RGD:1307157
    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
    RGD1307157
    Summary
    Predicted to enable identical protein binding activity and signaling receptor activity. Predicted to be involved in cell-cell adhesion. Predicted to act upstream of or within negative regulation of neurogenesis. Predicted to be located in plasma membrane. Orthologous to human PRTG (protogenin). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Liver (RPKM 12.2), Testes (RPKM 11.8) and 8 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Prtg in Genome Data Viewer
    Location:
    8q24
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (82429106..82538612)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (73548440..73657945)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (79489790..79593806)

    Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene U6 spliceosomal RNA Neighboring gene ribosomal protein S7, pseudogene 9 Neighboring gene uncharacterized LOC120094206 Neighboring gene small nucleolar RNA SNORA2/SNORA34 family Neighboring gene pygopus family PHD finger 1 Neighboring gene U6 spliceosomal RNA Neighboring gene dynein axonemal assembly factor 4

    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. Protogenin defines a transition stage during embryonic neurogenesis and prevents precocious neuronal differentiation. Wong YH, et al. J Neurosci, 2010 Mar 24. PMID 20335479, Free PMC Article
    2. Comparison of tear protein levels in breast cancer patients and healthy controls using a de novo proteomic approach. Böhm D, et al. Oncol Rep, 2012 Aug. PMID 22664934, Free PMC Article
    3. 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

    Function Evidence Code Pubs
    enables identical protein binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables signaling receptor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables signaling receptor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell-cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of neurogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within negative regulation of neurogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    protogenin
    Names
    protein Shen-Dan
    protogenin A
    protogenin homolog (Gallus gallus)
    shen-dan

    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_001037651.2 → NP_001032740.2  protogenin precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008
      UniProtKB/Swiss-Prot
      Q2VWP9
      UniProtKB/TrEMBL
      F1LNL1
      Related
      ENSRNOP00000071092.1, ENSRNOT00000091722.3
      Conserved Domains (6) summary
      cd00063
      Location:816 → 906
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam00041
      Location:619 → 694
      fn3; Fibronectin type III domain
      pfam07679
      Location:322 → 407
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:230 → 302
      Ig_3; Immunoglobulin domain
      cd00096
      Location:32 → 35
      Ig; Ig strand A [structural motif]
      cl11960
      Location:32 → 124
      Ig; Immunoglobulin 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_086026.1 Reference GRCr8

      Range
      82429106..82538612
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039081517.2 → XP_038937445.1  protogenin isoform X1

      UniProtKB/Swiss-Prot
      Q2VWP9
      UniProtKB/TrEMBL
      A6KEM4
      Conserved Domains (7) summary
      smart00410
      Location:135 → 217
      IG_like; Immunoglobulin like
      cd00063
      Location:815 → 905
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam00041
      Location:618 → 693
      fn3; Fibronectin type III domain
      pfam07679
      Location:321 → 406
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:229 → 301
      Ig_3; Immunoglobulin domain
      cd00096
      Location:32 → 35
      Ig; Ig strand A [structural motif]
      cl11960
      Location:32 → 124
      Ig; Immunoglobulin domain

    2. XM_039081518.2 → XP_038937446.1  protogenin isoform X2

      UniProtKB/Swiss-Prot
      Q2VWP9
      Conserved Domains (6) summary
      cd00063
      Location:781 → 871
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam00041
      Location:584 → 659
      fn3; Fibronectin type III domain
      pfam07679
      Location:287 → 372
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:195 → 267
      Ig_3; Immunoglobulin domain
      cd00096
      Location:3 → 9
      Ig; Ig strand A' [structural motif]
      cl11960
      Location:1 → 89
      Ig; Immunoglobulin domain

    3. XM_039081519.2 → XP_038937447.1  protogenin isoform X3

      UniProtKB/Swiss-Prot
      Q2VWP9
      Conserved Domains (6) summary
      cd00063
      Location:646 → 736
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam00041
      Location:449 → 524
      fn3; Fibronectin type III domain
      pfam07679
      Location:152 → 237
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:60 → 132
      Ig_3; Immunoglobulin domain
      cd00096
      Location:77 → 81
      Ig; Ig strand B [structural motif]
      cl11960
      Location:2 → 34
      Ig; Immunoglobulin domain

    4. XM_063265548.1 → XP_063121618.1  protogenin isoform X4

    RNA

    1. XR_010053966.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q2VWP9.1 GenPept UniProtKB/Swiss-Prot:Q2VWP9

    Gene LinkOut

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