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Ptpdc1 protein tyrosine phosphatase domain containing 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 291022, updated on 2-Nov-2024

Summary

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Official Symbol
Ptpdc1provided by RGD
Official Full Name
protein tyrosine phosphatase domain containing 1provided by RGD
Primary source
RGD:1307698
See related
EnsemblRapid:ENSRNOG00000086607 AllianceGenome:RGD:1307698
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to enable protein tyrosine phosphatase activity. Predicted to be involved in cilium assembly. Predicted to act upstream of or within smoothened signaling pathway. Predicted to be located in nucleoplasm. Predicted to be active in cytoplasm. Orthologous to human PTPDC1 (protein tyrosine phosphatase domain containing 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Testes (RPKM 69.3), Kidney (RPKM 48.9) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Ptpdc1 in Genome Data Viewer
Location:
17p14
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 17 NC_086035.1 (16235311..16284160)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 17 NC_051352.1 (16028964..16076512)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 17 NC_005116.4 (16333369..16381887)

Chromosome 17 - NC_086035.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102552096 Neighboring gene BARX homeobox 1 Neighboring gene uncharacterized LOC134482824 Neighboring gene small nucleolar RNA SNORA17 Neighboring gene uncharacterized LOC120097935 Neighboring gene microRNA let-7a-1

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. Functional characterization of putative cilia genes by high-content analysis. Lai CK, et al. Mol Biol Cell, 2011 Apr. PMID 21289087, Free PMC Article
  2. 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 protein tyrosine phosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in cilium assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within cilium assembly ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within smoothened signaling pathway 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 nucleoplasm ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
protein tyrosine phosphatase domain-containing protein 1
NP_001099574.1
XP_063132222.1
XP_063132223.1
XP_063132224.1
XP_063132225.1
XP_063132226.1
XP_063132227.1
XP_063132228.1
XP_063132229.1

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_001106104.1 → NP_001099574.1  protein tyrosine phosphatase domain-containing protein 1

    See identical proteins and their annotated locations for NP_001099574.1

    Status: PROVISIONAL

    Source sequence(s)
    CH473977
    UniProtKB/TrEMBL
    A6J6Y7, A6J6Y8
    Conserved Domains (1) summary
    cl21483
    Location:113 → 226
    PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...

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_086035.1 Reference GRCr8

    Range
    16235311..16284160
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_063276153.1 → XP_063132223.1  protein tyrosine phosphatase domain-containing protein 1 isoform X2

    Related
    ENSRNOP00000103066.1, ENSRNOT00000169259.1

  2. XM_063276158.1 → XP_063132228.1  protein tyrosine phosphatase domain-containing protein 1 isoform X6

    UniProtKB/TrEMBL
    A6J6Y7

  3. XM_063276159.1 → XP_063132229.1  protein tyrosine phosphatase domain-containing protein 1 isoform X7

  4. XM_063276157.1 → XP_063132227.1  protein tyrosine phosphatase domain-containing protein 1 isoform X6

    UniProtKB/TrEMBL
    A6J6Y7

  5. XM_063276156.1 → XP_063132226.1  protein tyrosine phosphatase domain-containing protein 1 isoform X5

    Related
    ENSRNOP00000098824.1, ENSRNOT00000171451.1

  6. XM_063276152.1 → XP_063132222.1  protein tyrosine phosphatase domain-containing protein 1 isoform X1

  7. XM_063276154.1 → XP_063132224.1  protein tyrosine phosphatase domain-containing protein 1 isoform X3

  8. XM_063276155.1 → XP_063132225.1  protein tyrosine phosphatase domain-containing protein 1 isoform X4

RNA

  1. XR_010058821.1 RNA Sequence

  2. XR_010058819.1 RNA Sequence

  3. XR_010058823.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version

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