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Ptch1 patched 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 89830, updated on 22-Aug-2021

Summary

Official Symbol
Ptch1provided by RGD
Official Full Name
patched 1provided by RGD
Primary source
RGD:621425
See related
Ensembl:ENSRNOG00000019354
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
Ptch; Ptch2
Summary
human homolog acts as a receptor for sonic hedgehog [RGD, Feb 2006]
Expression
Biased expression in Lung (RPKM 98.1), Kidney (RPKM 82.2) and 9 other tissues See more
Orthologs
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Genomic context

See Ptch1 in Genome Data Viewer
Location:
17p14
Exon count:
28
Annotation release Status Assembly Chr Location
108 current mRatBN7.2 (GCF_015227675.2) 17 NC_051352.1 (1542705..1607730)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 17 NC_005116.4 (1032242..1085885, complement)

Chromosome 17 - NC_051352.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102554174 Neighboring gene similar to ribosomal protein L27a Neighboring gene small nucleolar RNA SNORA76 Neighboring gene FA complementation group C Neighboring gene microRNA 3074 Neighboring gene microRNA 24-1 Neighboring gene aminopeptidase O

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

General gene information

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables cholesterol binding ISO
Inferred from Sequence Orthology
more info
 
enables cyclin binding ISO
Inferred from Sequence Orthology
more info
 
enables hedgehog family protein binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables hedgehog family protein binding ISO
Inferred from Sequence Orthology
more info
 
enables hedgehog receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables heparin binding ISO
Inferred from Sequence Orthology
more info
 
enables molecular_function ND
No biological Data available
more info
 
enables patched binding ISO
Inferred from Sequence Orthology
more info
 
enables protein-containing complex binding ISO
Inferred from Sequence Orthology
more info
 
enables smoothened binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables smoothened binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within animal organ morphogenesis ISO
Inferred from Sequence Orthology
more info
 
involved_in animal organ morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in brain development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within branching involved in ureteric bud morphogenesis ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within cell differentiation involved in kidney development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within cell fate determination ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within cell proliferation involved in metanephros development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within cellular response to cholesterol ISO
Inferred from Sequence Orthology
more info
 
involved_in cellular response to cholesterol ISO
Inferred from Sequence Orthology
more info
 
involved_in commissural neuron axon guidance IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within dorsal/ventral neural tube patterning ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within dorsal/ventral pattern formation ISO
Inferred from Sequence Orthology
more info
 
involved_in dorsal/ventral pattern formation ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within embryonic limb morphogenesis ISO
Inferred from Sequence Orthology
more info
 
involved_in embryonic limb morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within embryonic organ development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within epidermal cell fate specification ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within epidermis development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within glucose homeostasis ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within heart morphogenesis ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within hindlimb morphogenesis ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within in utero embryonic development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within keratinocyte proliferation ISO
Inferred from Sequence Orthology
more info
 
involved_in limb morphogenesis ISO
Inferred from Sequence Orthology
more info
 
involved_in liver regeneration IEP
Inferred from Expression Pattern
more info
PubMed 
acts_upstream_of_or_within mammary gland development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within mammary gland duct morphogenesis ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within mammary gland epithelial cell differentiation ISO
Inferred from Sequence Orthology
more info
 
involved_in metanephric collecting duct development ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of cell division ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of cell population proliferation ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of cell population proliferation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of epithelial cell proliferation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of multicellular organism growth ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of multicellular organism growth ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of osteoblast differentiation ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of smoothened signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
involved_in neural plate axis specification ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within neural tube closure ISO
Inferred from Sequence Orthology
more info
 
involved_in neural tube formation ISO
Inferred from Sequence Orthology
more info
 
involved_in neural tube patterning ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within pattern specification process ISO
Inferred from Sequence Orthology
more info
 
involved_in pharyngeal system development ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of cholesterol efflux ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within positive regulation of epidermal cell differentiation ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
involved_in prostate gland development IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in protein localization to plasma membrane ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within protein processing ISO
Inferred from Sequence Orthology
more info
 
involved_in protein processing ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within regulation of cell population proliferation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within regulation of growth ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within regulation of mitotic cell cycle ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within regulation of protein localization ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of protein localization ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of smoothened signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within response to chlorate ISO
Inferred from Sequence Orthology
more info
 
involved_in response to estradiol IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to mechanical stimulus IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to organic cyclic compound IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to retinoic acid IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to xenobiotic stimulus IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in signal transduction ISO
Inferred from Sequence Orthology
more info
 
involved_in smooth muscle tissue development ISO
Inferred from Sequence Orthology
more info
 
involved_in smoothened signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within smoothened signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in smoothened signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within smoothened signaling pathway involved in dorsal/ventral neural tube patterning ISO
Inferred from Sequence Orthology
more info
 
involved_in somite development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within spinal cord motor neuron differentiation ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
colocalizes_with Golgi apparatus ISO
Inferred from Sequence Orthology
more info
 
located_in apical part of cell ISO
Inferred from Sequence Orthology
more info
 
located_in axonal growth cone IDA
Inferred from Direct Assay
more info
PubMed 
located_in caveola ISO
Inferred from Sequence Orthology
more info
 
located_in cilium ISO
Inferred from Sequence Orthology
more info
 
located_in dendritic growth cone IDA
Inferred from Direct Assay
more info
PubMed 
located_in integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
located_in intracellular membrane-bounded organelle ISO
Inferred from Sequence Orthology
more info
 
located_in midbody ISO
Inferred from Sequence Orthology
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in perinuclear region of cytoplasm ISO
Inferred from Sequence Orthology
more info
 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in plasma membrane ISO
Inferred from Sequence Orthology
more info
 
located_in postsynaptic density IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
protein patched homolog 1
Names
patched homolog 2

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_001389256.1NP_001376185.1  protein patched homolog 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    JACYVU010000284
    Conserved Domains (1) summary
    TIGR00918
    Location:21140
    2A060602; The Eukaryotic (Putative) Sterol Transporter (EST) Family
  2. NM_053566.3NP_446018.1  protein patched homolog 1 isoform 1

    See identical proteins and their annotated locations for NP_446018.1

    Status: VALIDATED

    Source sequence(s)
    JACYVU010000284
    UniProtKB/TrEMBL
    Q6UY90
    Related
    ENSRNOP00000026287.5, ENSRNOT00000026287.5
    Conserved Domains (2) summary
    TIGR00918
    Location:291192
    2A060602; The Eukaryotic (Putative) Sterol Transporter (EST) Family
    pfam12349
    Location:448602
    Sterol-sensing; Sterol-sensing domain of SREBP cleavage-activation

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 108 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference mRatBN7.2 Primary Assembly

Genomic

  1. NC_051352.1 Reference mRatBN7.2 Primary Assembly

    Range
    1542705..1607730
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039096136.1XP_038952064.1  protein patched homolog 1 isoform X3

    Conserved Domains (1) summary
    TIGR00918
    Location:291140
    2A060602; The Eukaryotic (Putative) Sterol Transporter (EST) Family
  2. XM_039096137.1XP_038952065.1  protein patched homolog 1 isoform X4

    Conserved Domains (1) summary
    cl25655
    Location:11055
    Patched; Patched family
  3. XM_039096135.1XP_038952063.1  protein patched homolog 1 isoform X2

    Conserved Domains (1) summary
    cl25655
    Location:1781201
    Patched; Patched family
  4. XM_039096134.1XP_038952062.1  protein patched homolog 1 isoform X1

    Conserved Domains (1) summary
    TIGR00918
    Location:1781253
    2A060602; The Eukaryotic (Putative) Sterol Transporter (EST) Family
  5. XM_039096138.1XP_038952066.1  protein patched homolog 1 isoform X5

    Conserved Domains (1) summary
    cl25655
    Location:1620
    Patched; Patched family
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