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    Ptchd4 patched domain containing 4 [ Mus musculus (house mouse) ]

    Gene ID: 627626, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Ptchd4provided by MGI
    Official Full Name
    patched domain containing 4provided by MGI
    Primary source
    MGI:MGI:1920485
    See related
    Ensembl:ENSMUSG00000042256 AllianceGenome:MGI:1920485
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Gm321; 3110082D06Rik
    Summary
    Predicted to be active in membrane. Is expressed in central nervous system; foot mesenchyme; and hindlimb interdigital region. Orthologous to human PTCHD4 (patched domain containing 4). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    human all
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    Genomic context

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    See Ptchd4 in Genome Data Viewer
    Location:
    17 B3; 17 19.65 cM
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 17 NC_000083.7 (42626646..43004339)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (42315851..42507742)

    Chromosome 17 - NC_000083.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_42558 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene Neighboring gene STARR-seq mESC enhancer starr_42559 Neighboring gene STARR-seq mESC enhancer starr_42560 Neighboring gene STARR-seq mESC enhancer starr_42561 Neighboring gene serine palmitoyltransferase small subunit A pseudogene Neighboring gene STARR-seq mESC enhancer starr_42562 Neighboring gene STARR-seq mESC enhancer starr_42563 Neighboring gene STARR-seq mESC enhancer starr_42564 Neighboring gene STARR-seq mESC enhancer starr_42565 Neighboring gene STARR-seq mESC enhancer starr_42566 Neighboring gene STARR-seq mESC enhancer starr_42567 Neighboring gene STARR-seq mESC enhancer starr_42568 Neighboring gene STARR-seq mESC enhancer starr_42569 Neighboring gene STARR-seq mESC enhancer starr_42570 Neighboring gene opsin 5 Neighboring gene adhesion G protein-coupled receptor F4 Neighboring gene STARR-positive B cell enhancer mm9_chr17:42919148-42919448 Neighboring gene adhesion G protein-coupled receptor F2 Neighboring gene STARR-seq mESC enhancer starr_42571 Neighboring gene STARR-positive B cell enhancer ABC_E9167 Neighboring gene 40S ribosomal protein S2 pseudogene Neighboring gene CD2-associated protein

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Gata2, Nkx2-2 and Skor2 form a transcription factor network regulating development of a midbrain GABAergic neuron subtype with characteristics of REM-sleep regulatory neurons. Kirjavainen A, et al. Development, 2022 Jul 15. PMID 35815619
    2. BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. Pourhaghighi R, et al. Cell Syst, 2020 Apr 22. PMID 32325033, Free PMC Article
    3. Genetic determinants of micronucleus formation in vivo. Adams DJ, et al. Nature, 2024 Mar. PMID 38355793, Free PMC Article
    4. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548
    5. A high-resolution anatomical atlas of the transcriptome in the mouse embryo. Diez-Roux G, et al. PLoS Biol, 2011 Jan 18. PMID 21267068, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 

    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 MGI

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    Component Evidence Code Pubs
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    patched domain-containing protein 4
    Names
    patched domain-containing protein C6orf138 homolog

    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_001355270.1 → NP_001342199.1  patched domain-containing protein 4 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC110552, AC117246
      Consensus CDS
      CCDS89098.1
      UniProtKB/Swiss-Prot
      B9EKX1
      Related
      ENSMUSP00000156770.2, ENSMUST00000232968.2
      Conserved Domains (1) summary
      cl25655
      Location:84 → 870
      Patched; Patched family

    2. NM_028474.1 → NP_082750.1  patched domain-containing protein 4 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC110552, AC117246
      Consensus CDS
      CCDS50112.1
      UniProtKB/TrEMBL
      E9QMK6
      Related
      ENSMUSP00000047640.5, ENSMUST00000048691.6
      Conserved Domains (1) summary
      cl25655
      Location:81 → 867
      Patched; Patched family

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000083.7 Reference GRCm39 C57BL/6J

      Range
      42626646..43004339
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036160722.1 → XP_036016615.1  patched domain-containing protein 4 isoform X2

      UniProtKB/TrEMBL
      E9QMK6
      Conserved Domains (1) summary
      cl25655
      Location:81 → 867
      Patched; Patched family

    2. XM_006524754.5 → XP_006524817.1  patched domain-containing protein 4 isoform X5

      Conserved Domains (1) summary
      cl25655
      Location:145 → 809
      Patched; Patched family

    3. XM_006524752.4 → XP_006524815.1  patched domain-containing protein 4 isoform X3

      See identical proteins and their annotated locations for XP_006524815.1

      UniProtKB/Swiss-Prot
      B9EKX1
      Conserved Domains (1) summary
      cl25655
      Location:67 → 853
      Patched; Patched family

    4. XM_030249941.2 → XP_030105801.1  patched domain-containing protein 4 isoform X6

      Conserved Domains (1) summary
      cl25655
      Location:2 → 476
      Patched; Patched family

    5. XM_006524753.2 → XP_006524816.1  patched domain-containing protein 4 isoform X4

      Conserved Domains (1) summary
      cl25655
      Location:148 → 812
      Patched; Patched family

    6. XM_036160724.1 → XP_036016617.1  patched domain-containing protein 4 isoform X7

      UniProtKB/TrEMBL
      B7ZNK4
      Conserved Domains (1) summary
      cl25655
      Location:148 → 302
      Patched; Patched family

    7. XM_036160721.1 → XP_036016614.1  patched domain-containing protein 4 isoform X1

      UniProtKB/Swiss-Prot
      B9EKX1
      Conserved Domains (1) summary
      cl25655
      Location:84 → 870
      Patched; Patched family

    8. XM_036160723.1 → XP_036016616.1  patched domain-containing protein 4 isoform X6

      Conserved Domains (1) summary
      cl25655
      Location:2 → 476
      Patched; Patched family
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    B9EKX1.2 GenPept UniProtKB/Swiss-Prot:B9EKX1

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