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

Gene ID: 627626, updated on 11-Apr-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 integral component of membrane. 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, Apr 2022]
Expression
Low expression observed in reference dataset See more
Orthologs
human all
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Genomic context

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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
  • 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. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548
  4. 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
  5. Antisense transcription in the mammalian transcriptome. Katayama S, et al. Science, 2005 Sep 2. PMID 16141073

See all (13) 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
  

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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