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    Pkhd1l1 PKHD1 like 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 314917, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Pkhd1l1provided by RGD
    Official Full Name
    PKHD1 like 1provided by RGD
    Primary source
    RGD:1310406
    See related
    EnsemblRapid:ENSRNOG00000004398 AllianceGenome:RGD:1310406
    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 act upstream of or within sensory perception of sound. Predicted to be located in stereocilium coat and stereocilium tip. Human ortholog(s) of this gene implicated in autosomal recessive nonsyndromic deafness. Orthologous to human PKHD1L1 (PKHD1 like 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Heart (RPKM 118.4), Spleen (RPKM 81.0) and 8 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Pkhd1l1 in Genome Data Viewer
    Location:
    7q31
    Exon count:
    78
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 7 NC_086025.1 (77505063..77679994)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 7 NC_051342.1 (75620384..75795335)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 7 NC_005106.4 (83373022..83548944)

    Chromosome 7 - NC_086025.1Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA17 Neighboring gene NudC domain containing 1 Neighboring gene ENY2, transcription and export complex 2 subunit Neighboring gene estrogen receptor binding site associated antigen 9 Neighboring gene uncharacterized LOC134479721 Neighboring gene syntabulin

    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
    • 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. Arf4 is required for Mammalian development but dispensable for ciliary assembly. Follit JA, et al. PLoS Genet, 2014 Feb. PMID 24586199, Free PMC Article
    2. Gene and alternative splicing annotation with AIR. Florea L, et al. Genome Res, 2005 Jan. PMID 15632090, Free PMC Article
    3. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    5. 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

    Clone Names

    • MGC124881

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    acts_upstream_of_or_within sensory perception of sound ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in stereocilium coat ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in stereocilium tip ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    fibrocystin-L
    Names
    fibrocystin L
    polycystic kidney and hepatic disease 1-like 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_001034931.2 → NP_001030103.2  fibrocystin-L precursor

      Status: PROVISIONAL

      Source sequence(s)
      AI030678, BC105757, BF551112, BQ196166, CB713515, CB789394, CK600919, DY546293, FM096644, FM100521, FM106180, FM120324, JAXUCZ010000007
      UniProtKB/TrEMBL
      A0A8I6AHF3, D4A9R2
      Related
      ENSRNOP00000005958.8, ENSRNOT00000005958.9
      Conserved Domains (6) summary
      cd00603
      Location:2090 → 2175
      IPT_PCSR; IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the ...
      pfam01833
      Location:1830 → 1909
      TIG; IPT/TIG domain
      pfam10162
      Location:2184 → 2302
      G8; G8 domain
      pfam13229
      Location:3327 → 3506
      Beta_helix; Right handed beta helix region
      cl08459
      Location:341 → 467
      PA14; PA14 domain
      cl19115
      Location:1394 → 1497
      Cupredoxin; Cupredoxin superfamily

    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_086025.1 Reference GRCr8

      Range
      77505063..77679994
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039079161.2 → XP_038935089.1  fibrocystin-L isoform X1

      UniProtKB/TrEMBL
      A0A8I6AHF3
      Conserved Domains (6) summary
      cd00603
      Location:2089 → 2174
      IPT_PCSR; IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the ...
      pfam01833
      Location:1829 → 1908
      TIG; IPT/TIG domain
      pfam10162
      Location:2183 → 2301
      G8; G8 domain
      pfam13229
      Location:3326 → 3505
      Beta_helix; Right handed beta helix region
      cl08459
      Location:371 → 467
      PA14; PA14 domain
      cl19115
      Location:1394 → 1497
      Cupredoxin; Cupredoxin superfamily
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Other Literature Sources
    Chemical Information
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    Research Materials
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