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    pkhd1l1.2 PKHD1 like 1, tandem duplicate 2 [ Danio rerio (zebrafish) ]

    Gene ID: 569167, updated on 4-Jan-2025

    Summary

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    Official Symbol
    pkhd1l1.2provided by ZNC
    Official Full Name
    PKHD1 like 1, tandem duplicate 2provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-060503-789
    See related
    Ensembl:ENSDARG00000040004 AllianceGenome:ZFIN:ZDB-GENE-060503-789
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    pkhd-l2; si:ch211-244a23.1
    Summary
    Acts upstream of or within sensory perception of sound. Predicted to be located in membrane. 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, Jan 2025]
    Orthologs
    all
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    Genomic context

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    See pkhd1l1.2 in Genome Data Viewer
    Location:
    chromosome: 19
    Exon count:
    77
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 19 NC_007130.7 (22934621..22997680)
    105 previous assembly GRCz10 (GCF_000002035.5) 19 NC_007130.6 (23350298..23413329)

    Chromosome 19 - NC_007130.7Genomic Context describing neighboring genes Neighboring gene NudC domain containing 1 Neighboring gene PKHD1 like 1, tandem duplicate 1 Neighboring gene growth differentiation factor 6b Neighboring gene uncharacterized LOC137488437

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. A conserved function of Pkhd1l1, a mammalian hair cell stereociliary coat protein, in regulating hearing in zebrafish. Makrogkikas S, et al. J Neurogenet, 2023 Sep. PMID 36960824
    2. 15000 unique zebrafish EST clusters and their future use in microarray for profiling gene expression patterns during embryogenesis. Lo J, et al. Genome Res, 2003 Mar. PMID 12618376, Free PMC Article
    3. 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
    4. Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. Pasquier J, et al. BMC Genomics, 2016 May 18. PMID 27189481, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Process Evidence Code Pubs
    involved_in nervous system development IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within sensory perception of sound IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    PKHD1 like 1, tandem duplicate 2
    Names
    polycystic kidney and hepatic disease-like 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_001130399.1 → NP_001123871.1  PKHD1 like 1, tandem duplicate 2 isoform 1 precursor

      Status: PROVISIONAL

      Source sequence(s)
      BX649562
      UniProtKB/TrEMBL
      A0A8M1NI39, A0A8M3AVJ3, A8E7R5
      Related
      ENSDARP00000050455.8, ENSDART00000050456.10
      Conserved Domains (5) summary
      cd00603
      Location:1874 → 1961
      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:1690 → 1771
      TIG; IPT/TIG domain
      pfam10162
      Location:1968 → 2086
      G8; G8 domain
      pfam13229
      Location:2999 → 3105
      Beta_helix; Right handed beta helix region
      cl19115
      Location:1183 → 1280
      Cupredoxin; Cupredoxin superfamily

    2. NM_001166323.1 → NP_001159795.1  PKHD1 like 1, tandem duplicate 2 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001159795.1

      Status: PROVISIONAL

      Source sequence(s)
      EU864430
      UniProtKB/TrEMBL
      A0A8M3AVJ3, A0A8M6YTX7, D3G896
      Related
      ENSDARP00000105859.3, ENSDART00000124987.3
      Conserved Domains (5) summary
      cd00603
      Location:2047 → 2134
      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:1871 → 1952
      TIG; IPT/TIG domain
      pfam10162
      Location:2141 → 2259
      G8; G8 domain
      pfam13229
      Location:3284 → 3390
      Beta_helix; Right handed beta helix region
      cl19115
      Location:1359 → 1461
      Cupredoxin; Cupredoxin superfamily

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007130.7 Reference GRCz11 Primary Assembly

      Range
      22934621..22997680
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068215167.1 → XP_068071268.1  PKHD1 like 1, tandem duplicate 2 isoform X1

      UniProtKB/TrEMBL
      A0A8M6YTX7
      Related
      ENSDARP00000125726.1, ENSDART00000151737.4
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

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