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    PKD2L2 polycystin 2 like 2, transient receptor potential cation channel [ Homo sapiens (human) ]

    Gene ID: 27039, updated on 28-Oct-2024

    Summary

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    Official Symbol
    PKD2L2provided by HGNC
    Official Full Name
    polycystin 2 like 2, transient receptor potential cation channelprovided by HGNC
    Primary source
    HGNC:HGNC:9012
    See related
    Ensembl:ENSG00000078795 MIM:604669; AllianceGenome:HGNC:9012
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    TRPP5
    Summary
    Predicted to enable calcium channel activity. Predicted to be involved in detection of mechanical stimulus. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Broad expression in testis (RPKM 6.7), endometrium (RPKM 3.3) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PKD2L2 in Genome Data Viewer
    Location:
    5q31.2
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (137889457..137942747)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (138415893..138469143)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (137225146..137278436)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986368 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23188 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23189 Neighboring gene PKD2L2 divergent transcript Neighboring gene ReSE screen-validated silencer GRCh37_chr5:137199613-137199779 Neighboring gene myotilin Neighboring gene MPRA-validated peak5488 silencer Neighboring gene family with sequence similarity 13 member B Neighboring gene ReSE screen-validated silencer GRCh37_chr5:137338418-137338597 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23190 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:137366081-137366582 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23191 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:137367957-137368840 Neighboring gene uncharacterized LOC124901077 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23192 Neighboring gene FAM13B antisense RNA 1 Neighboring gene RNA, U6 small nuclear 1148, pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Identification and characterization of a novel polycystin family member, polycystin-L2, in mouse and human: sequence, expression, alternative splicing, and chromosomal localization. Guo L, et al. Genomics, 2000 Mar 15. PMID 10756092
    2. The calcium-binding EF-hand in polycystin-L is not a domain for channel activation and ensuing inactivation. Li Q, et al. FEBS Lett, 2002 Apr 10. PMID 11959145
    3. Genes homologous to the autosomal dominant polycystic kidney disease genes (PKD1 and PKD2). Veldhuisen B, et al. Eur J Hum Genet, 1999 Dec. PMID 10602361
    4. Polycystin channels and kidney disease. Stayner C, et al. Trends Pharmacol Sci, 2001 Nov. PMID 11698076
    5. Architecture of the human interactome defines protein communities and disease networks. Huttlin EL, et al. Nature, 2017 May 25. PMID 28514442, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    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 GOA

    Function Evidence Code Pubs
    enables calcium channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in calcium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in detection of mechanical stimulus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    polycystin-2-like protein 2
    Names
    polycystic kidney disease 2-like 2 protein
    polycystin-2L2
    polycystin-L2
    transient receptor potential cation channel subfamily P member 5

    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_001258448.2 → NP_001245377.1  polycystin-2-like protein 2 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has an alternate in-frame splice site in the central coding region and an additional exon in the 3' region, which results in an alternate translation stop codon, compared to variant 1. The resulting isoform (2) is shorter; it lacks an internal segment and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC106753, AC106791, AK301924, BG719682
      Consensus CDS
      CCDS58972.1
      UniProtKB/Swiss-Prot
      Q9NZM6
      Related
      ENSP00000425513.1, ENST00000502810.5
      Conserved Domains (1) summary
      cl27887
      Location:76 → 475
      PKD_channel; Polycystin cation channel

    2. NM_001258449.2 → NP_001245378.1  polycystin-2-like protein 2 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks two alternate in-frame exons in the central coding region, contains an alternate segment in the 3' region, which results in an alternate translation stop codon, compared to variant 1. The resulting isoform (3) is shorter; it lacks an internal segment and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC106753, BC044581
      Consensus CDS
      CCDS58971.1
      UniProtKB/Swiss-Prot
      Q9NZM6
      Related
      ENSP00000423382.1, ENST00000508638.5
      Conserved Domains (1) summary
      cl27887
      Location:76 → 382
      PKD_channel; Polycystin cation channel

    3. NM_001300921.2 → NP_001287850.1  polycystin-2-like protein 2 isoform 4

      See identical proteins and their annotated locations for NP_001287850.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (4) is longer and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC106753, AF182034, BG721989
      Consensus CDS
      CCDS78062.1
      UniProtKB/Swiss-Prot
      A6NK98, B4DXD2, E9PC91, E9PDG4, Q86YB4, Q9NZM6, Q9UNJ0
      Related
      ENSP00000424725.1, ENST00000508883.6
      Conserved Domains (1) summary
      cl27887
      Location:76 → 497
      PKD_channel; Polycystin cation channel

    4. NM_014386.4 → NP_055201.2  polycystin-2-like protein 2 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes isoform 1 of 602aa.
      Source sequence(s)
      AC106753, AF118125, BG721989
      Consensus CDS
      CCDS43367.1
      UniProtKB/Swiss-Prot
      Q9NZM6
      Related
      ENSP00000290431.5, ENST00000290431.5
      Conserved Domains (2) summary
      pfam08016
      Location:76 → 497
      PKD_channel; Polycystin cation channel
      pfam09805
      Location:513 → 593
      Nop25; Nucleolar protein 12 (25kDa)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      137889457..137942747
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017009343.3 → XP_016864832.1  polycystin-2-like protein 2 isoform X1

    2. XM_017009345.3 → XP_016864834.1  polycystin-2-like protein 2 isoform X4

    3. XM_011543318.4 → XP_011541620.1  polycystin-2-like protein 2 isoform X2

      UniProtKB/Swiss-Prot
      Q9NZM6
      Conserved Domains (2) summary
      pfam08016
      Location:42 → 463
      PKD_channel; Polycystin cation channel
      pfam09805
      Location:479 → 559
      Nop25; Nucleolar protein 12 (25kDa)

    4. XM_017009344.3 → XP_016864833.1  polycystin-2-like protein 2 isoform X3

      Conserved Domains (2) summary
      pfam08016
      Location:16 → 437
      PKD_channel; Polycystin cation channel
      pfam09805
      Location:453 → 533
      Nop25; Nucleolar protein 12 (25kDa)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      138415893..138469143
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054352379.1 → XP_054208354.1  polycystin-2-like protein 2 isoform X1

    2. XM_054352383.1 → XP_054208358.1  polycystin-2-like protein 2 isoform X4

    3. XM_054352381.1 → XP_054208356.1  polycystin-2-like protein 2 isoform X5

    4. XM_054352380.1 → XP_054208355.1  polycystin-2-like protein 2 isoform X2

    5. XM_054352382.1 → XP_054208357.1  polycystin-2-like protein 2 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NZM6.2 GenPept UniProtKB/Swiss-Prot:Q9NZM6

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