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

Gene ID: 27039, updated on 2-Nov-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, Nov 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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