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PKD1L2 polycystin 1 like 2 (gene/pseudogene) [ Homo sapiens (human) ]

Gene ID: 114780, updated on 27-Dec-2024

Summary

Official Symbol
PKD1L2provided by HGNC
Official Full Name
polycystin 1 like 2 (gene/pseudogene)provided by HGNC
Primary source
HGNC:HGNC:21715
See related
Ensembl:ENSG00000166473 MIM:607894; AllianceGenome:HGNC:21715
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PC1L2
Summary
This gene encodes a member of the polycystin protein family. This protein may function as a G-protein-coupled component or regulator of cation channel pores. The long isoform of this protein contains 11 transmembrane domains, a latrophilin/CL-1-like GPCR proteolytic site (GPS) domain, and a polycystin-1, lipoxygenase, alpha-toxin (PLAT) domain. Alternative splicing results in multiple transcript variants encoding distinct isoforms. This gene is a polymorphic pseudogene in humans. [provided by RefSeq, May 2022]
Annotation information
Annotation category: suggests misassembly
Note: Genetic polymorphisms result in both protein coding and non-coding alleles of this gene.
Expression
Biased expression in fat (RPKM 3.7), heart (RPKM 1.2) and 7 other tissues See more
Orthologs
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Genomic context

See PKD1L2 in Genome Data Viewer
Location:
16q23.2
Exon count:
43
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (81100875..81220394, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (87162065..87281147, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (81134480..81253999, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371361 Neighboring gene chromosome 16 open reading frame 46 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11176 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81110606-81111266 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81111267-81111925 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7751 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7752 Neighboring gene RNA, U6 small nuclear 1191, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81150474-81151032 Neighboring gene glycine cleavage system protein H Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81171151-81171768 Neighboring gene Sharpr-MPRA regulatory region 3111 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:81191716-81192216 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:81246022-81246522 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:81255488-81255706 Neighboring gene beta-carotene oxygenase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11178 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7753 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7754 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7755 Neighboring gene gigaxonin Neighboring gene microRNA 4720

Genomic regions, transcripts, and products

Expression

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

Description
Conduct disorder and ADHD: evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study.
EBI GWAS Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of polycystic kidney disease 1-like 2 (PKD1L2) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

General gene information

Clone Names

  • FLJ45333, DKFZp686J19100

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium channel activity  
enables calcium ion binding  
enables carbohydrate binding  
Component Evidence Code Pubs
is_active_in membrane  

General protein information

Preferred Names
polycystin-1-like protein 2
Names
PC1-like 2 protein
polycystic kidney disease 1-like 2
polycystin-1L2

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.

Genomic

  1. NG_033236.2 RefSeqGene

    Range
    5001..124542
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001076780.3NP_001070248.2  polycystin-1-like protein 2 isoform c precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks several 3' exons but includes an alternate 3' exon, and it thus differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (c) is shorter and has a distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AC092718, AC131888
  2. NM_001278423.2NP_001265352.1  polycystin-1-like protein 2 isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks several 5' and 3' exons but includes alternate 5' and 3' exons, and it thus differs in both UTRs, uses a downstream in-frame start codon and has an alternate 3' coding region, compared to variant 1. The encoded isoform (e) is shorter and has a distinct C-terminus, compared to isoform a.
    Source sequence(s)
    BC004562, DA326413
    Consensus CDS
    CCDS61999.1
    UniProtKB/Swiss-Prot
    Q7Z442
  3. NM_001278425.3NP_001265354.2  polycystin-1-like protein 2 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4, also known as short form) lacks several 5' exons but includes an alternate 5' exon, and it thus differs in the 5' UTR and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (d) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    ABBA01016982, AC092718, KF459692
    UniProtKB/TrEMBL
    A0AAG2UWM0
  4. NM_052892.5NP_443124.4  polycystin-1-like protein 2 isoform a precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1, also known as long form) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    ABBA01016982, AC092718, AC131888, KF459692
    UniProtKB/TrEMBL
    A0AAG2UWR4

RNA

  1. NR_126532.3 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1, non-coding), which represents the non-functional allele of this polymorphic pseudogene, has an indel that results in a frameshift to a premature termination codon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC092718, AC131888, AK131378, KF459692
    Related
    ENST00000525539.5

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    81100875..81220394 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791800.1 Reference GRCh38.p14 PATCHES

    Range
    149114..268655 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    87162065..87281147 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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