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PCNX2 pecanex 2 [ Homo sapiens (human) ]

Gene ID: 80003, updated on 3-Apr-2024

Summary

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Official Symbol
PCNX2provided by HGNC
Official Full Name
pecanex 2provided by HGNC
Primary source
HGNC:HGNC:8736
See related
Ensembl:ENSG00000135749 MIM:617656; AllianceGenome:HGNC:8736
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
PCNXL2
Summary
This gene contains coding mononucleotide repeats that are associated with tumors of high mcrosatellite instability (MSI-H). Defects in this gene are involved in the tumorigenesis of MSI-H colorectal carcinomas. [provided by RefSeq, Jun 2016]
Expression
Ubiquitous expression in brain (RPKM 5.2), ovary (RPKM 2.2) and 22 other tissues See more
Orthologs
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Genomic context

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Location:
1q42.2
Exon count:
40
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (232983435..233327329, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (232369777..232713706, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (233119181..233431471, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373201 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2733 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:233059320-233060519 Neighboring gene uncharacterized LOC107985361 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:233086091-233086632 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:233086633-233087172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:233088301-233088800 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:233113500-233114699 Neighboring gene nucleoside-triphosphatase, cancer-related Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:233215157-233215658 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:233215659-233216158 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:233250348-233251547 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:233264306-233264818 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:233264819-233265329 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:233314891-233316090 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:233370205-233370728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:233370729-233371250 Neighboring gene Sharpr-MPRA regulatory region 15021 Neighboring gene MPRA-validated peak771 silencer Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:233393606-233394805 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2738 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2739 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2740 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:233421783-233422284 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:233422285-233422784 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2741 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1959 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1960 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:233463573-233463724 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1962 Neighboring gene ribosomal protein S7 pseudogene 3 Neighboring gene mitogen-activated protein kinase kinase kinase 21 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:233507364-233507864 Neighboring gene RNA, U4 small nuclear 77, 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
  • 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. In silico functional and tumor suppressor role of hypothetical protein PCNXL2 with regulation of the Notch signaling pathway. Naveed M, et al. RSC Adv, 2018 Jun 8. PMID 35539910, Free PMC Article
  2. Genetic polymorphisms in the PCNXL2 gene are risk factors for thyroid cancer in the Chinese population. Hao R, et al. Future Oncol, 2021 Dec. PMID 34747634
  3. Identification of MARCKS, FLJ11383 and TAF1B as putative novel target genes in colorectal carcinomas with microsatellite instability. Kim NG, et al. Oncogene, 2002 Aug 1. PMID 12140758
  4. Transferability of type 2 diabetes implicated loci in multi-ethnic cohorts from Southeast Asia. Sim X, et al. PLoS Genet, 2011 Apr. PMID 21490949, Free PMC Article
  5. Genome-wide contribution of genotype by environment interaction to variation of diabetes-related traits. Zheng JS, et al. PLoS One, 2013. PMID 24204828, Free PMC Article

See all (17) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Genetic polymorphisms in the PCNXL2 gene are risk factors for thyroid cancer in the Chinese population.
    Title: Genetic polymorphisms in the PCNXL2 gene are risk factors for thyroid cancer in the Chinese population.
  2. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  3. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
  4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  5. Identification of MARCKS, FLJ11383 and TAF1B as putative novel target genes in colorectal carcinomas with microsatellite instability.
    Title: Identification of MARCKS, FLJ11383 and TAF1B as putative novel target genes in colorectal carcinomas with microsatellite instability.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide contribution of genotype by environment interaction to variation of diabetes-related traits.
EBI GWAS Catalog
Transferability of type 2 diabetes implicated loci in multi-ethnic cohorts from Southeast Asia.
EBI GWAS Catalog

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

Clone Names

  • FLJ11383, KIAA0435

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
Component Evidence Code Pubs
is_active_in cellular_component ND
No biological Data available
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
pecanex-like protein 2
Names
pecanex homolog 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.

Genomic

  1. NG_050912.2 RefSeqGene

    Range
    36604..348894
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001328607.3 → NP_001315536.1  pecanex-like protein 2 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate exon in place of all but the first exon compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AL133380

  2. NM_014801.4 → NP_055616.3  pecanex-like protein 2 isoform 1

    See identical proteins and their annotated locations for NP_055616.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK021445, AK055374, AK074078, AK097229, AL122003, AL133380, AL139342, CT004972, DR731333
    Consensus CDS
    CCDS44335.1
    UniProtKB/Swiss-Prot
    A6NKB5, O43162, Q5T9Z8, Q5TDF1, Q8TEP4, Q96HP9, Q9HAL8
    Related
    ENSP00000258229.8, ENST00000258229.14
    Conserved Domains (1) summary
    pfam05041
    Location:1619 → 1843
    Pecanex_C; Pecanex protein (C-terminus)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    232983435..233327329 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047430870.1 → XP_047286826.1  pecanex-like protein 2 isoform X1

  2. XM_047430871.1 → XP_047286827.1  pecanex-like protein 2 isoform X2

  3. XM_011544278.3 → XP_011542580.2  pecanex-like protein 2 isoform X4

  4. XM_047430873.1 → XP_047286829.1  pecanex-like protein 2 isoform X6

  5. XM_047430872.1 → XP_047286828.1  pecanex-like protein 2 isoform X3

  6. XM_006711816.4 → XP_006711879.1  pecanex-like protein 2 isoform X5

    Conserved Domains (1) summary
    pfam07263
    Location:472 → 641
    DMP1; Dentin matrix protein 1 (DMP1)

RNA

  1. XR_001737430.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    232369777..232713706 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054338848.1 → XP_054194823.1  pecanex-like protein 2 isoform X1

  2. XM_054338849.1 → XP_054194824.1  pecanex-like protein 2 isoform X2

  3. XM_054338851.1 → XP_054194826.1  pecanex-like protein 2 isoform X4

  4. XM_054338853.1 → XP_054194828.1  pecanex-like protein 2 isoform X7

  5. XM_054338850.1 → XP_054194825.1  pecanex-like protein 2 isoform X3

  6. XM_054338852.1 → XP_054194827.1  pecanex-like protein 2 isoform X5

RNA

  1. XR_008486166.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_024938.2: Suppressed sequence

    Description
    NM_024938.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
A6NKB5.3 GenPept UniProtKB/Swiss-Prot:A6NKB5

Gene LinkOut

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