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CNPY3-GNMT CNPY3-GNMT readthrough [ Homo sapiens (human) ]

Gene ID: 107080644, updated on 10-Oct-2023

Summary

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Gene symbol
CNPY3-GNMT
Gene description
CNPY3-GNMT readthrough
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
Summary
This locus represents naturally occurring readthrough transcription between the upstream CNPY3 (canopy FGF signaling regulator 3) and the downstream GNMT (glycine N-methyltransferase) genes. Readthrough transcripts may encode proteins that have amino acid similarity with proteins encoded by both individual genes. [provided by RefSeq, Jan 2016]
Expression
Broad expression in liver (RPKM 49.8), pancreas (RPKM 18.8) and 19 other tissues See more
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Genomic context

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Location:
6p21.1
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (42929480..42963880)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (42758548..42793018)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (42897218..42931618)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24575 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24576 Neighboring gene chromosome 6 open reading frame 226 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17209 Neighboring gene pre T cell antigen receptor alpha Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:42896611-42897112 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:42897113-42897614 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:42906342-42906844 Neighboring gene canopy FGF signaling regulator 3 Neighboring gene long intergenic non-protein coding RNA 2976 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:42928211-42928712 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24581 Neighboring gene RPL24 pseudogene 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:42935679-42935875 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:42938260-42939130 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:42939131-42939999 Neighboring gene glycine N-methyltransferase Neighboring gene peroxisomal biogenesis factor 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:42946179-42947120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24582 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:42947525-42947721 Neighboring gene uncharacterized LOC124900215 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:42948960-42949178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24583 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17211 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17212 Neighboring gene Sharpr-MPRA regulatory region 14905 Neighboring gene protein phosphatase 2 regulatory subunit B'delta Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:42979352-42979852 Neighboring gene male-enhanced antigen 1

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. Expression of conjoined genes: another mechanism for gene regulation in eukaryotes. Prakash T, et al. PLoS One, 2010 Oct 12. PMID 20967262, Free PMC Article

GeneRIFs: Gene References Into Functions

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

Genotypes

General gene information

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Readthrough CNPY3-GNMT

Included genes: CNPY3, GNMT

General protein information

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Preferred Names
Glycine N-methyltransferase-like

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_001318856.2 → NP_001305785.1  Glycine N-methyltransferase-like isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains an alternate exon in the 3' gene region and initiates translation at an alternate start codon compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AI074613, AL035587, BQ947041, FY210916
    Conserved Domains (1) summary
    pfam12847
    Location:6 → 111
    Methyltransf_18; Methyltransferase domain

  2. NM_001318857.2 → NP_001305786.1  Glycine N-methyltransferase-like isoform 1 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AI074613, AL035587, FY210916
    Conserved Domains (1) summary
    pfam12847
    Location:52 → 116
    Methyltransf_18; Methyltransferase domain

  3. NM_001318858.2 → NP_001305787.1  Glycine N-methyltransferase-like isoform 3 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' gene region compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AI074613, AL035587, FY213777

RNA

  1. NR_134890.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) contains an alternate exon in the 5' gene region and lacks an exon in the 3' gene region 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)
    AI074613, AL035587, FY210916, FY213816

  2. NR_134891.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks an exon in the 3' gene region 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)
    AI074613, AL035587, FY213370

  3. NR_134892.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) contains an alternate exon and lacks an exon in the 3' gene region 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)
    AI074613, AL035587, BQ947041, FY210916

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    42929480..42963880
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    42758548..42793018
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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