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PMF1-BGLAP PMF1-BGLAP readthrough [ Homo sapiens (human) ]

Gene ID: 100527963, updated on 3-Dec-2023

Summary

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Official Symbol
PMF1-BGLAPprovided by HGNC
Official Full Name
PMF1-BGLAP readthroughprovided by HGNC
Primary source
HGNC:HGNC:42953
See related
Ensembl:ENSG00000260238 AllianceGenome:HGNC:42953
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
PMF1; PMF-1
Summary
This locus represents naturally occurring read-through transcription between the neighboring PMF1 (polyamine-modulated factor 1) and BGLAP (bone gamma-carboxyglutamate Gla protein) genes on chromosome 1. Alternative splicing results in multiple transcript variants encoding isoforms that share sequence identity with the upstream gene product, but they contain distinct C-termini due to frameshifts versus the downstream gene coding sequence. [provided by RefSeq, Dec 2010]
Expression
Ubiquitous expression in thyroid (RPKM 18.8), bone marrow (RPKM 17.3) and 25 other tissues See more
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Genomic context

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Location:
1q22
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (156212988..156243332)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (155351442..155381789)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (156182779..156213123)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900449 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1851 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1853 Neighboring gene solute carrier family 25 member 44 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1854 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1855 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1856 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1422 Neighboring gene polyamine modulated factor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1857 Neighboring gene BGLAP promoter region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1423 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1424 Neighboring gene Sharpr-MPRA regulatory region 3040 Neighboring gene bone gamma-carboxyglutamate protein Neighboring gene progestin and adipoQ receptor family member 6 Neighboring gene SMG5 nonsense mediated mRNA decay factor Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156250697-156251670 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1425 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:156252643-156253614 Neighboring gene Sharpr-MPRA regulatory regions 9834 and 13552 Neighboring gene transmembrane protein 79 Neighboring gene glycosylated lysosomal membrane protein

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. Meta-analysis of genome-wide association studies identifies 1q22 as a susceptibility locus for intracerebral hemorrhage. Woo D, et al. Am J Hum Genet, 2014 Apr 3. PMID 24656865, Free PMC Article
  2. 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
  3. A High-Density Map for Navigating the Human Polycomb Complexome. Hauri S, et al. Cell Rep, 2016 Oct 4. PMID 27705803
  4. Integrative oncogene-dependency mapping identifies RIT1 vulnerabilities and synergies in lung cancer. Vichas A, et al. Nat Commun, 2021 Aug 9. PMID 34373451, Free PMC Article
  5. RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination. Choudhury NR, et al. BMC Biol, 2017 Nov 8. PMID 29117863, Free PMC Article

See all (8) citations in PubMed

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

EBI GWAS Catalog

Description
Meta-analysis of genome-wide association studies identifies 1q22 as a susceptibility locus for intracerebral hemorrhage.
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

Readthrough PMF1-BGLAP

Included genes: BGLAP, PMF1

Homology

Clone Names

  • FLJ12287

General protein information

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Preferred Names
PMF1-BGLAP protein
Names
polyamine-modulated factor 1

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_001199661.1 → NP_001186590.1  PMF1-BGLAP protein isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AL135927, CD388852
    UniProtKB/Swiss-Prot
    Q6P1K2
    Related
    ENSP00000357259.4, ENST00000368276.8
    Conserved Domains (1) summary
    pfam03980
    Location:71 → 127
    Nnf1; Nnf1

  2. NM_001199662.1 → NP_001186591.1  PMF1-BGLAP protein isoform 2

    See identical proteins and their annotated locations for NP_001186591.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site that causes a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AL135927, CD049192
    UniProtKB/TrEMBL
    U3KQ54
    Related
    ENSP00000475561.1, ENST00000490491.5
    Conserved Domains (1) summary
    pfam03980
    Location:71 → 169
    Nnf1; Nnf1

  3. NM_001199663.1 → NP_001186592.1  PMF1-BGLAP protein isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1.
    Source sequence(s)
    AL135927, BC033656
    UniProtKB/Swiss-Prot
    Q6P1K2
    Related
    ENSP00000324909.5, ENST00000320139.5
    Conserved Domains (1) summary
    pfam03980
    Location:71 → 128
    Nnf1; Nnf1

  4. NM_001199664.1 → NP_001186593.1  PMF1-BGLAP protein isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks two exons in the central region and uses an alternate splice site that causes a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (4) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AL135927, FY213424
    UniProtKB/TrEMBL
    A0A087WT04
    Related
    ENSP00000458021.2, ENST00000567140.3
    Conserved Domains (1) summary
    pfam03980
    Location:59 → 100
    Nnf1; Nnf1

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
    156212988..156243332
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    155351442..155381789
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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