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SYNJ2BP-COX16 SYNJ2BP-COX16 readthrough [ Homo sapiens (human) ]

Gene ID: 100529257, updated on 17-Sep-2024

Summary

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Official Symbol
SYNJ2BP-COX16provided by HGNC
Official Full Name
SYNJ2BP-COX16 readthroughprovided by HGNC
Primary source
HGNC:HGNC:48350
See related
Ensembl:ENSG00000258644 AllianceGenome:HGNC:48350
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 read-through transcription between the neighboring SYNJ2BP (synaptojanin 2 binding protein) and COX16 (COX16 cytochrome c oxidase assembly homolog (S. cerevisiae)) genes on chromosome 14. The read-through transcript produces a fusion protein that shares sequence identity with each individual gene product. Alternate splicing results in multiple transcript variants that encode different isoforms. [provided by RefSeq, Feb 2011]
Expression
Ubiquitous expression in kidney (RPKM 44.4), duodenum (RPKM 43.6) and 25 other tissues See more
Orthologs
all
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Genomic context

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See SYNJ2BP-COX16 in Genome Data Viewer
Location:
14q24.2
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (70325081..70417090, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (64531030..64623200, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (70791798..70883807, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928046 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5886 Neighboring gene uncharacterized LOC105370552 Neighboring gene ADAM metallopeptidase domain 21 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:70755991-70756492 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:70768308-70768998 Neighboring gene uncharacterized LOC124903340 Neighboring gene cytochrome c oxidase assembly factor COX16 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:70816287-70817486 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8651 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8652 Neighboring gene RNA, U2 small nuclear 51, pseudogene Neighboring gene synaptojanin 2 binding protein Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:70866018-70866578 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:70883594-70884793 Neighboring gene uncharacterized LOC124903339 Neighboring gene MPRA-validated peak2189 silencer Neighboring gene ADAM metallopeptidase domain 21 Neighboring gene ADAM metallopeptidase domain 20 pseudogene 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 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. Gene-age interactions in blood pressure regulation: a large-scale investigation with the CHARGE, Global BPgen, and ICBP Consortia. Simino J, et al. Am J Hum Genet, 2014 Jul 3. PMID 24954895, 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. Global Interactome Mapping of Mitochondrial Intermembrane Space Proteases Identifies a Novel Function for HTRA2. Botham A, et al. Proteomics, 2019 Dec. PMID 31617661
  4. HDLBP Promotes Hepatocellular Carcinoma Proliferation and Sorafenib Resistance by Suppressing Trim71-dependent RAF1 Degradation. Yuan J, et al. Cell Mol Gastroenterol Hepatol, 2023. PMID 36244648, Free PMC Article
  5. A proximity-dependent biotinylation map of a human cell. Go CD, et al. Nature, 2021 Jul. PMID 34079125

See all (6) 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
Gene-age interactions in blood pressure regulation: a large-scale investigation with the CHARGE, Global BPgen, and ICBP Consortia.
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

General protein information

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Preferred Names
SYNJ2BP-COX16 protein

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_001202547.2 → NP_001189476.1  SYNJ2BP-COX16 protein isoform 1

    See identical proteins and their annotated locations for NP_001189476.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AL356804, FY210787
    Conserved Domains (3) summary
    COG0265
    Location:16 → 77
    DegQ; Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
    cd00992
    Location:13 → 97
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    pfam14138
    Location:133 → 173
    COX16; Cytochrome c oxidase assembly protein COX16

  2. NM_001202548.2 → NP_001189477.1  SYNJ2BP-COX16 protein isoform 2

    See identical proteins and their annotated locations for NP_001189477.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has multiple differences in the coding region but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AL356804, FY213836
    UniProtKB/TrEMBL
    A0A087WYV9, A0A087X1F5
    Related
    ENSP00000482133.1, ENST00000621525.4
    Conserved Domains (3) summary
    COG0265
    Location:16 → 77
    DegQ; Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
    cd00992
    Location:13 → 97
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    pfam14138
    Location:100 → 164
    COX16; Cytochrome c oxidase assembly protein COX16

  3. NM_001202549.2 → NP_001189478.1  SYNJ2BP-COX16 protein isoform 3

    See identical proteins and their annotated locations for NP_001189478.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AL356804, FY213292
    UniProtKB/TrEMBL
    A0A087X1F5
    Related
    ENSP00000484161.1, ENST00000617124.4
    Conserved Domains (2) summary
    cd00992
    Location:13 → 97
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    pfam14138
    Location:98 → 140
    COX16; Cytochrome c oxidase assembly protein COX16

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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    70325081..70417090 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    64531030..64623200 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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