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

    Gene ID: 100529257, updated on 4-Jan-2025

    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: 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

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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)

    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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