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    C16orf89 chromosome 16 open reading frame 89 [ Homo sapiens (human) ]

    Gene ID: 146556, updated on 10-Dec-2024

    Summary

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    Official Symbol
    C16orf89provided by HGNC
    Official Full Name
    chromosome 16 open reading frame 89provided by HGNC
    Primary source
    HGNC:HGNC:28687
    See related
    Ensembl:ENSG00000153446 AllianceGenome:HGNC:28687
    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 gene is expressed predominantly in the thyroid. Based on expression patterns similar to thyroid transcription factors and proteins, this gene may function in the development and function of the thyroid. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
    Expression
    Biased expression in thyroid (RPKM 83.5), lung (RPKM 41.7) and 7 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See C16orf89 in Genome Data Viewer
    Location:
    16p13.3
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (5042772..5065956, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (5072272..5095444, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (5094123..5115957, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:5008323-5008858 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:5019509-5020008 Neighboring gene Sharpr-MPRA regulatory region 439 Neighboring gene SEC14 like lipid binding 5 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:5051228-5051419 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:5060637-5061160 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:5061161-5061684 Neighboring gene Sharpr-MPRA regulatory region 11332 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:5078448-5079647 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:5083173-5083674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10347 Neighboring gene NAGPA antisense RNA 1 Neighboring gene N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase Neighboring gene Sharpr-MPRA regulatory region 9075 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10348 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10349 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10350 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:5132135-5132636 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:5132637-5133136 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:5134229-5135141 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:5139758-5140258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:5140259-5140759 Neighboring gene ALG1 chitobiosyldiphosphodolichol beta-mannosyltransferase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:5145374-5145926 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:5147415-5148040 Neighboring gene eukaryotic elongation factor 2 lysine methyltransferase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7174 Neighboring gene uncharacterized LOC107984828 Neighboring gene ectonucleotide pyrophosphatase/phosphodiesterase 7 pseudogene 14

    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. Initial characterization of C16orf89, a novel thyroid-specific gene. Afink GB, et al. Thyroid, 2010 Jul. PMID 20578903
    2. A transcript finishing initiative for closing gaps in the human transcriptome. Sogayar MC, et al. Genome Res, 2004 Jul. PMID 15197164, Free PMC Article
    3. Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries. Otsuki T, et al. DNA Res, 2005. PMID 16303743
    4. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. Clark HF, et al. Genome Res, 2003 Oct. PMID 12975309, Free PMC Article
    5. Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. Bennett EJ, et al. Cell, 2010 Dec 10. PMID 21145461, Free PMC Article

    See all (10) 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

    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

    Clone Names

    • MGC45438

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein homodimerization activity IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular exosome HDA PubMed 
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    UPF0764 protein C16orf89

    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_030316.2 RefSeqGene

      Range
      5000..26834
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001098514.3 → NP_001091984.2  UPF0764 protein C16orf89 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001091984.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate acceptor splice site at the 3' terminal exon compared to variant 1. This results in a frame-shift and a shorter isoform (2) with a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC026458
      Consensus CDS
      CCDS45404.2
      UniProtKB/Swiss-Prot
      Q6UX73
      Related
      ENSP00000420566.2, ENST00000472572.8
      Conserved Domains (1) summary
      pfam15882
      Location:60 → 340
      DUF4735; Domain of unknown function (DUF4735)

    2. NM_152459.5 → NP_689672.4  UPF0764 protein C16orf89 isoform 1 precursor

      See identical proteins and their annotated locations for NP_689672.4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC026458
      Consensus CDS
      CCDS42116.2
      UniProtKB/Swiss-Prot
      B4DUM5, Q6UX73, Q8N2I3, Q8N4T1
      UniProtKB/TrEMBL
      A0A0A0MT71
      Related
      ENSP00000324672.5, ENST00000315997.5
      Conserved Domains (1) summary
      pfam15882
      Location:60 → 319
      DUF4735; Domain of unknown function (DUF4735)

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      5042772..5065956 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005255143.4 → XP_005255200.2  UPF0764 protein C16orf89 isoform X2

      Conserved Domains (1) summary
      pfam15882
      Location:60 → 318
      DUF4735; Domain of unknown function (DUF4735)

    2. XM_017022974.2 → XP_016878463.1  UPF0764 protein C16orf89 isoform X1

    3. XM_017022972.2 → XP_016878461.1  UPF0764 protein C16orf89 isoform X1

    4. XM_011522392.3 → XP_011520694.1  UPF0764 protein C16orf89 isoform X3

      Conserved Domains (2) summary
      pfam13900
      Location:137 → 184
      GVQW; Putative domain of unknown function
      pfam15882
      Location:1 → 133
      DUF4735; Domain of unknown function (DUF4735)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      5072272..5095444 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054379687.1 → XP_054235662.1  UPF0764 protein C16orf89 isoform X2

    2. XM_054379685.1 → XP_054235660.1  UPF0764 protein C16orf89 isoform X1

    3. XM_054379686.1 → XP_054235661.1  UPF0764 protein C16orf89 isoform X1

    4. XM_054379688.1 → XP_054235663.1  UPF0764 protein C16orf89 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6UX73.2 GenPept UniProtKB/Swiss-Prot:Q6UX73

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