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

Gene ID: 146556, updated on 27-Nov-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
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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: 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. 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

Gene LinkOut

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