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TRIM59-IFT80 TRIM59-IFT80 readthrough (NMD candidate) [ Homo sapiens (human) ]

Gene ID: 100174949, updated on 10-Oct-2023

Summary

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Official Symbol
TRIM59-IFT80provided by HGNC
Official Full Name
TRIM59-IFT80 readthrough (NMD candidate)provided by HGNC
Primary source
HGNC:HGNC:56756
See related
Ensembl:ENSG00000248710
Gene type
ncRNA
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
IFT80-L
Summary
This locus represents naturally occurring readthrough transcription between the neighboring TRIM59 (tripartite motif containing 59) and IFT80 (intraflagellar transport 80) genes on chromosome 3. The readthrough transcript is unlikely to produce a protein product. [provided by RefSeq, Jun 2017]
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Genomic context

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Location:
3q25.33
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (160227454..160485747, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (163002051..163260360, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (159945241..160203535, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene IL12A antisense RNA 1 Neighboring gene uncharacterized LOC124906252 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:159756960-159757562 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:159794247-159794746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:159815928-159816428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:159816429-159816929 Neighboring gene Sharpr-MPRA regulatory region 6612 Neighboring gene bromodomain containing 7 pseudogene 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:159896251-159896847 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:159896848-159897443 Neighboring gene Sharpr-MPRA regulatory region 14309 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14854 Neighboring gene chromosome 3 open reading frame 80 Neighboring gene intraflagellar transport 80 Neighboring gene ribosomal protein L35a pseudogene 10 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:160117119-160117481 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14855 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:160149190-160150389 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:160166710-160167230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20758 Neighboring gene microRNA 16-2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:160167750-160168269 Neighboring gene microRNA 15b Neighboring gene structural maintenance of chromosomes 4 Neighboring gene beta-1,3-glucuronyltransferase 3 pseudogene 1 Neighboring gene tripartite motif containing 59 Neighboring gene RNA, U7 small nuclear 136 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14856 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14857 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:160283422-160284621 Neighboring gene karyopherin subunit alpha 4 Neighboring gene small Cajal body-specific RNA 7 Neighboring gene keratin 8 pseudogene 12

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. Identification and characterization of a long isoform of human IFT80, IFT80-L. Huang W, et al. Biochem Biophys Res Commun, 2008 Sep 5. PMID 18601909
  2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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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)

Genotypes

General gene information

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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.

RNA

  1. NR_148401.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC024221, AC079594, BC068444
    Related
    ENST00000483754.1

  2. NR_148402.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC024221, AC079594

  3. NR_148403.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC024221, AC079594

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    160227454..160485747 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    163002051..163260360 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Molecular Biology Databases