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SUGT1P4-STRA6LP-CCDC180 SUGT1P4-STRA6LP-CCDC180 readthrough [ Homo sapiens (human) ]

Gene ID: 57653, updated on 17-Sep-2024

Summary

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Official Symbol
SUGT1P4-STRA6LP-CCDC180provided by HGNC
Official Full Name
SUGT1P4-STRA6LP-CCDC180 readthroughprovided by HGNC
Primary source
HGNC:HGNC:53835
See related
Ensembl:ENSG00000255036 AllianceGenome:HGNC:53835
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
LOC100499484-C9ORF174
Summary
This locus represents a set of read-through transcripts spanning an upstream pseudogene (GeneID:100499484) extending into a downstream protein-coding locus (GeneID:100499483). All of the read-through transcripts are candidates for nonsense-mediated decay (NMD), so they are not thought to express a protein. [provided by RefSeq, Aug 2010]
Expression
Biased expression in testis (RPKM 13.8), lung (RPKM 2.2) and 11 other tissues See more
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Genomic context

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See SUGT1P4-STRA6LP-CCDC180 in Genome Data Viewer
Location:
9q22.33
Exon count:
51
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (97238426..97377295)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (109410229..109549254)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (100000708..100139577)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ankyrin repeat domain 18C, pseudogene Neighboring gene SUGT1P4-STRA6LP readthrough Neighboring gene uncharacterized LOC124902224 Neighboring gene NANOG hESC enhancer GRCh37_chr9:99994442-99995039 Neighboring gene Sharpr-MPRA regulatory region 7929 Neighboring gene vomeronasal 1 receptor 52 pseudogene Neighboring gene SUGT1 pseudogene 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:100033649-100034149 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:100057407-100057584 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20098 Neighboring gene Sharpr-MPRA regulatory region 563 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100074371-100074871 Neighboring gene STRA6 like, pseudogene Neighboring gene coiled-coil domain containing 180 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28658 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28659 Neighboring gene microRNA 1302-8 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100148028-100148534 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100148535-100149040 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:100150291-100150855 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28661 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:100161577-100161764 Neighboring gene uncharacterized LOC286359 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr9:100174359-100174860 and GRCh37_chr9:100174861-100175360 Neighboring gene tudor domain containing 7 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:100226535-100227734 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28663

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. Candidate gene/loci studies in cleft lip/palate and dental anomalies finds novel susceptibility genes for clefts. Vieira AR, et al. Genet Med, 2008 Sep. PMID 18978678, Free PMC Article
  2. Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. Nagase T, et al. DNA Res, 2000 Apr 28. PMID 10819331
  3. High-throughput analyses of hnRNP H1 dissects its multi-functional aspect. Uren PJ, et al. RNA Biol, 2016. PMID 26760575, Free PMC Article
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039
  5. 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

What's a GeneRIF?
  1. Observational study of gene-disease association. (HuGE Navigator)
    Title: Candidate gene/loci studies in cleft lip/palate and dental anomalies finds novel susceptibility genes for clefts.
Submit: New GeneRIF Correction

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)

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

Other Names

  • Behcet's Disease Associated Gene 1
  • LOC100499484-C9orf174 readthrough

Clone Names

  • KIAA1529, MGC131724

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_036527.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks three alternate exons, an internal segment, and uses an alternate splice site, compared to variant 1.
    Source sequence(s)
    AB040962, AL512590, AL590705
    Related
    ENST00000375206.6

  2. NR_036528.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript.
    Source sequence(s)
    AL512590, AL590705, BC144521
    Related
    ENST00000534123.5

  3. NR_036529.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks 7 alternate exons and an internal segment, compared to variant 1.
    Source sequence(s)
    AL512590, AL590705, BC144521, BC144522
    Related
    ENST00000532526.5

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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    97238426..97377295
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    109410229..109549254
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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