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

    Gene ID: 57653, updated on 10-Oct-2023

    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_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (97238426..97377295)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (109410229..109549254)
    105.20220307 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
    • 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_2023_10

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Molecular Biology Databases
    Research Materials