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    LINC03040 long intergenic non-protein coding RNA 3040 [ Homo sapiens (human) ]

    Gene ID: 221416, updated on 10-Dec-2024

    Summary

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    Official Symbol
    LINC03040provided by HGNC
    Official Full Name
    long intergenic non-protein coding RNA 3040provided by HGNC
    Primary source
    HGNC:HGNC:28692
    See related
    Ensembl:ENSG00000181577 AllianceGenome:HGNC:28692
    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
    C6orf223
    Expression
    Biased expression in lung (RPKM 1.6), duodenum (RPKM 0.5) and 11 other tissues See more
    Orthologs
    all
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    Genomic context

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    See LINC03040 in Genome Data Viewer
    Location:
    6p21.1
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (44000585..44007612)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (43832289..43839314)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (43968322..43975349)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375070 Neighboring gene long intergenic non-protein coding RNA 1512 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43878694-43879258 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43879259-43879821 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43880895-43881684 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24622 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43893291-43894024 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43911713-43912238 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43918399-43919384 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43932755-43933254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24623 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43952691-43953286 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43957693-43958202 Neighboring gene uncharacterized LOC124901321 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43961654-43962154 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24624 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43972319-43972950 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:43977969-43979168 Neighboring gene stem cell inhibitory RNA transcript Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:44007317-44008074 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:44009776-44010524 Neighboring gene Sharpr-MPRA regulatory region 2143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24625 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44019358-44019952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44022316-44022816 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24626 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:44030458-44031420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24627 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24628 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17247 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17248 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24629 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24630 Neighboring gene Sharpr-MPRA regulatory region 9341 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91788 Neighboring gene Sharpr-MPRA regulatory region 15428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44069931-44070480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44070481-44071029 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91802 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91811 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44075151-44075650 Neighboring gene ribosomal protein L29 pseudogene 16 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91827 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91835 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91840 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17250 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17251 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17252 Neighboring gene mitochondrial ribosomal protein L14 Neighboring gene transmembrane protein 63B

    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. Identification of cis- and trans-acting genetic variants explaining up to half the variation in circulating vascular endothelial growth factor levels. Debette S, et al. Circ Res, 2011 Aug 19. PMID 21757650, Free PMC Article
    2. RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination. Choudhury NR, et al. BMC Biol, 2017 Nov 8. PMID 29117863, Free PMC Article
    3. A reference map of the human binary protein interactome. Luck K, et al. Nature, 2020 Apr. PMID 32296183, Free PMC Article
    4. 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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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Identification of cis- and trans-acting genetic variants explaining up to half the variation in circulating vascular endothelial growth factor levels.
    EBI GWAS Catalog

    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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    Homology

    Other Names

    • uncharacterized protein C6orf223

    Clone Names

    • MGC45491

    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_160954.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL109615
      Related
      ENST00000336600.7

    2. NR_160955.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL109615

    3. NR_160956.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL109615

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      44000585..44007612
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      43832289..43839314
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001171992.2: Suppressed sequence

      Description
      NM_001171992.2: This RefSeq was removed because it is now thought that this gene does not encode a protein.

    2. NM_001324369.1: Suppressed sequence

      Description
      NM_001324369.1: This RefSeq was removed because it is now thought that this gene does not encode a protein.

    3. NM_153246.6: Suppressed sequence

      Description
      NM_153246.6: This RefSeq was removed because it is now thought that this gene does not encode a protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N319.2 GenPept UniProtKB/Swiss-Prot:Q8N319

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