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LINC01007 long intergenic non-protein coding RNA 1007 [ Homo sapiens (human) ]

Gene ID: 100506527, updated on 10-Oct-2023

Summary

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Official Symbol
LINC01007provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 1007provided by HGNC
Primary source
HGNC:HGNC:48973
See related
Ensembl:ENSG00000233123 AllianceGenome:HGNC:48973
Gene type
ncRNA
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Expression
Restricted expression toward brain (RPKM 2.3) See more
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Genomic context

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Location:
7q22.1
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (101562755..101569006, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (102882655..102888905, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (101206035..101212286, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18483 Neighboring gene E2F1 mRNA stabilizing lncRNA Neighboring gene intraflagellar transport 22 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18484 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101015900-101016438 Neighboring gene collagen type XXVI alpha 1 chain Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101029559-101030174 Neighboring gene Sharpr-MPRA regulatory region 586 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:101041899-101042500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101044285-101044812 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101054568-101055111 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:101063681-101064232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:101064233-101064784 Neighboring gene NANOG hESC enhancer GRCh37_chr7:101065582-101066107 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101079627-101080270 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101080271-101080912 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:101081787-101082746 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101104635-101105147 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101128605-101129258 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101129259-101129911 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101137182-101137752 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101137753-101138322 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101146871-101147560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101147561-101148250 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101150569-101151328 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101185407-101186075 Neighboring gene Sharpr-MPRA regulatory region 7535 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:101207140-101208002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:101208003-101208864 Neighboring gene uncharacterized LOC107986832 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101241532-101242460 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101242461-101243388 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18486 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101257215-101258142 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101258143-101259071 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:101259072-101259999 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:101262113-101262652 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:101262653-101263192 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101267192-101268119 Neighboring gene myosin light chain 10

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. Large-scale concatenation cDNA sequencing. Yu W, et al. Genome Res, 1997 Apr. PMID 9110174, Free PMC Article
  2. A "double adaptor" method for improved shotgun library construction. Andersson B, et al. Anal Biochem, 1996 Apr 5. PMID 8619474
  3. Toward a complete human genome sequence. Sanger Center, et al. Genome Res, 1998 Nov. PMID 9847074
  4. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
  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

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

General gene information

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Markers

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_103747.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript.
    Source sequence(s)
    AC004953, AF131787, BC027906
    Related
    ENST00000434537.2

  2. NR_103748.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in its 3' terminal exon, compared to variant 1.
    Source sequence(s)
    AC004953, AF131787
    Related
    ENST00000437900.1

  3. NR_103749.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains alternate 3' exon structure, compared to variant 1.
    Source sequence(s)
    AF131787, DA533941
    Related
    ENST00000451953.1

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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    101562755..101569006 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    102882655..102888905 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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