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LINC01854 long intergenic non-protein coding RNA 1854 [ Homo sapiens (human) ]

Gene ID: 151121, updated on 10-Oct-2023

Summary

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Official Symbol
LINC01854provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 1854provided by HGNC
Primary source
HGNC:HGNC:52670
See related
Ensembl:ENSG00000204460 AllianceGenome:HGNC:52670
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
Low expression observed in reference dataset See more
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Genomic context

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Location:
2q21.1
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (129242173..129273891, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (129670494..129702352, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (129999746..130031464, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124907888 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16517 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129523559-129524071 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129527772-129528310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129528311-129528849 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:129533429-129534628 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129547330-129547830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129569784-129570284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129592419-129593118 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:129621764-129622354 Neighboring gene uncharacterized LOC101927881 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:129816763-129816957 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:129944797-129945329 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:129950197-129951124 Neighboring gene uncharacterized LOC105373612 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:130056887-130057388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16518 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16519 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16520 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:130188987-130189488 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:130189489-130189988 Neighboring gene uncharacterized LOC105373613

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. Discovery of genetic biomarkers contributing to variation in drug response of cytidine analogues using human lymphoblastoid cell lines. Li L, et al. BMC Genomics, 2014 Feb 1. PMID 24483146, Free PMC Article
  2. Genome-wide association study of chemotherapeutic agent-induced severe neutropenia/leucopenia for patients in Biobank Japan. Low SK, et al. Cancer Sci, 2013 Aug. PMID 23648065, Free PMC Article
  3. 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
  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

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Discovery of genetic biomarkers contributing to variation in drug response of cytidine analogues using human lymphoblastoid cell lines.
EBI GWAS Catalog
Genome-wide association study of chemotherapeutic agent-induced severe neutropenia/leucopenia for patients in Biobank Japan.
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)

Genotypes

General gene information

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Markers

Clone Names

  • MGC120750, MGC138193, AC079586.1

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_122040.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript.
    Source sequence(s)
    AC079586, AK056598, DA821832, DA825295
    Related
    ENST00000375987.3

  2. NR_122041.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an internal exon and uses an alternate splice site, resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AC079586, AK056598, DA821832, DA825295

  3. NR_122042.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an internal exon, resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AC079586, AK056598, DA821832, DA824517, DA825295

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    129242173..129273891 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    129670494..129702352 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001033657.1: Suppressed sequence

    Description
    NM_001033657.1: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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