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LINC01404 long intergenic non-protein coding RNA 1404 [ Homo sapiens (human) ]

Gene ID: 105369980, updated on 10-Oct-2023

Summary

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Official Symbol
LINC01404provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 1404provided by HGNC
Primary source
HGNC:HGNC:50689
See related
Ensembl:ENSG00000258240
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:
12q24.11
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (110951683..110957818, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (110930866..110937001, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (111389487..111395622, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:111355215-111355716 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:111355717-111356216 Neighboring gene VISTA enhancer hs2149 Neighboring gene VISTA enhancer hs2493 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:111373669-111374362 Neighboring gene Sharpr-MPRA regulatory region 3484 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:111375751-111376443 Neighboring gene long intergenic non-protein coding RNA 1405 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:111394805-111396004 Neighboring gene myosin light chain 2 Neighboring gene uncharacterized LOC105369981 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:111478778-111479544 Neighboring gene VISTA enhancer hs611 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:111498362-111498864 Neighboring gene NANOG hESC enhancer GRCh37_chr12:111510029-111510544 Neighboring gene cut like homeobox 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7029 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7030 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:111537905-111538524 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:111542473-111542974 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:111598487-111599098 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:111620445-111620945 Neighboring gene uncharacterized LOC124903018 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:111631064-111631574

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. 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

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)

Genotypes

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_135001.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) reprsents the longer transcript.
    Source sequence(s)
    DA146183, DA302221, HY021340
    Related
    ENST00000548329.1

  2. NR_135002.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site, resulting in a shorter transcript than variant 1.
    Source sequence(s)
    DA146183, DA148561, HY021340
    Related
    ENST00000546852.5

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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    110951683..110957818 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    110930866..110937001 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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