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LINC00598 long intergenic non-protein coding RNA 598 [ Homo sapiens (human) ]

Gene ID: 646982, updated on 10-Oct-2023

Summary

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Official Symbol
LINC00598provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 598provided by HGNC
Primary source
HGNC:HGNC:42770
See related
Ensembl:ENSG00000215483 MIM:619008; AllianceGenome:HGNC:42770
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
lncFOXO1
Expression
Low expression observed in reference dataset See more
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Genomic context

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Location:
13q14.11
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (40347132..40481004, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (39566232..39699981, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (40921269..41055143, complement)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein L17 pseudogene 51 Neighboring gene RNY3 pseudogene 9 Neighboring gene Sharpr-MPRA regulatory region 8959 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:40926515-40927014 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:40956871-40957426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7603 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7604 Neighboring gene LINC00598 intron ENCODE-defined enhancer Neighboring gene RN7SK pseudogene 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:41019797-41020402 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5279 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:41092118-41093317 Neighboring gene Sharpr-MPRA regulatory region 6999 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr13:41114319-41114868 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr13:41114869-41115418 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:41115419-41115966 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:41119870-41120370 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:41120371-41120871 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:41137465-41138218 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7608 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7609 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7610 Neighboring gene forkhead box O1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7611 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7612 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:41225852-41226373 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:41226374-41226894 Neighboring gene ring finger protein, LIM domain interacting pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5281 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5280 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5282 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5283 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7613 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr13:41254046-41254810 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:41254811-41255575 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:41255576-41256340 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5285 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:41286412-41286912 Neighboring gene microRNA 320d-1

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. Identification of a novel fusion gene, TTL, fused to ETV6 in acute lymphoblastic leukemia with t(12;13)(p13;q14), and its implication in leukemogenesis. Qiao Y, et al. Leukemia, 2003 Jun. PMID 12764377
  2. Long noncoding RNA linc00598 regulates CCND2 transcription and modulates the G1 checkpoint. Jeong OS, et al. Sci Rep, 2016 Aug 30. PMID 27572135, Free PMC Article
  3. The long non-coding RNA lncFOXO1 suppresses growth of human breast cancer cells through association with BAP1. Xi J, et al. Int J Oncol, 2017 May. PMID 28339037
  4. A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder. Wang KS, et al. Schizophr Res, 2010 Dec. PMID 20889312
  5. Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. Anderson CA, et al. Nat Genet, 2011 Mar. PMID 21297633, Free PMC Article

See all (6) citations in PubMed

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
A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder.
EBI GWAS Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
EBI GWAS Catalog
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Other Names

  • twelve-thirteen translocation leukemia transcript (non-protein coding)

Clone Names

  • FLJ21437

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_024505.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (TTL-T) differs in the 3' end compared to variant TTL-B2.
    Source sequence(s)
    AL391724
    Related
    ENST00000616706.4

  2. NR_024506.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (TTL-B1) lacks an alternate exon compared to variant TTL-B2.
    Source sequence(s)
    AL391724, AL445143

  3. NR_024507.3 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (TTL-B2) represents the longest transcript.
    Source sequence(s)
    AL391724, AL445143

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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    40347132..40481004 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    39566232..39699981 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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