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

Summary

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

Location:: 13q14.11

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	13	NC_000013.11 (40347132..40481006, complement)
RS_2023_03	current	T2T-CHM13v2.0 (GCF_009914755.1)	13	NC_060937.1 (39566232..39699983, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (40921269..41055143, complement)

Chromosome 13 - NC_000013.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

data indicate that linc00598 plays an important role in cell cycle regulation and proliferation through its ability to regulate the transcription of CCND2.
Title: Long noncoding RNA linc00598 regulates CCND2 transcription and modulates the G1 checkpoint.
lncFOXO1 suppressed the growth of breast cancer by increasing FOXO1 transcription. Moreover, we found that lncFOXO1 associated with BRCA-1-associated protein 1 (BAP1) and regulates its binding and the level of mono-ubiquitinated H2A at K119 (ubH2AK119) at FOXO1 promoter
Title: The long non-coding RNA lncFOXO1 suppresses growth of human breast cancer cells through association with BAP1.

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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 EBI GWAS CatalogPubMed
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. EBI GWAS Catalog EBI GWAS CatalogPubMed

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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Markers

NoName (e-PCR)
- UniSTS:80690

SHGC-153427 (e-PCR)
- UniSTS:177742

SHGC-111293 (e-PCR)
- UniSTS:168284

D10S16 (e-PCR)
- UniSTS:155756

RH70375 (e-PCR)
- UniSTS:80262

RH93071 (e-PCR)
- UniSTS:88202

D13S648 (e-PCR)
- UniSTS:149750

Other Names

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

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

NR_024505.1 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, AY116214

Related

ENST00000616706.4
NR_024506.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (TTL-B1) lacks an alternate exon compared to variant TTL-B2.

Source sequence(s)

AL445143, AY116214, AY116215
NR_024507.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (TTL-B2) represents the longest transcript.

Source sequence(s)

AL445143, AY116214, AY116216