LINC00598 long intergenic non-protein coding RNA 598

2007-11-01 Jean-Loup Huret Affiliation

Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France

Identity

HGNC

LINC00598

LOCATION

13q14

LOCUSID

646982

ALIAS

lncFOXO1

DNA/RNA

Description

Start at 39,822,377 bp from pter; the gene spans 119,929 bases on minus strand.

Transcription

Three splicing forms, namely: TTL-T, TTL-B1 and -B2. TTL-T is 2090 bp long and composed of exons 1-8. The longest open-reading frame contains exons 4, 5, and part of exon 6; it encods a 133 amino acids peptid. TTL-B1 transcript is 3450 bp long and is composed of exons 4, 5, and part of exon 9. TTL-B2, 3588 bp long is composed of exons 4, 5, and part of exon 8a.

Proteins

Note

This gene/protein remains poorly known: there has been no study on it since the princeps paper by Qiao et al (2003).

Expression

Ubiquitous expression (lung, liver, spleen, thymus, and bone marrow); major expression in brain and testis.

Homology

TTL has no homology to known genes.

Implicated in

Entity name

t(12;13)(p13;q14) in B-cell acute lymphoblastic leukaemia (B-ALL) --> ETV6 /LINC00598

Note

Only one case to date.

Hybrid gene

Both reciprocal transcripts, TTL/ETV6 and ETV6/TTL, were detected. ETV6/TTL fusion transcript
The other transcript, TTL/ETV6, comprises 5 TTL exons 1 to 5 or to 8a, fused to ETV6 from exon 2. The predicted 530 amino acids fusion protein consists mostly of ETV6 with both HLH and ETS domains, and could have modified transcriptional activities. On the other hand, a loss of function of ETV6 and/or of TTL.could play the critical role in leukemogenesis.

Article Bibliography

Pubmed ID	Last Year	Title	Authors
12764377	2003	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

Other Information

Locus ID:

NCBI: 646982
HGNC: 42770
Ensembl: ENSG00000215483

Variants:

dbSNP: 646982
ClinVar: 646982
TCGA: ENSG00000215483
COSMIC: LINC00598

RNA/Proteins

Expression (GTEx)

Adipose - Subcutaneous

Adipose - Visceral

Adrenal Gland

Artery - Aorta

Artery - Tibial

Bladder

Brain - Amygdala

Brain - Anterior cingulate cortex

Brain - Caudate

Brain - Cerebellar Hemisphere

Brain - Cerebellum

Brain - Cortex

Brain - Frontal Cortex

Brain - Hippocampus

Brain - Hypothalamus

Brain - Nucleus accumbens

Brain - Putamen

Brain - Spinal cord

Brain - Substantia nigra

Breast - Mammary Tissue

Cells - Cultured fibroblasts

Cells - EBV - transformed lymphocytes

Cervix - Ectocervix

Cervix - Endocervix

Colon - Sigmoid

Colon - Transverse

Esophagus - Gastroesophageal Junction

Esophagus - Mucosa

Esophagus - Muscularis

Fallopian Tube

Heart - Atrial Appendage

Heart - Left Ventricle

Kidney - Cortex

Kidney - Medulla

Liver

Lung

Minor Salivary Gland

Muscle - Skeletal

Nerve - Tibial

Ovary

Pancreas

Pituitary

Prostate

Skin - Not Sun Exposed

Skin - Sun Exposed

Small Intestine - Terminal Ileum

Spleen

Stomach

Testis

Thyroid

Uterus

Vagina

Whole Blood

References

Pubmed ID	Year	Title	Citations
28339037	2017	The long non-coding RNA lncFOXO1 suppresses growth of human breast cancer cells through association with BAP1.	11
28339037	2017	The long non-coding RNA lncFOXO1 suppresses growth of human breast cancer cells through association with BAP1.	11
27572135	2016	Long noncoding RNA linc00598 regulates CCND2 transcription and modulates the G1 checkpoint.	10
27572135	2016	Long noncoding RNA linc00598 regulates CCND2 transcription and modulates the G1 checkpoint.	10

Citation

Jean-Loup Huret

LINC00598 long intergenic non-protein coding RNA 598

Atlas Genet Cytogenet Oncol Haematol. 2007-11-01

Online version: http://atlasgeneticsoncology.org/gene/529/linc00598-long-intergenic-non-protein-coding-rna-598