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LINC00598 long intergenic non-protein coding RNA 598

Written2007-11Jean-Loup Huret
Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France

(Note : for Links provided by Atlas : click)

Identity

Alias_symbol (synonym)TTL
Other aliasFLJ21437
LOC646982
TTL/TEL
TTL-T
TTL-B1
TTL-B2
HGNC (Hugo) LINC00598
LocusID (NCBI) 646982
Atlas_Id 529
Location 13q14  [Link to chromosome band 13q14]
Location_base_pair Starts at 40450934 and ends at 40481006 bp from pter ( according to hg19-Feb_2009)  [Mapping LINC00598.png]
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
Note Not to be confused with: TTL : tubulin tyrosine ligase (2q13), nor with "transthyretin-like (TTL) gene family", a family to which belongs TTR (transthyretin, 18q12).

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.

Protein

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

Note
  
Entity t(12;13)(p13;q14) in B-cell acute lymphoblastic leukaemia (B-ALL) --> ETV6 /LINC00598
Note Only one case to date.
Hybrid/Mutated 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.
  

Bibliography

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, Ogawa S, Hangaishi A, Yuji K, Izutsu K, Kunisato A, Imai Y, Wang L, Hosoya N, Nannya Y, Sato Y, Maki K, Mitani K, Hirai H.
Leukemia. 2003 Jun; 17(6): 1112-20.
PMID 12764377
 

Citation

This paper should be referenced as such :
Huret, JL
TTL (twelve-thirteen translocation leukemia)
Atlas Genet Cytogenet Oncol Haematol. 2008;12(4):295-295.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/TTLID529ch13q14.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 1 ]
  t(12;13)(p13;q14) LIN00598/ETV6


External links

Nomenclature
HGNC (Hugo)LINC00598   42770
Cards
AtlasTTLID529ch13q14
Entrez_Gene (NCBI)LINC00598  646982  long intergenic non-protein coding RNA 598
AliaseslncFOXO1
GeneCards (Weizmann)LINC00598
Ensembl hg19 (Hinxton)ENSG00000215483 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000215483 [Gene_View]  chr13:40450934-40481006 [Contig_View]  LINC00598 [Vega]
ICGC DataPortalENSG00000215483
TCGA cBioPortalLINC00598
AceView (NCBI)LINC00598
Genatlas (Paris)LINC00598
WikiGenes646982
SOURCE (Princeton)LINC00598
Genetics Home Reference (NIH)LINC00598
Genomic and cartography
GoldenPath hg38 (UCSC)LINC00598  -     chr13:40450934-40481006 -  13q14.11   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)LINC00598  -     13q14.11   [Description]    (hg19-Feb_2009)
EnsemblLINC00598 - 13q14.11 [CytoView hg19]  LINC00598 - 13q14.11 [CytoView hg38]
Mapping of homologs : NCBILINC00598 [Mapview hg19]  LINC00598 [Mapview hg38]
Gene and transcription
Genbank (Entrez)AK025090 AY116214 AY116215 AY116216
RefSeq transcript (Entrez)
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)LINC00598
Cluster EST : UnigeneHs.287664 [ NCBI ]
CGAP (NCI)Hs.287664
Alternative Splicing GalleryENSG00000215483
Gene ExpressionLINC00598 [ NCBI-GEO ]   LINC00598 [ EBI - ARRAY_EXPRESS ]   LINC00598 [ SEEK ]   LINC00598 [ MEM ]
Gene Expression Viewer (FireBrowse)LINC00598 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
BioGPS (Tissue expression)646982
GTEX Portal (Tissue expression)LINC00598
Human Protein AtlasENSG00000215483-LINC00598 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Conserved Domain (NCBI)LINC00598
DMDM Disease mutations646982
Blocks (Seattle)LINC00598
Human Protein Atlas [tissue]ENSG00000215483-LINC00598 [tissue]
Protein Interaction databases
FunCoupENSG00000215483
BioGRIDLINC00598
STRING (EMBL)LINC00598
ZODIACLINC00598
Ontologies - Pathways
Huge Navigator LINC00598 [HugePedia]
snp3D : Map Gene to Disease646982
BioCentury BCIQLINC00598
ClinGenLINC00598
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD646982
Clinical trialLINC00598
Miscellaneous
canSAR (ICR)LINC00598 (select the gene name)
Probes
Litterature
PubMed6 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineLINC00598
EVEXLINC00598
GoPubMedLINC00598
iHOPLINC00598
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Thu Oct 12 16:36:17 CEST 2017

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