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MALAT1 (metastasis associated lung adenocarcinoma transcript 1 (non-protein coding))

Identity

Alias_symbol (synonym)PRO1073
MALAT-1
NCRNA00047
HCN
NEAT2
LINC00047
mascRNA
Other aliasPRO2853
HGNC (Hugo) MALAT1
LocusID (NCBI) 378938
Atlas_Id 41266
Location 11q13.1  [Link to chromosome band 11q13]
Location_base_pair Starts at 65265233 and ends at 65273983 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
ACTN4 (19q13.2) / MALAT1 (11q13.1)ALB (4q13.3) / MALAT1 (11q13.1)ALDH7A1 (5q23.2) / MALAT1 (11q13.1)
APP (21q21.3) / MALAT1 (11q13.1)ARHGEF3 (3p14.3) / MALAT1 (11q13.1)ASAP1 (8q24.21) / MALAT1 (11q13.1)
ATF7IP (12p13.1) / MALAT1 (11q13.1)ATP11C (Xq27.1) / MALAT1 (11q13.1)ATP5I (4p16.3) / MALAT1 (11q13.1)
AURKAIP1 (1p36.33) / MALAT1 (11q13.1)BABAM1 (19p13.11) / MALAT1 (11q13.1)CDK14 (7q21.13) / MALAT1 (11q13.1)
CNTRL (9q33.2) / MALAT1 (11q13.1)DDB1 (11q12.2) / MALAT1 (11q13.1)DGKB (7p21.2) / MALAT1 (11q13.1)
DNM2 (19p13.2) / MALAT1 (11q13.1)DNMT1 (19p13.2) / MALAT1 (11q13.1)DUSP27 (1q24.1) / MALAT1 (11q13.1)
EBAG9 (8q23.2) / MALAT1 (11q13.1)ENPP2 (8q24.12) / MALAT1 (11q13.1)EPHA5 (4q13.1) / MALAT1 (11q13.1)
ERGIC1 (5q35.1) / MALAT1 (11q13.1)FAM234B (12p13.1) / MALAT1 (11q13.1)FAM81B (5q15) / MALAT1 (11q13.1)
FGFR4 (5q35.2) / MALAT1 (11q13.1)FKBP15 (9q32) / MALAT1 (11q13.1)FOCAD (9p21.3) / MALAT1 (11q13.1)
GNAI1 (7q21.11) / MALAT1 (11q13.1)GUCY1A2 (11q22.3) / MALAT1 (11q13.1)HMBOX1 (8p21.1) / MALAT1 (11q13.1)
IGF1R (15q26.3) / MALAT1 (11q13.1)IRF3 (19q13.33) / MALAT1 (11q13.1)IVD (15q15.1) / MALAT1 (11q13.1)
KLK3 (19q13.33) / MALAT1 (11q13.1)KMO (1q43) / MALAT1 (11q13.1)LEMD2 (6p21.31) / MALAT1 (11q13.1)
MALAT1 (11q13.1) / ALK (2p23.2)MALAT1 (11q13.1) / ANKRD44 (2q33.1)MALAT1 (11q13.1) / APOB (2p24.1)
MALAT1 (11q13.1) / B3GNT2 (2p15)MALAT1 (11q13.1) / BHLHE40 (3p26.1)MALAT1 (11q13.1) / CCNI (4q21.1)
MALAT1 (11q13.1) / CD59 (11p13)MALAT1 (11q13.1) / CDH2 (18q12.1)MALAT1 (11q13.1) / CEMIP (15q25.1)
MALAT1 (11q13.1) / CLGN (4q31.1)MALAT1 (11q13.1) / CNOT8 (5q33.2)MALAT1 (11q13.1) / COQ10B (2q33.1)
MALAT1 (11q13.1) / CTSZ (20q13.32)MALAT1 (11q13.1) / CYLC2 (9q31.1)MALAT1 (11q13.1) / DBN1 (5q35.3)
MALAT1 (11q13.1) / EIF3J (15q21.1)MALAT1 (11q13.1) / ESR1 (6q25.1)MALAT1 (11q13.1) / FKBP15 (9q32)
MALAT1 (11q13.1) / GAPDH (12p13.31)MALAT1 (11q13.1) / GNA12 (7p22.3)MALAT1 (11q13.1) / HBA2 (16p13.3)
MALAT1 (11q13.1) / HDAC3 (5q31.3)MALAT1 (11q13.1) / HNRNPUL1 (19q13.2)MALAT1 (11q13.1) / HS1BP3 (2p24.1)
MALAT1 (11q13.1) / HSP90AA1 (14q32.31)MALAT1 (11q13.1) / IGF2 (11p15.5)MALAT1 (11q13.1) / IPO13 (1p34.1)
MALAT1 (11q13.1) / LAMB1 (7q31.1)MALAT1 (11q13.1) / LAMP2 (Xq24)MALAT1 (11q13.1) / LDAH (2p24.1)
MALAT1 (11q13.1) / LIFR (5p13.1)MALAT1 (11q13.1) / LRP1B (2q22.1)MALAT1 (11q13.1) / MALAT1 (11q13.1)
MALAT1 (11q13.1) / MAML2 (11q21)MALAT1 (11q13.1) / MAP4K3 (2p22.1)MALAT1 (11q13.1) / MBD3 (19p13.3)
MALAT1 (11q13.1) / MEG3 (14q32.2)MALAT1 (11q13.1) / MGAT4B (5q35.3)MALAT1 (11q13.1) / MIR548H3 (6q16.1)
MALAT1 (11q13.1) / MLH1 (3p22.2)MALAT1 (11q13.1) / MNT (17p13.3)MALAT1 (11q13.1) / MUC7 (4q13.3)
MALAT1 (11q13.1) / MX2 (21q22.3)MALAT1 (11q13.1) / NASP (1p34.1)MALAT1 (11q13.1) / NCOR2 (12q24.31)
MALAT1 (11q13.1) / NEDD4L (18q21.31)MALAT1 (11q13.1) / NSRP1 (17q11.2)MALAT1 (11q13.1) / NUP210 (3p25.1)
MALAT1 (11q13.1) / NUP58 (13q12.13)MALAT1 (11q13.1) / OSBPL6 (2q31.2)MALAT1 (11q13.1) / OST4 (2p23.3)
MALAT1 (11q13.1) / OXR1 (8q23.1)MALAT1 (11q13.1) / PCCA (13q32.3)MALAT1 (11q13.1) / PLCL1 (2q33.1)
MALAT1 (11q13.1) / PLEKHB1 (11q13.4)MALAT1 (11q13.1) / PSPH (7p11.2)MALAT1 (11q13.1) / RAB5B (12q13.2)
MALAT1 (11q13.1) / RAD21L1 (20p13)MALAT1 (11q13.1) / RCVRN (17p13.1)MALAT1 (11q13.1) / RPL13 (16q24.3)
MALAT1 (11q13.1) / RPN1 (3q21.3)MALAT1 (11q13.1) / RPS6 (9p22.1)MALAT1 (11q13.1) / S100A10 (1q21.3)
MALAT1 (11q13.1) / SETDB1 (1q21.3)MALAT1 (11q13.1) / SFXN1 (5q35.2)MALAT1 (11q13.1) / SPG21 (15q22.31)
MALAT1 (11q13.1) / SPRED1 (15q14)MALAT1 (11q13.1) / STK3 (8q22.2)MALAT1 (11q13.1) / TBC1D10A (22q12.2)
MALAT1 (11q13.1) / TFEB (6p21.1)MALAT1 (11q13.1) / TG (8q24.22)MALAT1 (11q13.1) / TMBIM6 (12q13.12)
MALAT1 (11q13.1) / TMC5 (16p12.3)MALAT1 (11q13.1) / TPD52L2 (20q13.33)MALAT1 (11q13.1) / TPM1 (15q22.2)
MALAT1 (11q13.1) / TPP1 (11p15.4)MALAT1 (11q13.1) / TRA2B (3q27.2)MALAT1 (11q13.1) / TRIM2 (4q31.3)
MALAT1 (11q13.1) / TUBB4A (19p13.3)MALAT1 (11q13.1) / U2AF2 (19q13.42)MALAT1 (11q13.1) / USO1 (4q21.1)
MALAT1 (11q13.1) / XPNPEP1 (10q25.1)MALAT1 (11q13.1) / ZAK (2q31.1)MALAT1 (11q13.1) / ZFAND5 (9q21.13)
MALAT1 (11q13.1) / retro-NXF5 ()MAP2K2 (19p13.3) / MALAT1 (11q13.1)MAP3K13 (3q27.2) / MALAT1 (11q13.1)
MDS2 (1p36.11) / MALAT1 (11q13.1)MEMO1 (2p23.1) / MALAT1 (11q13.1)MOGS (2p13.1) / MALAT1 (11q13.1)
MYOT (5q31.2) / MALAT1 (11q13.1)NCKAP5 (2q21.2) / MALAT1 (11q13.1)PARN (16p13.12) / MALAT1 (11q13.1)
PART1 (5q12.1) / MALAT1 (11q13.1)PJA2 (5q21.3) / MALAT1 (11q13.1)PRH1-PRR4 (12p13.2) / MALAT1 (11q13.1)
PRKAG2 (7q36.1) / MALAT1 (11q13.1)PTBP1 (19p13.3) / MALAT1 (11q13.1)PTP4A2 (1p35.2) / MALAT1 (11q13.1)
RAPGEF1 (9q34.13) / MALAT1 (11q13.1)RGL3 (19p13.2) / MALAT1 (11q13.1)RGS5 (1q23.3) / MALAT1 (11q13.1)
RMND5A (2p11.2) / MALAT1 (11q13.1)RPAIN (17p13.2) / MALAT1 (11q13.1)RPL13 (16q24.3) / MALAT1 (11q13.1)
RPS6 (9p22.1) / MALAT1 (11q13.1)RUNX1T1 (8q21.3) / MALAT1 (11q13.1)SCAF11 (12q12) / MALAT1 (11q13.1)
SCN8A (12q13.13) / MALAT1 (11q13.1)SEC24B (4q25) / MALAT1 (11q13.1)SLC9A3R1 (17q25.1) / MALAT1 (11q13.1)
SPG7 (16q24.3) / MALAT1 (11q13.1)TAX1BP1 (7p15.2) / MALAT1 (11q13.1)THRAP3 (1p34.3) / MALAT1 (11q13.1)
TMED10 (14q24.3) / MALAT1 (11q13.1)TMPRSS2 (21q22.3) / MALAT1 (11q13.1)TRIM41 (5q35.3) / MALAT1 (11q13.1)
UIMC1 (5q35.2) / MALAT1 (11q13.1)WDR70 (5p13.2) / MALAT1 (11q13.1)XIST (Xq13.2) / MALAT1 (11q13.1)

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 8 ]
  Kidney: Renal cell carcinoma with inv(X)(p11q12) NONO/TFE3
Liver: Mesenchymal hamartoma with t(11;19)(q11;q13) MALAT1/MHLB1
Kidney: Renal cell carcinomas with MiT family translocation
Kidney: Renal cell carcinoma with t(X;17)(p11;q25) ASPSCR1/TFE3
Kidney: Renal cell carcinoma with t(6;11)(p21;q12) MALAT1/TFEB
Kidney: Renal cell carcinoma with t(X;17)(p11;q23) CLTC/TFE3
Kidney: Renal cell carcinoma with t(X;1)(p11;q21) PRCC/TFE3
Kidney: Renal cell carcinoma with t(X;1)(p11;p34) SFPQ/TFE3


External links

Nomenclature
HGNC (Hugo)MALAT1   29665
Cards
Entrez_Gene (NCBI)MALAT1  378938  metastasis associated lung adenocarcinoma transcript 1 (non-protein coding)
AliasesHCN; LINC00047; NCRNA00047; NEAT2; 
PRO2853; mascRNA
GeneCards (Weizmann)MALAT1
Ensembl hg19 (Hinxton)ENSG00000251562 [Gene_View]  chr11:65265233-65273983 [Contig_View]  MALAT1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000251562 [Gene_View]  chr11:65265233-65273983 [Contig_View]  MALAT1 [Vega]
ICGC DataPortalENSG00000251562
TCGA cBioPortalMALAT1
AceView (NCBI)MALAT1
Genatlas (Paris)MALAT1
WikiGenes378938
SOURCE (Princeton)MALAT1
Genetics Home Reference (NIH)MALAT1
Genomic and cartography
GoldenPath hg19 (UCSC)MALAT1  -     chr11:65265233-65273983 +  11q13.1   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)MALAT1  -     11q13.1   [Description]    (hg38-Dec_2013)
EnsemblMALAT1 - 11q13.1 [CytoView hg19]  MALAT1 - 11q13.1 [CytoView hg38]
Mapping of homologs : NCBIMALAT1 [Mapview hg19]  MALAT1 [Mapview hg38]
OMIM607924   
Gene and transcription
Genbank (Entrez)AF001542 AI805768 AJ535465 AK130345 AL050210
RefSeq transcript (Entrez)
RefSeq genomic (Entrez)NC_000011 NC_018922 NT_167190 NW_004929380
Consensus coding sequences : CCDS (NCBI)MALAT1
Cluster EST : UnigeneHs.642877 [ NCBI ]
CGAP (NCI)Hs.642877
Alternative Splicing GalleryENSG00000251562
Gene ExpressionMALAT1 [ NCBI-GEO ]   MALAT1 [ EBI - ARRAY_EXPRESS ]   MALAT1 [ SEEK ]   MALAT1 [ MEM ]
Gene Expression Viewer (FireBrowse)MALAT1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)378938
GTEX Portal (Tissue expression)MALAT1
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9UHZ2   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9UHZ2  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9UHZ2
Splice isoforms : SwissVarQ9UHZ2
PhosPhoSitePlusQ9UHZ2
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Conserved Domain (NCBI)MALAT1
DMDM Disease mutations378938
Blocks (Seattle)MALAT1
SuperfamilyQ9UHZ2
Human Protein AtlasENSG00000251562
Peptide AtlasQ9UHZ2
IPIIPI00006107   IPI00019779   
Protein Interaction databases
DIP (DOE-UCLA)Q9UHZ2
IntAct (EBI)Q9UHZ2
FunCoupENSG00000251562
BioGRIDMALAT1
STRING (EMBL)MALAT1
ZODIACMALAT1
Ontologies - Pathways
QuickGOQ9UHZ2
Ontology : AmiGO
Ontology : EGO-EBI
NDEx NetworkMALAT1
Atlas of Cancer Signalling NetworkMALAT1
Wikipedia pathwaysMALAT1
Orthology - Evolution
OrthoDB378938
GeneTree (enSembl)ENSG00000251562
Phylogenetic Trees/Animal Genes : TreeFamMALAT1
HOVERGENQ9UHZ2
HOGENOMQ9UHZ2
Homologs : HomoloGeneMALAT1
Homology/Alignments : Family Browser (UCSC)MALAT1
Gene fusions - Rearrangements
Fusion : MitelmanASAP1/MALAT1 [8q24.21/11q13.1]  [t(8;11)(q24;q13)]  
Fusion : MitelmanMALAT1/ALK [11q13.1/2p23.2]  [t(2;11)(p23;q13)]  
Fusion : MitelmanMALAT1/IGF2 [11q13.1/11p15.5]  [t(11;11)(p15;q13)]  
Fusion : MitelmanMALAT1/TFEB [11q13.1/6p21.1]  [t(6;11)(p21;q13)]  
Fusion : MitelmanPTP4A2/MALAT1 [1p35.2/11q13.1]  [t(1;11)(p35;q13)]  
Fusion : MitelmanTAX1BP1/MALAT1 [7p15.2/11q13.1]  [t(7;11)(p15;q13)]  
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerMALAT1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)MALAT1
dbVarMALAT1
ClinVarMALAT1
1000_GenomesMALAT1 
Exome Variant ServerMALAT1
ExAC (Exome Aggregation Consortium)MALAT1 (select the gene name)
Genetic variants : HAPMAP378938
Genomic Variants (DGV)MALAT1 [DGVbeta]
DECIPHER (Syndromes)11:65265233-65273983  ENSG00000251562
CONAN: Copy Number AnalysisMALAT1 
Mutations
ICGC Data PortalMALAT1 
TCGA Data PortalMALAT1 
Broad Tumor PortalMALAT1
OASIS PortalMALAT1 [ Somatic mutations - Copy number]
Cancer Gene: CensusMALAT1 
Somatic Mutations in Cancer : COSMICMALAT1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDMALAT1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch MALAT1
DgiDB (Drug Gene Interaction Database)MALAT1
DoCM (Curated mutations)MALAT1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)MALAT1 (select a term)
intoGenMALAT1
Cancer3DMALAT1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM607924   
Orphanet
MedgenMALAT1
Genetic Testing Registry MALAT1
NextProtQ9UHZ2 [Medical]
TSGene378938
GENETestsMALAT1
Huge Navigator MALAT1 [HugePedia]
snp3D : Map Gene to Disease378938
BioCentury BCIQMALAT1
ClinGenMALAT1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD378938
Chemical/Pharm GKB GenePA134935778
Clinical trialMALAT1
Miscellaneous
canSAR (ICR)MALAT1 (select the gene name)
Probes
Litterature
PubMed71 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineMALAT1
EVEXMALAT1
GoPubMedMALAT1
iHOPMALAT1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Mar 14 13:14:17 CET 2017

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