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Center for Computational Systems Medicine
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Gene summary

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Gene structures and expression levels

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Exon skipping events with PSIs in TCGA

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Exon skipping events with PSIs in GTEx

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Open reading frame (ORF) annotation in the exon skipping event

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Exon skipping events in the canonical protein sequence

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SNVs in the skipped exons with depth of coverage

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon

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Related drugs with this gene

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Related diseases with this gene

Gene summary for MLLT3

check button Gene summary
Gene informationGene symbol

MLLT3

Gene ID

4300

Gene nameMLLT3, super elongation complex subunit
SynonymsAF9|YEATS3
Cytomap

9p21.3

Type of geneprotein-coding
Descriptionprotein AF-9ALL1-fused gene from chromosome 9 proteinYEATS domain-containing protein 3myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog); translocated to, 3myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translo
Modification date20180519
UniProtAcc

P42568

ContextPubMed: MLLT3 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract]
- Title (PMID)

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
MLLT3

GO:0045893

positive regulation of transcription, DNA-templated

25417107|27105114

MLLT3

GO:0090090

negative regulation of canonical Wnt signaling pathway

19591803


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Exon skipping events across known transcript of Ensembl for MLLT3 from UCSC genome browser

check buttonSkipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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Gene isoform structures and expression levels for MLLT3

check button Expression levels of gene isoforms across TCGA.
gencode gene structure

check button Expression levels of gene isoforms across GTEx.
gencode gene structure


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Exon skipping events with PSIs in TCGA for MLLT3

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_502964920345074:20346572:20353522:20353594:20354805:2035487720353522:20353594ENSG00000171843.11ENST00000488705.1,ENST00000380321.1,ENST00000380338.4,ENST00000429426.2
exon_skip_502966920345074:20346572:20354805:20354877:20360739:2036083920354805:20354877ENSG00000171843.11ENST00000355930.6,ENST00000380323.1
exon_skip_502967920346403:20346572:20360739:20360839:20363473:2036356720360739:20360839ENSG00000171843.11ENST00000469261.1
exon_skip_502968920353522:20353594:20354805:20354877:20360739:2036083920354805:20354877ENSG00000171843.11ENST00000380321.1,ENST00000380338.4,ENST00000429426.2
exon_skip_502971920365666:20365742:20380204:20380325:20382378:2038245020380204:20380325ENSG00000171843.11ENST00000491137.1
exon_skip_502973920365666:20365742:20410558:20410668:20411813:2041193620410558:20410668ENSG00000171843.11ENST00000468513.1
exon_skip_502975920365666:20365742:20413718:20414423:20448120:2044826420413718:20414423ENSG00000171843.11ENST00000355930.6,ENST00000380338.4,ENST00000429426.2

check button PSI values of skipped exons in TCGA.
psi tcga

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Exon skipping events with PSIs in GTEx for MLLT3

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_502964920345074:20346572:20353522:20353594:20354805:2035487720353522:20353594ENSG00000171843.11ENST00000380338.4,ENST00000429426.2,ENST00000488705.1,ENST00000380321.1
exon_skip_502966920345074:20346572:20354805:20354877:20360739:2036083920354805:20354877ENSG00000171843.11ENST00000355930.6,ENST00000380323.1
exon_skip_502967920346403:20346572:20360739:20360839:20363473:2036356720360739:20360839ENSG00000171843.11ENST00000469261.1
exon_skip_502968920353522:20353594:20354805:20354877:20360739:2036083920354805:20354877ENSG00000171843.11ENST00000380338.4,ENST00000429426.2,ENST00000380321.1
exon_skip_502969920363473:20363603:20365666:20365742:20413718:2041442320365666:20365742ENSG00000171843.11ENST00000380338.4,ENST00000355930.6,ENST00000429426.2,ENST00000475957.1
exon_skip_502971920365666:20365742:20380204:20380325:20382378:2038245020380204:20380325ENSG00000171843.11ENST00000491137.1
exon_skip_502975920365666:20365742:20413718:20414423:20448120:2044826420413718:20414423ENSG00000171843.11ENST00000380338.4,ENST00000355930.6,ENST00000429426.2

check button PSI values of skipped exons in GTEx.
psi gtex

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for MLLT3

check button Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000003803382035352220353594In-frame
ENST000003803382035480520354877In-frame
ENST000003803382041371820414423In-frame

check button Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000003803382036566620365742Frame-shift
ENST000003803382035352220353594In-frame
ENST000003803382035480520354877In-frame
ENST000003803382041371820414423In-frame

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Infer the effects of exon skipping event on protein functional features for MLLT3

check button Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.
prot feature distribution

check button Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST00000380338678956820413718204144237081412140375
ENST000003803386789568203548052035487717191790477501
ENST000003803386789568203535222035359417911862501525

check button Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST00000380338678956820413718204144237081412140375
ENST000003803386789568203548052035487717191790477501
ENST000003803386789568203535222035359417911862501525

check button Lost protein functional features of individual exon skipping events in TCGA.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
P425681403751568ChainID=PRO_0000215921;Note=Protein AF-9
P42568140375149194Compositional biasNote=Poly-Ser
P42568140375339339Cross-linkNote=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:25218447,ECO:0000244|PubMed:28112733;Dbxref=PMID:25218447,PMID:28112733
P42568140375288288Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648
P42568140375294294Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:18691976,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:18691976,PMID:23186163
P42568140375295300MotifNote=Nuclear localization signal;Ontology_term=ECO:0000255;evidence=ECO:0000255
P42568140375173173Sequence conflictNote=S->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
P42568140375375375SiteNote=KMT2A/MLL1 fusion point (in acute myeloid leukemia patient CO);Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8506309;Dbxref=PMID:8506309
P425684775011568ChainID=PRO_0000215921;Note=Protein AF-9
P42568477501483483Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:18691976,ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:18691976,PMID:20068231,PMID
P42568477501481481SiteNote=KMT2A/MLL1 fusion point (in acute myeloid leukemia patient F1);Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8506309;Dbxref=PMID:8506309
P425685015251568ChainID=PRO_0000215921;Note=Protein AF-9
P42568501525504515HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2LM0
P42568501525523531HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2LM0


check button Lost protein functional features of individual exon skipping events in GTEx.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
P425681403751568ChainID=PRO_0000215921;Note=Protein AF-9
P42568140375149194Compositional biasNote=Poly-Ser
P42568140375339339Cross-linkNote=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:25218447,ECO:0000244|PubMed:28112733;Dbxref=PMID:25218447,PMID:28112733
P42568140375288288Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648
P42568140375294294Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:18691976,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:18691976,PMID:23186163
P42568140375295300MotifNote=Nuclear localization signal;Ontology_term=ECO:0000255;evidence=ECO:0000255
P42568140375173173Sequence conflictNote=S->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
P42568140375375375SiteNote=KMT2A/MLL1 fusion point (in acute myeloid leukemia patient CO);Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8506309;Dbxref=PMID:8506309
P425684775011568ChainID=PRO_0000215921;Note=Protein AF-9
P42568477501483483Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:18691976,ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:18691976,PMID:20068231,PMID
P42568477501481481SiteNote=KMT2A/MLL1 fusion point (in acute myeloid leukemia patient F1);Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8506309;Dbxref=PMID:8506309
P425685015251568ChainID=PRO_0000215921;Note=Protein AF-9
P42568501525504515HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2LM0
P42568501525523531HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2LM0


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SNVs in the skipped exons for MLLT3

check button - Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.
lollipop

check button - Differential PSIs between mutated versus non-mutated samples.

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
LIHCTCGA-DD-A1EG-01exon_skip_502967
20360740203608392036075420360754Frame_Shift_DelT-p.T473fs
LIHCTCGA-DD-A1EG-01exon_skip_502975
20413719204144232041391320413913Frame_Shift_DelA-p.S312fs
SKCMTCGA-EE-A2ME-06exon_skip_502975
20413719204144232041395220413952Frame_Shift_DelT-p.R298fs
UCECTCGA-D1-A17H-01exon_skip_502975
20413719204144232041395220413952Frame_Shift_DelT-p.R298fs
LIHCTCGA-DD-A3A0-01exon_skip_502975
20413719204144232041416320414163Frame_Shift_DelT-p.K227fs
CESCTCGA-DR-A0ZM-01exon_skip_502975
20413719204144232041406520414065Nonsense_MutationGCp.S260*
UCECTCGA-AP-A056-01exon_skip_502975
20413719204144232041413220414132Nonsense_MutationCAp.E238*
UCECTCGA-AX-A05Z-01exon_skip_502975
20413719204144232041413220414132Nonsense_MutationCAp.E238*
UCSTCGA-ND-A4WC-01exon_skip_502975
20413719204144232041413220414132Nonsense_MutationCAp.E238*
UCSTCGA-ND-A4WC-01exon_skip_502975
20413719204144232041413220414132Nonsense_MutationCAp.E238X

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE20413719204144232041386920413869Frame_Shift_DelT-p.K325fs
C33A_CERVIX20413719204144232041395220413952Frame_Shift_DelT-p.R298fs
CL34_LARGE_INTESTINE20413719204144232041395220413952Frame_Shift_DelT-p.R298fs
COLO684_ENDOMETRIUM20413719204144232041395220413952Frame_Shift_DelT-p.R298fs
COLO704_OVARY20413719204144232041395220413952Frame_Shift_DelT-p.R298fs
BICR18_UPPER_AERODIGESTIVE_TRACT20413719204144232041398520413985Frame_Shift_DelT-p.I287fs
BICR18_UPPER_AERODIGESTIVE_TRACT20413719204144232041398920413989Frame_Shift_DelC-p.P286fs
639V_URINARY_TRACT20413719204144232041395120413952Frame_Shift_Ins-Tp.R298fs
DV90_LUNG20413719204144232041395120413952Frame_Shift_Ins-Tp.R298fs
HCC2157_BREAST20413719204144232041395120413952Frame_Shift_Ins-Tp.R298fs
KELLY_AUTONOMIC_GANGLIA20413719204144232041395120413952Frame_Shift_Ins-Tp.R298fs
KMRC3_KIDNEY20413719204144232041395120413952Frame_Shift_Ins-Tp.R298fs
KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE20413719204144232041395120413952Frame_Shift_Ins-Tp.R298fs
NCIH1341_LUNG20413719204144232041395120413952Frame_Shift_Ins-Tp.R298fs
RERFLCAD1_LUNG20413719204144232041395120413952Frame_Shift_Ins-Tp.R298fs
RS5_FIBROBLAST20413719204144232041395120413952Frame_Shift_Ins-Tp.R298fs
SCC15_UPPER_AERODIGESTIVE_TRACT20413719204144232041395120413952Frame_Shift_Ins-Tp.R298fs
SKMEL5_SKIN20413719204144232041395120413952Frame_Shift_Ins-Tp.R298fs
SW1271_LUNG20413719204144232041395120413952Frame_Shift_Ins-Tp.R298fs
TT_OESOPHAGUS20413719204144232041395120413952Frame_Shift_Ins-Tp.R298fs
YD8_UPPER_AERODIGESTIVE_TRACT20413719204144232041395120413952Frame_Shift_Ins-Tp.R298fs
BICR18_UPPER_AERODIGESTIVE_TRACT20413719204144232041398320413984Frame_Shift_Ins-GCp.I287fs
ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE20413719204144232041427520414307In_Frame_DelCTACTGCTGCTGCTGCTGCTGCTACTGCTGCTG-p.179_190SSSSSSSSSSSS>S
OE33_OESOPHAGUS20413719204144232041427520414295In_Frame_DelCTACTGCTGCTGCTGCTGCTG-p.183_190SSSSSSSS>S
NCIH1339_LUNG20413719204144232041427820414286In_Frame_DelCTGCTGCTG-p.186_189SSSS>S
EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE20413719204144232041429620414298In_Frame_DelCTA-p.182_183SS>S
PFEIFFER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE20413719204144232041436220414376In_Frame_DelCTGCTGCTGCTGCTA-p.156_161SSSSSS>S
IGROV1_OVARY20413719204144232041437120414376In_Frame_DelCTGCTA-p.156_158SSS>S
MERO82_LUNG20413719204144232041427720414278In_Frame_Ins-CTGp.189_189S>SS
AN3CA_ENDOMETRIUM20413719204144232041427720414278In_Frame_Ins-CTGp.189_189S>SS
TE617T_SOFT_TISSUE20413719204144232041435420414355In_Frame_Ins-GCTp.163_164SS>SSS
TC138_BONE20413719204144232041436420414365In_Frame_Ins-CTGp.160_160S>SS
TGW_AUTONOMIC_GANGLIA20360740203608392036081320360813Missense_MutationCTp.S453N
JHUEM7_ENDOMETRIUM20360740203608392036082220360822Missense_MutationCTp.G450D
SW684_SOFT_TISSUE20413719204144232041373220413732Missense_MutationGAp.S371F
MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE20413719204144232041377420413774Missense_MutationTAp.D357V
MON_SOFT_TISSUE20413719204144232041395920413960Missense_MutationGGTTp.A295E
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE20413719204144232041405120414051Missense_MutationGCp.P265A
BICR18_UPPER_AERODIGESTIVE_TRACT20413719204144232041405120414051Missense_MutationGCp.P265A
NCIH1703_LUNG20413719204144232041407520414075Missense_MutationTCp.K257E
GEO_LARGE_INTESTINE20413719204144232041410220414102Missense_MutationCTp.V248I
ES6_BONE20413719204144232041413220414132Missense_MutationCGp.E238Q
BICR18_UPPER_AERODIGESTIVE_TRACT20413719204144232041415120414151Missense_MutationTGp.E231D
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE20413719204144232041415120414151Missense_MutationTGp.E231D
OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE20413719204144232041415120414151Missense_MutationTGp.E231D
JHUEM7_ENDOMETRIUM20413719204144232041421520414215Missense_MutationTCp.D210G
EFE184_ENDOMETRIUM20413719204144232041428420414284Missense_MutationCTp.S187N
SW48_LARGE_INTESTINE20413719204144232041439820414398Missense_MutationCGp.S149T
U266B1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE20413719204144232041423120414231Nonsense_MutationCAp.E205*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for MLLT3

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for MLLT3


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for MLLT3


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RelatedDrugs for MLLT3

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for MLLT3

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
MLLT3C0005586Bipolar Disorder1PSYGENET