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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 TRERF1

check button Gene summary
Gene informationGene symbol

TRERF1

Gene ID

55809

Gene nametranscriptional regulating factor 1
SynonymsBCAR2|HSA277276|RAPA|TREP132|TReP-132|dJ139D8.5
Cytomap

6p21.1

Type of geneprotein-coding
Descriptiontranscriptional-regulating factor 1breast cancer anti-estrogen resistance 2rapa-1rapa-2transcriptional regulating protein 132zinc finger protein rapazinc finger transcription factor TReP-132
Modification date20180523
UniProtAcc

Q96PN7

ContextPubMed: TRERF1 [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
TRERF1

GO:0045893

positive regulation of transcription, DNA-templated

11349124


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Exon skipping events across known transcript of Ensembl for TRERF1 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 TRERF1

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 TRERF1

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_459578642200418:42200630:42203942:42204149:42210985:4221109942203942:42204149ENSG00000124496.8ENST00000541110.1,ENST00000372922.4,ENST00000354325.2
exon_skip_459580642200418:42200666:42203942:42204149:42210985:4221109942203942:42204149ENSG00000124496.8ENST00000340840.2,ENST00000372917.4
exon_skip_459584642225872:42225939:42227076:42227461:42232441:4223259242227076:42227461ENSG00000124496.8ENST00000340840.2,ENST00000372917.4,ENST00000354325.2
exon_skip_459585642227076:42227461:42230997:42231306:42232441:4223259242230997:42231306ENSG00000124496.8ENST00000541110.1
exon_skip_459588642227076:42227461:42231057:42231306:42232441:4223259242231057:42231306ENSG00000124496.8ENST00000372922.4
exon_skip_459590642233488:42233535:42235891:42237586:42268375:4226848742235891:42237586ENSG00000124496.8ENST00000541110.1,ENST00000340840.2,ENST00000372922.4,ENST00000372917.4,ENST00000354325.2
exon_skip_459597642268375:42268487:42330684:42330817:42418914:4241899942330684:42330817ENSG00000124496.8ENST00000340840.2,ENST00000354325.2
exon_skip_459598642268375:42268487:42330734:42330817:42418914:4241899942330734:42330817ENSG00000124496.8ENST00000541110.1,ENST00000372922.4,ENST00000372917.4

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

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Exon skipping events with PSIs in GTEx for TRERF1

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_459578642200418:42200630:42203942:42204149:42210985:4221109942203942:42204149ENSG00000124496.8ENST00000541110.1,ENST00000372922.4,ENST00000354325.2
exon_skip_459580642200418:42200666:42203942:42204149:42210985:4221109942203942:42204149ENSG00000124496.8ENST00000372917.4,ENST00000340840.2
exon_skip_459584642225872:42225939:42227076:42227461:42232441:4223259242227076:42227461ENSG00000124496.8ENST00000372917.4,ENST00000340840.2,ENST00000354325.2
exon_skip_459585642227076:42227461:42230997:42231306:42232441:4223259242230997:42231306ENSG00000124496.8ENST00000541110.1
exon_skip_459588642227076:42227461:42231057:42231306:42232441:4223259242231057:42231306ENSG00000124496.8ENST00000372922.4
exon_skip_459590642233488:42233535:42235891:42237586:42268375:4226848742235891:42237586ENSG00000124496.8ENST00000541110.1,ENST00000372917.4,ENST00000372922.4,ENST00000340840.2,ENST00000354325.2
exon_skip_459597642268375:42268487:42330684:42330817:42418914:4241899942330684:42330817ENSG00000124496.8ENST00000340840.2,ENST00000354325.2
exon_skip_459598642268375:42268487:42330734:42330817:42418914:4241899942330734:42330817ENSG00000124496.8ENST00000541110.1,ENST00000372917.4,ENST00000372922.4

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 TRERF1

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
ENST0000037292242235891422375863UTR-3CDS
ENST0000037292242330734423308173UTR-3UTR
ENST000003729224220394242204149In-frame
ENST000003729224223105742231306In-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
ENST0000037292242235891422375863UTR-3CDS
ENST0000037292242330734423308173UTR-3UTR
ENST000003729224220394242204149In-frame
ENST000003729224223105742231306In-frame

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Infer the effects of exon skipping event on protein functional features for TRERF1

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
ENST0000037292273031200422310574223130621992447545628
ENST00000372922730312004220394242204149342336299531022

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
ENST0000037292273031200422310574223130621992447545628
ENST00000372922730312004220394242204149342336299531022

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
Q96PN7545628546628Alternative sequenceID=VSP_015645;Note=In isoform 2%2C isoform 3%2C isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2
Q96PN754562811200ChainID=PRO_0000197134;Note=Transcriptional-regulating factor 1
Q96PN7545628553749Compositional biasNote=Pro-rich
Q96PN75456284391200RegionNote=Interaction with CREBBP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11349124;Dbxref=PMID:11349124
Q96PN7953102210221022Alternative sequenceID=VSP_015646;Note=In isoform 3 and isoform 5. A->ADCRCHVTPFLPQ;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2
Q96PN7953102211200ChainID=PRO_0000197134;Note=Transcriptional-regulating factor 1
Q96PN79531022956982Compositional biasNote=Glu-rich
Q96PN79531022954954Modified residueNote=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:21406692;Dbxref=PMID:21406692
Q96PN79531022955955Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:21406692;Dbxref=PMID:21406692
Q96PN7953102210191019Natural variantID=VAR_050199;Note=N->T;Dbxref=dbSNP:rs35978318
Q96PN795310224391200RegionNote=Interaction with CREBBP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11349124;Dbxref=PMID:11349124
Q96PN7953102210131037Zinc fingerNote=C2H2-type 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00042


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
Q96PN7545628546628Alternative sequenceID=VSP_015645;Note=In isoform 2%2C isoform 3%2C isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2
Q96PN754562811200ChainID=PRO_0000197134;Note=Transcriptional-regulating factor 1
Q96PN7545628553749Compositional biasNote=Pro-rich
Q96PN75456284391200RegionNote=Interaction with CREBBP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11349124;Dbxref=PMID:11349124
Q96PN7953102210221022Alternative sequenceID=VSP_015646;Note=In isoform 3 and isoform 5. A->ADCRCHVTPFLPQ;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2
Q96PN7953102211200ChainID=PRO_0000197134;Note=Transcriptional-regulating factor 1
Q96PN79531022956982Compositional biasNote=Glu-rich
Q96PN79531022954954Modified residueNote=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:21406692;Dbxref=PMID:21406692
Q96PN79531022955955Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:21406692;Dbxref=PMID:21406692
Q96PN7953102210191019Natural variantID=VAR_050199;Note=N->T;Dbxref=dbSNP:rs35978318
Q96PN795310224391200RegionNote=Interaction with CREBBP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11349124;Dbxref=PMID:11349124
Q96PN7953102210131037Zinc fingerNote=C2H2-type 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00042


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SNVs in the skipped exons for TRERF1

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_459578
exon_skip_459580
42203943422041494220403042204030Frame_Shift_DelG-p.P1013fs
SKCMTCGA-BF-AAP1-01exon_skip_459578
exon_skip_459580
42203943422041494220403042204036Frame_Shift_DelGGGGACG-p.PVP1011fs
STADTCGA-HF-7132-01exon_skip_459584
42227077422274614222722642227226Frame_Shift_DelG-p.P707fs
STADTCGA-D7-A6EZ-01exon_skip_459584
42227077422274614222741742227417Frame_Shift_DelC-p.E663fs
STADTCGA-D7-A6EZ-01exon_skip_459584
42227077422274614222741742227417Frame_Shift_DelC-p.P644fs
STADTCGA-BR-4361-01exon_skip_459585
42230998422313064223111242231112Frame_Shift_DelG-p.S611fs
STADTCGA-BR-4361-01exon_skip_459588
42231058422313064223111242231112Frame_Shift_DelG-p.S611fs
LIHCTCGA-G3-A3CJ-01exon_skip_459590
42235892422375864223616142236161Frame_Shift_DelG-p.L390fs
STADTCGA-FP-A4BE-01exon_skip_459590
42235892422375864223616142236161Frame_Shift_DelG-p.L390fs
STADTCGA-HU-A4G8-01exon_skip_459590
42235892422375864223616142236161Frame_Shift_DelG-p.L390fs
LIHCTCGA-DD-A39Y-01exon_skip_459590
42235892422375864223622242236222Frame_Shift_DelA-p.I369fs
BLCATCGA-E7-A3Y1-01exon_skip_459590
42235892422375864223649242236492Frame_Shift_DelC-p.G279fs
LIHCTCGA-DD-A3A0-01exon_skip_459590
42235892422375864223688742236887Frame_Shift_DelG-p.Q148fs
LIHCTCGA-DD-A3A0-01exon_skip_459590
42235892422375864223718642237186Frame_Shift_DelG-p.P48fs
BLCATCGA-ZF-AA52-01exon_skip_459585
42230998422313064223100842231009Frame_Shift_Ins-Gp.R645fs
KIRCTCGA-A3-3308-01exon_skip_459585
42230998422313064223100842231009Frame_Shift_Ins-Gp.H645fs
KIRCTCGA-A3-3363-01exon_skip_459585
42230998422313064223100842231009Frame_Shift_Ins-Gp.H645fs
LIHCTCGA-BC-A112-01exon_skip_459590
42235892422375864223700042237001Frame_Shift_Ins-Cp.T110fs
KIRCTCGA-A3-3319-01exon_skip_459590
42235892422375864223716242237163Frame_Shift_Ins-Gp.L56fs
LUADTCGA-44-2656-01exon_skip_459590
42235892422375864223716242237163Frame_Shift_Ins-Gp.H56fs
BLCATCGA-BL-A0C8-01exon_skip_459590
42235892422375864223613742236137Nonsense_MutationGAp.Q398*
SKCMTCGA-FW-A3R5-06exon_skip_459590
42235892422375864223619142236191Nonsense_MutationGAp.Q380*
SKCMTCGA-FW-A3R5-06exon_skip_459590
42235892422375864223619142236191Nonsense_MutationGAp.Q380X
SKCMTCGA-EE-A29S-06exon_skip_459590
42235892422375864223700642237006Nonsense_MutationCTp.W108*
SKCMTCGA-EE-A29S-06exon_skip_459590
42235892422375864223700642237006Nonsense_MutationCTp.W108X
BLCATCGA-CF-A47X-01exon_skip_459590
42235892422375864223718442237184Nonsense_MutationGAp.Q49*
UCECTCGA-D1-A17Q-01exon_skip_459597
42330685423308174233068442330684Splice_SiteCTe0+1

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
CAL51_BREAST42230998422313064223111242231112Frame_Shift_DelG-p.P610fs
CAL51_BREAST42231058422313064223111242231112Frame_Shift_DelG-p.P610fs
SNU407_LARGE_INTESTINE42230998422313064223111242231112Frame_Shift_DelG-p.P610fs
SNU407_LARGE_INTESTINE42231058422313064223111242231112Frame_Shift_DelG-p.P610fs
SKUT1_SOFT_TISSUE42235892422375864223616142236161Frame_Shift_DelG-p.L390fs
U2OS_BONE42235892422375864223621142236217Frame_Shift_DelGAGCCCA-p.LGS371fs
LOVO_LARGE_INTESTINE42203943422041494220413042204132In_Frame_DelTCT-p.959_960EE>E
BICR18_UPPER_AERODIGESTIVE_TRACT42235892422375864223591542235916In_Frame_Ins-TGGp.471_472LS>LPS
CW9019_SOFT_TISSUE42203943422041494220398042203980Missense_MutationGAp.S1010L
NCIH1793_LUNG42203943422041494220399942203999Missense_MutationGTp.Q1004K
YD38_UPPER_AERODIGESTIVE_TRACT42203943422041494220402542204025Missense_MutationAGp.L995P
SNUC1_LARGE_INTESTINE42203943422041494220402542204025Missense_MutationAGp.L995P
MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE42203943422041494220404042204040Missense_MutationGAp.P990L
CW2_LARGE_INTESTINE42203943422041494220409142204091Missense_MutationCAp.R973M
MZ7MEL_SKIN42203943422041494220410742204107Missense_MutationCTp.D968N
SW684_SOFT_TISSUE42203943422041494220412242204122Missense_MutationCTp.E963K
HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE42227077422274614222709842227098Missense_MutationGAp.R750W
HT115_LARGE_INTESTINE42227077422274614222716442227164Missense_MutationGTp.L728I
HEC6_ENDOMETRIUM42227077422274614222718242227182Missense_MutationCAp.G722W
NCIH1703_LUNG42227077422274614222727142227271Missense_MutationATp.V692D
BICR18_UPPER_AERODIGESTIVE_TRACT42227077422274614222727242227272Missense_MutationCTp.V692I
PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE42227077422274614222727442227274Missense_MutationCTp.R691H
EW1_BONE42227077422274614222727542227275Missense_MutationGAp.R691C
PACADD137_PANCREAS42227077422274614222730842227308Missense_MutationCTp.A680T
MFE296_ENDOMETRIUM42227077422274614222732642227326Missense_MutationCTp.A674T
CCK81_LARGE_INTESTINE42227077422274614222734742227347Missense_MutationGAp.P667S
NK92MI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE42227077422274614222740042227400Missense_MutationTCp.Q649R
NCIH727_LUNG42230998422313064223112342231123Missense_MutationCAp.V607F
NCIH727_LUNG42231058422313064223112342231123Missense_MutationCAp.V607F
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE42230998422313064223116542231166Missense_MutationGATTp.L593I
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE42231058422313064223116542231166Missense_MutationGATTp.L593I
SNU1040_LARGE_INTESTINE42230998422313064223118942231189Missense_MutationGAp.P585S
SNU1040_LARGE_INTESTINE42231058422313064223118942231189Missense_MutationGAp.P585S
SNU1040_LARGE_INTESTINE42230998422313064223119442231194Missense_MutationATp.V583D
SNU1040_LARGE_INTESTINE42231058422313064223119442231194Missense_MutationATp.V583D
HEC6_ENDOMETRIUM42230998422313064223120342231203Missense_MutationGAp.T580M
HEC6_ENDOMETRIUM42231058422313064223120342231203Missense_MutationGAp.T580M
UO31_KIDNEY42235892422375864223592542235925Missense_MutationACp.H468Q
SNU175_LARGE_INTESTINE42235892422375864223595642235956Missense_MutationCAp.G458V
NTERA2CLD1_TESTIS42235892422375864223611342236113Missense_MutationGTp.Q406K
NCIH1688_LUNG42235892422375864223612542236125Missense_MutationGAp.R402C
SNU1040_LARGE_INTESTINE42235892422375864223635042236350Missense_MutationAGp.Y327H
SUDHL16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE42235892422375864223638042236380Missense_MutationGAp.R317W
MRKNU1_BREAST42235892422375864223643642236436Missense_MutationGAp.S298L
COLO792_SKIN42235892422375864223649442236494Missense_MutationCGp.G279R
HEC59_ENDOMETRIUM42235892422375864223651442236514Missense_MutationGAp.P272L
HEC59_ENDOMETRIUM42235892422375864223652142236521Missense_MutationAGp.Y270H
BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE42235892422375864223657242236572Missense_MutationCAp.A253S
EFO27_OVARY42235892422375864223658142236581Missense_MutationGAp.P250S
SNUC5_LARGE_INTESTINE42235892422375864223662842236628Missense_MutationTCp.Y234C
HCC2998_LARGE_INTESTINE42235892422375864223665042236650Missense_MutationGAp.P227S
NCIH1573_LUNG42235892422375864223665942236659Missense_MutationCTp.G224R
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE42235892422375864223672842236728Missense_MutationAGp.Y201H
ES2_OVARY42235892422375864223675942236759Missense_MutationCTp.M190I
HT115_LARGE_INTESTINE42235892422375864223678442236784Missense_MutationCTp.R182H
BB30PBL_MATCHED_NORMAL_TISSUE42235892422375864223678442236784Missense_MutationCTp.R182H
KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE42235892422375864223683842236838Missense_MutationTCp.Q164R
HEC6_ENDOMETRIUM42235892422375864223685542236855Missense_MutationCAp.Q158H
HSC4_UPPER_AERODIGESTIVE_TRACT42235892422375864223689542236895Missense_MutationGCp.S145C
YD38_UPPER_AERODIGESTIVE_TRACT42235892422375864223704842237048Missense_MutationTAp.H94L
MFE296_ENDOMETRIUM42235892422375864223705842237058Missense_MutationGAp.P91S
SW1463_LARGE_INTESTINE42235892422375864223707242237072Missense_MutationCTp.G86E
HMCB_SKIN42235892422375864223716642237166Missense_MutationGAp.P55S
CAL62_THYROID42235892422375864223719242237192Missense_MutationTAp.D46V
KPMRTRY_SOFT_TISSUE42235892422375864223720242237202Missense_MutationCTp.G43S
AU565_BREAST42235892422375864223724642237246Missense_MutationAGp.V28A
YD38_UPPER_AERODIGESTIVE_TRACT42235892422375864223728242237282Missense_MutationCTp.S16N
A673_BONE42203943422041494220401442204014Nonsense_MutationCAp.E999*
RERFLCKJ_LUNG42235892422375864223647042236470Nonsense_MutationCAp.E287*
SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE42235892422375864223695342236953Nonsense_MutationGAp.Q126*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TRERF1

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 TRERF1


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TRERF1


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RelatedDrugs for TRERF1

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 TRERF1

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
TRERF1C1458155Mammary Neoplasms1CTD_human