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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 LARP7

check button Gene summary
Gene informationGene symbol

LARP7

Gene ID

51574

Gene nameLa ribonucleoprotein domain family member 7
SynonymsALAZS|HDCMA18P|PIP7S
Cytomap

4q25

Type of geneprotein-coding
Descriptionla-related protein 7P-TEFb-interaction protein for 7SK stability
Modification date20180522
UniProtAcc

Q4G0J3

ContextPubMed: LARP7 [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

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Exon skipping events across known transcript of Ensembl for LARP7 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 LARP7

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 LARP7

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_4258174113558348:113558395:113558799:113558943:113565580:113565644113558799:113558943ENSG00000174720.11ENST00000509061.1
exon_skip_4258184113558348:113558395:113558799:113558943:113565823:113565855113558799:113558943ENSG00000174720.11ENST00000508577.1
exon_skip_4258234113558348:113558395:113565823:113565924:113567506:113567607113565823:113565924ENSG00000174720.11ENST00000509622.1
exon_skip_4258304113558680:113558759:113565823:113565924:113567506:113567607113565823:113565924ENSG00000174720.11ENST00000505216.1
exon_skip_4258324113558680:113558759:113565823:113566027:113567506:113567607113565823:113566027ENSG00000174720.11ENST00000324052.6,ENST00000505034.1
exon_skip_4258354113558799:113558943:113565580:113565644:113565823:113565855113565580:113565644ENSG00000174720.11ENST00000509061.1
exon_skip_4258384113565823:113566027:113566706:113566818:113567506:113567607113566706:113566818ENSG00000174720.11ENST00000512589.1
exon_skip_4258404113567506:113567607:113567743:113567827:113567946:113568058113567743:113567827ENSG00000174720.11ENST00000324052.6,ENST00000505034.1,ENST00000344442.5,ENST00000505216.1,ENST00000509622.1,ENST00000509061.1
exon_skip_4258484113568874:113568990:113570690:113570842:113571616:113571738113570690:113570842ENSG00000174720.11ENST00000324052.6,ENST00000511529.1,ENST00000513553.1,ENST00000344442.5,ENST00000509622.1,ENST00000509061.1

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

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Exon skipping events with PSIs in GTEx for LARP7

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_4258174113558348:113558395:113558799:113558943:113565580:113565644113558799:113558943ENSG00000174720.11ENST00000509061.1
exon_skip_4258184113558348:113558395:113558799:113558943:113565823:113565855113558799:113558943ENSG00000174720.11ENST00000508577.1
exon_skip_4258234113558348:113558395:113565823:113565924:113567506:113567607113565823:113565924ENSG00000174720.11ENST00000509622.1
exon_skip_4258304113558680:113558759:113565823:113565924:113567506:113567607113565823:113565924ENSG00000174720.11ENST00000505216.1
exon_skip_4258324113558680:113558759:113565823:113566027:113567506:113567607113565823:113566027ENSG00000174720.11ENST00000505034.1,ENST00000324052.6
exon_skip_4258354113558799:113558943:113565580:113565644:113565823:113565855113565580:113565644ENSG00000174720.11ENST00000509061.1
exon_skip_4258384113565823:113566027:113566706:113566818:113567506:113567607113566706:113566818ENSG00000174720.11ENST00000512589.1
exon_skip_4258404113567506:113567607:113567743:113567827:113567946:113568058113567743:113567827ENSG00000174720.11ENST00000344442.5,ENST00000509061.1,ENST00000509622.1,ENST00000505034.1,ENST00000324052.6,ENST00000505216.1
exon_skip_4258484113568874:113568990:113570690:113570842:113571616:113571738113570690:113570842ENSG00000174720.11ENST00000344442.5,ENST00000509061.1,ENST00000509622.1,ENST00000513553.1,ENST00000324052.6,ENST00000511529.1

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 LARP7

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
ENST000003240521135658231135660275CDS-5UTR
ENST00000324052113570690113570842Frame-shift
ENST00000344442113570690113570842Frame-shift
ENST00000324052113567743113567827In-frame
ENST00000344442113567743113567827In-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
ENST000003240521135658231135660275CDS-5UTR
ENST00000324052113570690113570842Frame-shift
ENST00000344442113570690113570842Frame-shift
ENST00000324052113567743113567827In-frame
ENST00000344442113567743113567827In-frame

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Infer the effects of exon skipping event on protein functional features for LARP7

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
ENST000003240522174582113567743113567827454537101129
ENST000003444422303582113567743113567827582665101129

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
ENST000003240522174582113567743113567827454537101129
ENST000003444422303582113567743113567827582665101129

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
Q4G0J31011291368Alternative sequenceID=VSP_024021;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2
Q4G0J31011291368Alternative sequenceID=VSP_024021;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2
Q4G0J3101129106110Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4WKR
Q4G0J3101129106110Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4WKR
Q4G0J3101129127130Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4WKR
Q4G0J3101129127130Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4WKR
Q4G0J31011291582ChainID=PRO_0000281143;Note=La-related protein 7
Q4G0J31011291582ChainID=PRO_0000281143;Note=La-related protein 7
Q4G0J310112928122DomainNote=HTH La-type RNA-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00332
Q4G0J310112928122DomainNote=HTH La-type RNA-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00332
Q4G0J3101129125203DomainNote=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00176
Q4G0J3101129125203DomainNote=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00176
Q4G0J3101129122125HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4WKR
Q4G0J3101129122125HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4WKR
Q4G0J3101129128128MutagenesisNote=Loss of 7SK RNA-binding and marked decrease in 7SK RNP complex formation. Y->D;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18249148;Dbxref=PMID:18249148
Q4G0J3101129128128MutagenesisNote=Loss of 7SK RNA-binding and marked decrease in 7SK RNP complex formation. Y->D;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18249148;Dbxref=PMID:18249148


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
Q4G0J31011291368Alternative sequenceID=VSP_024021;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2
Q4G0J31011291368Alternative sequenceID=VSP_024021;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.2
Q4G0J3101129106110Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4WKR
Q4G0J3101129106110Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4WKR
Q4G0J3101129127130Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4WKR
Q4G0J3101129127130Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4WKR
Q4G0J31011291582ChainID=PRO_0000281143;Note=La-related protein 7
Q4G0J31011291582ChainID=PRO_0000281143;Note=La-related protein 7
Q4G0J310112928122DomainNote=HTH La-type RNA-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00332
Q4G0J310112928122DomainNote=HTH La-type RNA-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00332
Q4G0J3101129125203DomainNote=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00176
Q4G0J3101129125203DomainNote=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00176
Q4G0J3101129122125HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4WKR
Q4G0J3101129122125HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4WKR
Q4G0J3101129128128MutagenesisNote=Loss of 7SK RNA-binding and marked decrease in 7SK RNP complex formation. Y->D;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18249148;Dbxref=PMID:18249148
Q4G0J3101129128128MutagenesisNote=Loss of 7SK RNA-binding and marked decrease in 7SK RNP complex formation. Y->D;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18249148;Dbxref=PMID:18249148


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SNVs in the skipped exons for LARP7

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
STADTCGA-SW-A7EA-01exon_skip_425830
exon_skip_425823
113565824113565924113565896113565896Frame_Shift_DelA-p.E31fs
STADTCGA-SW-A7EA-01exon_skip_425832
113565824113566027113565896113565896Frame_Shift_DelA-p.E31fs
BLCATCGA-ZF-AA4W-01exon_skip_425848
113570691113570842113570754113570754Frame_Shift_DelA-p.L409fs
HNSCTCGA-F7-A624-01exon_skip_425848
113570691113570842113570754113570754Frame_Shift_DelA-p.L409fs
LIHCTCGA-G3-A3CJ-01exon_skip_425848
113570691113570842113570754113570754Frame_Shift_DelA-p.L409fs
STADTCGA-BR-4201-01exon_skip_425848
113570691113570842113570754113570754Frame_Shift_DelA-p.L409X
STADTCGA-BR-8368-01exon_skip_425848
113570691113570842113570754113570754Frame_Shift_DelA-p.L409X
STADTCGA-BR-8372-01exon_skip_425848
113570691113570842113570754113570754Frame_Shift_DelA-p.L409X
STADTCGA-CG-5726-01exon_skip_425848
113570691113570842113570754113570754Frame_Shift_DelA-p.L409X
UCECTCGA-AP-A05N-01exon_skip_425848
113570691113570842113570754113570754Frame_Shift_DelA-p.L409fs
UCECTCGA-AX-A060-01exon_skip_425848
113570691113570842113570754113570754Frame_Shift_DelA-p.L409fs
UCECTCGA-BG-A0M4-01exon_skip_425848
113570691113570842113570754113570754Frame_Shift_DelA-p.L409fs
UCECTCGA-BG-A0MQ-01exon_skip_425848
113570691113570842113570754113570754Frame_Shift_DelA-p.L409fs
UCECTCGA-D1-A17A-01exon_skip_425848
113570691113570842113570754113570754Frame_Shift_DelA-p.L409fs
KICHTCGA-KL-8332-01exon_skip_425830
exon_skip_425823
113565824113565924113565882113565883Frame_Shift_Ins-Ap.K19fs
KICHTCGA-KL-8332-01exon_skip_425832
113565824113566027113565882113565883Frame_Shift_Ins-Ap.K19fs
ESCATCGA-Z6-A9VB-01exon_skip_425848
113570691113570842113570753113570754Frame_Shift_Ins-Ap.T405fs
LUSCTCGA-34-5927-01exon_skip_425830
exon_skip_425823
113565824113565924113565913113565913Nonsense_MutationCTp.R37*
LUSCTCGA-34-5927-01exon_skip_425832
113565824113566027113565913113565913Nonsense_MutationCTp.R37*

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
HEC1A_ENDOMETRIUM113565824113565924113565896113565896Frame_Shift_DelA-p.E24fs
HEC1A_ENDOMETRIUM113565824113566027113565896113565896Frame_Shift_DelA-p.E24fs
HEC1_ENDOMETRIUM113565824113565924113565896113565896Frame_Shift_DelA-p.E24fs
HEC1_ENDOMETRIUM113565824113566027113565896113565896Frame_Shift_DelA-p.E24fs
HEC1B_ENDOMETRIUM113565824113565924113565896113565896Frame_Shift_DelA-p.E24fs
HEC1B_ENDOMETRIUM113565824113566027113565896113565896Frame_Shift_DelA-p.E24fs
TE11_OESOPHAGUS113570691113570842113570701113570701Frame_Shift_DelA-p.M385fs
T3M10_LUNG113570691113570842113570706113570709Frame_Shift_DelTTTG-p.DL386fs
DV90_LUNG113570691113570842113570754113570754Frame_Shift_DelA-p.L402fs
HCT15_LARGE_INTESTINE113570691113570842113570754113570754Frame_Shift_DelA-p.L402fs
LOVO_LARGE_INTESTINE113570691113570842113570754113570754Frame_Shift_DelA-p.L402fs
DG75_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE113570691113570842113570754113570754Frame_Shift_DelA-p.L402fs
P30OHK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE113570691113570842113570754113570754Frame_Shift_DelA-p.L402fs
CW2_LARGE_INTESTINE113567744113567827113567773113567774Frame_Shift_Ins-Ap.K112fs
T3M10_LUNG113570691113570842113570709113570710Frame_Shift_Ins-AAp.K388fs
HEC151_ENDOMETRIUM113570691113570842113570753113570754Frame_Shift_Ins-Ap.LK402fs
IM95_STOMACH113570691113570842113570753113570754Frame_Shift_Ins-Ap.LK402fs
COLO684_ENDOMETRIUM113565824113565924113565898113565898Missense_MutationAGp.K25E
COLO684_ENDOMETRIUM113565824113566027113565898113565898Missense_MutationAGp.K25E
HEC251_ENDOMETRIUM113565824113565924113565914113565914Missense_MutationGAp.R30Q
HEC251_ENDOMETRIUM113565824113566027113565914113565914Missense_MutationGAp.R30Q
NCIH1573_LUNG113565824113565924113565914113565914Missense_MutationGTp.R30L
NCIH1573_LUNG113565824113566027113565914113565914Missense_MutationGTp.R30L
SH10TC_STOMACH113565824113566027113566016113566016Missense_MutationCAp.S64Y
RCM1_LARGE_INTESTINE113567744113567827113567757113567757Missense_MutationGTp.G106V
NCIH1651_LUNG113570691113570842113570750113570750Missense_MutationCTp.S401F
COLO320_LARGE_INTESTINE113570691113570842113570750113570750Missense_MutationCTp.S401F
DU145_PROSTATE113570691113570842113570807113570807Missense_MutationGTp.G420V
CCLFPEDS0008T_SOFT_TISSUE113570691113570842113570829113570829Missense_MutationGAp.M427I
CCLFPEDS0008T_SOFT_TISSUE113570691113570842113570835113570835Missense_MutationTAp.N429K
CHLA266_SOFT_TISSUE113570691113570842113570836113570836Missense_MutationGAp.E430K
CW9019_SOFT_TISSUE113570691113570842113570836113570836Missense_MutationGAp.E430K
KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE113565824113565924113565913113565913Nonsense_MutationCTp.R30*
KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE113565824113566027113565913113565913Nonsense_MutationCTp.R30*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LARP7

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 LARP7


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LARP7


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RelatedDrugs for LARP7

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 LARP7

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
LARP7C3714756Intellectual Disability1CTD_human