ExonSkipDB Logo

Home

Download

Statistics

Landscape

Help

Contact

Center for Computational Systems Medicine
leaf

Gene summary

leaf

Gene structures and expression levels

leaf

Exon skipping events with PSIs in TCGA

leaf

Exon skipping events with PSIs in GTEx

leaf

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

leaf

Exon skipping events in the canonical protein sequence

leaf

SNVs in the skipped exons with depth of coverage

leaf

Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

leaf

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon

leaf

Related drugs with this gene

leaf

Related diseases with this gene

Gene summary for HERC4

check button Gene summary
Gene informationGene symbol

HERC4

Gene ID

26091

Gene nameHECT and RLD domain containing E3 ubiquitin protein ligase 4
Synonyms-
Cytomap

10q21.3

Type of geneprotein-coding
Descriptionprobable E3 ubiquitin-protein ligase HERC4HECT domain and RCC1-like domain-containing protein 4HECT-type E3 ubiquitin transferase HERC4hect domain and RLD 4
Modification date20180522
UniProtAcc

Q5GLZ8

ContextPubMed: HERC4 [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

Top

Exon skipping events across known transcript of Ensembl for HERC4 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

Top

Gene isoform structures and expression levels for HERC4

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

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


Top

Exon skipping events with PSIs in TCGA for HERC4

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_496701069692353:69692537:69695909:69695992:69699344:6969940869695909:69695992ENSG00000148634.11ENST00000395198.3,ENST00000373700.4,ENST00000277817.6,ENST00000473533.2,ENST00000395187.2,ENST00000427635.2
exon_skip_496721069695909:69695992:69699344:69699411:69700695:6970086269699344:69699411ENSG00000148634.11ENST00000395198.3,ENST00000373700.4,ENST00000277817.6,ENST00000473533.2,ENST00000395187.2,ENST00000427635.2
exon_skip_496771069699344:69699411:69700695:69700862:69714351:6971449569700695:69700862ENSG00000148634.11ENST00000395198.3,ENST00000373700.4,ENST00000277817.6,ENST00000473533.2,ENST00000395187.2,ENST00000427635.2
exon_skip_496811069714719:69714887:69716634:69716733:69726439:6972655969716634:69716733ENSG00000148634.11ENST00000373700.4,ENST00000473533.2,ENST00000395187.2,ENST00000427635.2
exon_skip_496821069716634:69716733:69718869:69718893:69726439:6972655969718869:69718893ENSG00000148634.11ENST00000395198.3,ENST00000277817.6,ENST00000412272.2
exon_skip_496831069726439:69726559:69747799:69747901:69748419:6974859269747799:69747901ENSG00000148634.11ENST00000427635.2
exon_skip_496841069726439:69726559:69748419:69748592:69749967:6974999869748419:69748592ENSG00000148634.11ENST00000395198.3,ENST00000373700.4,ENST00000277817.6,ENST00000473533.2,ENST00000460168.1,ENST00000395187.2,ENST00000412272.2
exon_skip_496901069748419:69748592:69749967:69750157:69750660:6975077269749967:69750157ENSG00000148634.11ENST00000395198.3,ENST00000373700.4,ENST00000277817.6,ENST00000473533.2,ENST00000395187.2,ENST00000427635.2,ENST00000412272.2
exon_skip_496941069752362:69752439:69773782:69773943:69785302:6978543369773782:69773943ENSG00000148634.11ENST00000395198.3,ENST00000373700.4,ENST00000277817.6,ENST00000473533.2,ENST00000395187.2,ENST00000412272.2
exon_skip_496951069773782:69773943:69785302:69785433:69792534:6979262669785302:69785433ENSG00000148634.11ENST00000395198.3,ENST00000373700.4,ENST00000277817.6,ENST00000395187.2,ENST00000427635.2,ENST00000412272.2
exon_skip_496971069785302:69785433:69792534:69792626:69793721:6979394369792534:69792626ENSG00000148634.11ENST00000395198.3,ENST00000373700.4,ENST00000277817.6,ENST00000395187.2,ENST00000427635.2,ENST00000412272.2
exon_skip_497011069792575:69792626:69793721:69793943:69797849:6979792669793721:69793943ENSG00000148634.11ENST00000395198.3,ENST00000373700.4,ENST00000277817.6,ENST00000395187.2,ENST00000427635.2,ENST00000463478.1,ENST00000412272.2
exon_skip_497041069797849:69797926:69799173:69799245:69804160:6980431569799173:69799245ENSG00000148634.11ENST00000513996.1
exon_skip_497101069797849:69797926:69804160:69804320:69832639:6983285469804160:69804320ENSG00000148634.11ENST00000395198.3,ENST00000373700.4,ENST00000427635.2,ENST00000412272.2
exon_skip_497141069832891:69832943:69833413:69833443:69834900:6983498369833413:69833443ENSG00000148634.11ENST00000395198.3,ENST00000513996.1,ENST00000373700.4,ENST00000395185.3,ENST00000473533.2,ENST00000395187.2,ENST00000492996.2,ENST00000412272.2

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

Top

Exon skipping events with PSIs in GTEx for HERC4

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_496701069692353:69692537:69695909:69695992:69699344:6969940869695909:69695992ENSG00000148634.11ENST00000277817.6,ENST00000395198.3,ENST00000427635.2,ENST00000473533.2,ENST00000373700.4,ENST00000395187.2
exon_skip_496721069695909:69695992:69699344:69699411:69700695:6970086269699344:69699411ENSG00000148634.11ENST00000277817.6,ENST00000395198.3,ENST00000427635.2,ENST00000473533.2,ENST00000373700.4,ENST00000395187.2
exon_skip_496771069699344:69699411:69700695:69700862:69714351:6971449569700695:69700862ENSG00000148634.11ENST00000277817.6,ENST00000395198.3,ENST00000427635.2,ENST00000473533.2,ENST00000373700.4,ENST00000395187.2
exon_skip_496811069714719:69714887:69716634:69716733:69726439:6972655969716634:69716733ENSG00000148634.11ENST00000427635.2,ENST00000473533.2,ENST00000373700.4,ENST00000395187.2
exon_skip_496821069716634:69716733:69718869:69718893:69726439:6972655969718869:69718893ENSG00000148634.11ENST00000277817.6,ENST00000412272.2,ENST00000395198.3
exon_skip_496831069726439:69726559:69747799:69747901:69748419:6974859269747799:69747901ENSG00000148634.11ENST00000427635.2
exon_skip_496841069726439:69726559:69748419:69748592:69749967:6974999869748419:69748592ENSG00000148634.11ENST00000277817.6,ENST00000412272.2,ENST00000395198.3,ENST00000473533.2,ENST00000373700.4,ENST00000395187.2,ENST00000460168.1
exon_skip_496901069748419:69748592:69749967:69750157:69750660:6975077269749967:69750157ENSG00000148634.11ENST00000277817.6,ENST00000412272.2,ENST00000395198.3,ENST00000427635.2,ENST00000473533.2,ENST00000373700.4,ENST00000395187.2
exon_skip_496941069752362:69752439:69773782:69773943:69785302:6978543369773782:69773943ENSG00000148634.11ENST00000277817.6,ENST00000412272.2,ENST00000395198.3,ENST00000473533.2,ENST00000373700.4,ENST00000395187.2
exon_skip_496951069773782:69773943:69785302:69785433:69792534:6979262669785302:69785433ENSG00000148634.11ENST00000277817.6,ENST00000412272.2,ENST00000395198.3,ENST00000427635.2,ENST00000373700.4,ENST00000395187.2
exon_skip_496971069785302:69785433:69792534:69792626:69793721:6979394369792534:69792626ENSG00000148634.11ENST00000277817.6,ENST00000412272.2,ENST00000395198.3,ENST00000427635.2,ENST00000373700.4,ENST00000395187.2
exon_skip_497001069785302:69785433:69793721:69793943:69797849:6979792669793721:69793943ENSG00000148634.11ENST00000473533.2
exon_skip_497011069792575:69792626:69793721:69793943:69797849:6979792669793721:69793943ENSG00000148634.11ENST00000277817.6,ENST00000412272.2,ENST00000395198.3,ENST00000427635.2,ENST00000373700.4,ENST00000395187.2,ENST00000463478.1
exon_skip_497041069797849:69797926:69799173:69799245:69804160:6980431569799173:69799245ENSG00000148634.11ENST00000513996.1
exon_skip_497101069797849:69797926:69804160:69804320:69832639:6983285469804160:69804320ENSG00000148634.11ENST00000412272.2,ENST00000395198.3,ENST00000427635.2,ENST00000373700.4
exon_skip_497141069832891:69832943:69833413:69833443:69834900:6983498369833413:69833443ENSG00000148634.11ENST00000412272.2,ENST00000395198.3,ENST00000473533.2,ENST00000373700.4,ENST00000395187.2,ENST00000513996.1,ENST00000395185.3,ENST00000492996.2

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

* Skipped exon sequences.

Top

Open reading frame (ORF) annotation in the exon skipping event for HERC4

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
ENST0000039519869833413698334433UTR-3UTR
ENST000003951986969590969695992Frame-shift
ENST000003951986969934469699411Frame-shift
ENST000003951986970069569700862Frame-shift
ENST000003951986974841969748592Frame-shift
ENST000003951986974996769750157Frame-shift
ENST000003951986977378269773943Frame-shift
ENST000003951986978530269785433Frame-shift
ENST000003951986979253469792626Frame-shift
ENST000003951986980416069804320Frame-shift
ENST000003951986971886969718893In-frame
ENST000003951986979372169793943In-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
ENST0000039519869833413698334433UTR-3UTR
ENST000003951986969590969695992Frame-shift
ENST000003951986969934469699411Frame-shift
ENST000003951986970069569700862Frame-shift
ENST000003951986974841969748592Frame-shift
ENST000003951986974996769750157Frame-shift
ENST000003951986977378269773943Frame-shift
ENST000003951986978530269785433Frame-shift
ENST000003951986979253469792626Frame-shift
ENST000003951986980416069804320Frame-shift
ENST000003951986971886969718893In-frame
ENST000003951986979372169793943In-frame

Top

Infer the effects of exon skipping event on protein functional features for HERC4

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
ENST00000395198446210576979372169793943712933154228

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
ENST00000395198446210576979372169793943712933154228

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
Q5GLZ81542281111057Alternative sequenceID=VSP_023175;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15676274;Dbxref=PMID:15676274
Q5GLZ81542281181057Alternative sequenceID=VSP_023176;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:15676274;Dbxref=PMID:15489334,PMID:15676274
Q5GLZ815422811057ChainID=PRO_0000278216;Note=Probable E3 ubiquitin-protein ligase HERC4
Q5GLZ8154228102154RepeatNote=RCC1 3
Q5GLZ8154228156207RepeatNote=RCC1 4
Q5GLZ8154228208259RepeatNote=RCC1 5


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
Q5GLZ81542281111057Alternative sequenceID=VSP_023175;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15676274;Dbxref=PMID:15676274
Q5GLZ81542281181057Alternative sequenceID=VSP_023176;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:15676274;Dbxref=PMID:15489334,PMID:15676274
Q5GLZ815422811057ChainID=PRO_0000278216;Note=Probable E3 ubiquitin-protein ligase HERC4
Q5GLZ8154228102154RepeatNote=RCC1 3
Q5GLZ8154228156207RepeatNote=RCC1 4
Q5GLZ8154228208259RepeatNote=RCC1 5


Top

SNVs in the skipped exons for HERC4

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
BRCATCGA-E9-A1N8-01exon_skip_49670
69695910696959926969591469695917Frame_Shift_DelTTTG-p.Q891fs
LIHCTCGA-DD-A3A0-01exon_skip_49670
69695910696959926969591869695918Frame_Shift_DelT-p.K890fs
BLCATCGA-DK-A1AC-01exon_skip_49684
69748420697485926974851369748513Frame_Shift_DelC-p.L571fs
LIHCTCGA-DD-A1EG-01exon_skip_49694
69773783697739436977381169773811Frame_Shift_DelG-p.P347fs
LIHCTCGA-DD-A3A0-01exon_skip_49694
69773783697739436977383869773838Frame_Shift_DelG-p.P338fs
LIHCTCGA-DD-A3A0-01exon_skip_49701
69793722697939436979381169793811Frame_Shift_DelC-p.G199fs
BRCATCGA-A8-A08R-01exon_skip_49701
69793722697939436979382669793829Frame_Shift_DelTGCA-p.M193fs
BLCATCGA-G2-AA3C-01exon_skip_49694
69773783697739436977388069773881Frame_Shift_Ins-Tp.N324fs
LIHCTCGA-G3-A3CJ-01exon_skip_49695
69785303697854336978541269785412Nonsense_MutationCAp.G267X
LUADTCGA-05-4397-01exon_skip_49701
69793722697939436979392069793920Nonsense_MutationGAp.Q163*
LUADTCGA-MN-A4N4-01exon_skip_49701
69793722697939436979392369793923Nonsense_MutationCAp.G162*
BLCATCGA-MV-A51V-01exon_skip_49710
69804161698043206980418569804185Nonsense_MutationGCp.S121*
CHOLTCGA-W6-AA0S-01exon_skip_49695
69785303697854336978543569785435Splice_SiteTA.
KIRPTCGA-G7-A8LB-01exon_skip_49710
69804161698043206980416069804160Splice_SiteCT.

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
SARC9371_BONE69695910696959926969595669695956Missense_MutationCTp.E878K
MZ7MEL_SKIN69695910696959926969597369695973Missense_MutationCTp.G872D
RCC10RGB_KIDNEY69700696697008626970070569700705Missense_MutationTCp.D840G
SBC1_LUNG69700696697008626970070569700705Missense_MutationTCp.D840G
SNGM_ENDOMETRIUM69700696697008626970080869700808Missense_MutationTCp.I806V
RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE69700696697008626970083369700833Missense_MutationCAp.L797F
GP2D_LARGE_INTESTINE69716635697167336971669669716696Missense_MutationACp.F663C
GP5D_LARGE_INTESTINE69716635697167336971669669716696Missense_MutationACp.F663C
HEC151_ENDOMETRIUM69748420697485926974844869748448Missense_MutationGAp.A593V
CAOV3_OVARY69748420697485926974846969748469Missense_MutationATp.F586Y
SNU1_STOMACH69748420697485926974849769748497Missense_MutationCTp.G577S
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE69749968697501576975004569750045Missense_MutationGCp.S519C
JHUEM7_ENDOMETRIUM69749968697501576975013769750137Missense_MutationCAp.K488N
MCF7_BREAST69749968697501576975015069750150Missense_MutationGTp.A484D
CAMA1_BREAST69785303697854336978538169785381Missense_MutationTAp.N277I
769P_KIDNEY69792535697926266979254369792543Missense_MutationGTp.L257I
MIAPACA2_PANCREAS69792535697926266979256669792566Missense_MutationCGp.C249S
BT474_BREAST69792535697926266979259969792599Missense_MutationGAp.S238L
GP2D_LARGE_INTESTINE69792535697926266979262169792621Missense_MutationATp.Y231N
GP5D_LARGE_INTESTINE69792535697926266979262169792621Missense_MutationATp.Y231N
JEG3_PLACENTA69793722697939436979376169793761Missense_MutationGAp.R216C
SW684_SOFT_TISSUE69793722697939436979389369793893Missense_MutationCTp.G172S
OCUBM_BREAST69793722697939436979389969793899Missense_MutationCAp.G170C
HT115_LARGE_INTESTINE69793722697939436979391369793913Missense_MutationTGp.K165T
JHU029_UPPER_AERODIGESTIVE_TRACT69793722697939436979394069793940Missense_MutationCTp.S156N
KM12_LARGE_INTESTINE69804161698043206980418069804180Missense_MutationCTp.E123K
NCIH1563_LUNG69804161698043206980428269804282Missense_MutationCAp.V89F

Top

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for HERC4

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value
exon_skip_496951069773782:69773943:69785302:69785433:69792534:6979262669785302:69785433ENST00000395198.3,ENST00000373700.4,ENST00000277817.6,ENST00000395187.2,ENST00000427635.2,ENST00000412272.2ESCArs3834396chr10:69785435T/TA7.63e-04
exon_skip_496951069773782:69773943:69785302:69785433:69792534:6979262669785302:69785433ENST00000395198.3,ENST00000373700.4,ENST00000277817.6,ENST00000395187.2,ENST00000427635.2,ENST00000412272.2ESCArs3834396chr10:69785435T/TA7.63e-04

Top

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for HERC4


Top

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for HERC4


Top

RelatedDrugs for HERC4

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

Top

RelatedDiseases for HERC4

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