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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 PHACTR2

check button Gene summary
Gene informationGene symbol

PHACTR2

Gene ID

9749

Gene namephosphatase and actin regulator 2
SynonymsC6orf56
Cytomap

6q24.2

Type of geneprotein-coding
Descriptionphosphatase and actin regulator 2
Modification date20180519
UniProtAcc

O75167

ContextPubMed: PHACTR2 [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 PHACTR2 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 PHACTR2

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 PHACTR2

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_4545886143999309:143999346:144033152:144033320:144070121:144070202144033152:144033320ENSG00000112419.10ENST00000402863.3,ENST00000397980.3,ENST00000367582.3,ENST00000440869.2,ENST00000451827.2
exon_skip_4545906144033152:144033320:144070121:144070202:144074890:144075049144070121:144070202ENSG00000112419.10ENST00000305766.6,ENST00000402863.3,ENST00000367584.4,ENST00000397980.3,ENST00000367582.3,ENST00000427704.2,ENST00000440869.2
exon_skip_4545916144033152:144033320:144070121:144070202:144086397:144086611144070121:144070202ENSG00000112419.10ENST00000451827.2
exon_skip_4545966144070121:144070202:144074890:144075049:144086397:144086611144074890:144075049ENSG00000112419.10ENST00000305766.6,ENST00000367584.4,ENST00000420771.2,ENST00000542769.1,ENST00000367582.3
exon_skip_4545986144074890:144075049:144081537:144081777:144086397:144086611144081537:144081777ENSG00000112419.10ENST00000427704.2,ENST00000440869.2
exon_skip_4545996144074890:144075049:144086397:144086935:144093394:144093594144086397:144086935ENSG00000112419.10ENST00000305766.6,ENST00000367584.4,ENST00000367582.3
exon_skip_4546006144086397:144086935:144093394:144093594:144095195:144095352144093394:144093594ENSG00000112419.10ENST00000305766.6,ENST00000367584.4,ENST00000367582.3,ENST00000427704.2,ENST00000440869.2

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

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Exon skipping events with PSIs in GTEx for PHACTR2

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_4545886143999309:143999346:144033152:144033320:144070121:144070202144033152:144033320ENSG00000112419.10ENST00000440869.2,ENST00000367582.3,ENST00000402863.3,ENST00000451827.2,ENST00000397980.3
exon_skip_4545906144033152:144033320:144070121:144070202:144074890:144075049144070121:144070202ENSG00000112419.10ENST00000367584.4,ENST00000427704.2,ENST00000305766.6,ENST00000440869.2,ENST00000367582.3,ENST00000402863.3,ENST00000397980.3
exon_skip_4545916144033152:144033320:144070121:144070202:144086397:144086611144070121:144070202ENSG00000112419.10ENST00000451827.2
exon_skip_4545966144070121:144070202:144074890:144075049:144086397:144086611144074890:144075049ENSG00000112419.10ENST00000367584.4,ENST00000305766.6,ENST00000367582.3,ENST00000542769.1,ENST00000420771.2
exon_skip_4545986144074890:144075049:144081537:144081777:144086397:144086611144081537:144081777ENSG00000112419.10ENST00000427704.2,ENST00000440869.2
exon_skip_4545996144074890:144075049:144086397:144086935:144093394:144093594144086397:144086935ENSG00000112419.10ENST00000367584.4,ENST00000305766.6,ENST00000367582.3
exon_skip_4546006144086397:144086935:144093394:144093594:144095195:144095352144093394:144093594ENSG00000112419.10ENST00000367584.4,ENST00000427704.2,ENST00000305766.6,ENST00000440869.2,ENST00000367582.3

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 PHACTR2

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
ENST00000427704144093394144093594Frame-shift
ENST00000427704144070121144070202In-frame
ENST00000427704144081537144081777In-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
ENST00000427704144093394144093594Frame-shift
ENST00000427704144070121144070202In-frame
ENST00000427704144081537144081777In-frame

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Infer the effects of exon skipping event on protein functional features for PHACTR2

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
ENST0000042770495486341440701211440702023123926087
ENST000004277049548634144081537144081777552791140220

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
ENST0000042770495486341440701211440702023123926087
ENST000004277049548634144081537144081777552791140220

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


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


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SNVs in the skipped exons for PHACTR2

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.
PHACTR2_COAD_exon_skip_454598_psi_boxplot.png
boxplot
PHACTR2_STAD_exon_skip_454598_psi_boxplot.png
boxplot
PHACTR2_THCA_exon_skip_454598_psi_boxplot.png
boxplot

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
ESCATCGA-2H-A9GI-01exon_skip_454588
144033153144033320144033170144033170Frame_Shift_DelG-p.A11fs
ESCATCGA-2H-A9GI-01exon_skip_454588
144033153144033320144033170144033170Frame_Shift_DelG-p.A22fs
ESCATCGA-2H-A9GI-01exon_skip_454588
144033153144033320144033170144033170Frame_Shift_DelG-p.K21fs
LIHCTCGA-DD-A39Y-01exon_skip_454596
144074891144075049144075008144075008Frame_Shift_DelA-p.E127fs
LIHCTCGA-G3-A3CJ-01exon_skip_454596
144074891144075049144075008144075008Frame_Shift_DelA-p.E127fs
COADTCGA-AZ-4615-01exon_skip_454598
144081538144081777144081696144081696Frame_Shift_DelA-p.I193fs
UCECTCGA-D1-A17D-01exon_skip_454598
144081538144081777144081696144081696Frame_Shift_DelA-p.K205fs
KIRCTCGA-B2-4098-01exon_skip_454599
144086398144086935144086414144086414Frame_Shift_DelA-p.S237X
STADTCGA-HU-A4H8-01exon_skip_454599
144086398144086935144086414144086414Frame_Shift_DelA-p.S237fs
UCECTCGA-BG-A0VZ-01exon_skip_454599
144086398144086935144086414144086414Frame_Shift_DelA-p.S237fs
COADTCGA-AA-3663-01exon_skip_454599
144086398144086935144086746144086746Frame_Shift_DelC-p.A257fs
STADTCGA-HU-8602-01exon_skip_454599
144086398144086935144086746144086746Frame_Shift_DelC-p.A348fs
BLCATCGA-GV-A40E-01exon_skip_454598
144081538144081777144081695144081696Frame_Shift_Ins-Ap.I193fs
COADTCGA-AU-6004-01exon_skip_454598
144081538144081777144081695144081696Frame_Shift_Ins-Ap.I193fs
HNSCTCGA-KU-A6H7-06exon_skip_454598
144081538144081777144081695144081696Frame_Shift_Ins-Ap.IK193fs
LUADTCGA-91-6849-01exon_skip_454598
144081538144081777144081695144081696Frame_Shift_Ins-Ap.I193fs
LUADTCGA-91-6849-01exon_skip_454598
144081538144081777144081695144081696Frame_Shift_Ins-Ap.IK193fs
THCATCGA-EL-A3GX-01exon_skip_454598
144081538144081777144081695144081696Frame_Shift_Ins-Ap.IK193fs
STADTCGA-HU-A4GQ-01exon_skip_454598
144081538144081777144081696144081697Frame_Shift_Ins-Ap.I204fs
ACCTCGA-OR-A5LB-01exon_skip_454599
144086398144086935144086413144086414Frame_Shift_Ins-Ap.*226fs
ACCTCGA-OR-A5LB-01exon_skip_454599
144086398144086935144086413144086414Frame_Shift_Ins-Ap.S237fs
PRADTCGA-XK-AAIW-01exon_skip_454599
144086398144086935144086413144086414Frame_Shift_Ins-Ap.*226fs
STADTCGA-BR-4368-01exon_skip_454599
144086398144086935144086414144086415Frame_Shift_Ins-Ap.S237fs
STADTCGA-BR-7707-01exon_skip_454599
144086398144086935144086414144086415Frame_Shift_Ins-Ap.S237fs
STADTCGA-CG-4306-01exon_skip_454599
144086398144086935144086414144086415Frame_Shift_Ins-Ap.S237fs
COADTCGA-AZ-6598-01exon_skip_454599
144086398144086935144086745144086746Frame_Shift_Ins-Cp.A257fs
COADTCGA-CM-5861-01exon_skip_454599
144086398144086935144086745144086746Frame_Shift_Ins-Cp.A257fs
KIRCTCGA-A3-3363-01exon_skip_454599
144086398144086935144086745144086746Frame_Shift_Ins-Cp.P337fs
KIRCTCGA-A3-3365-01exon_skip_454599
144086398144086935144086745144086746Frame_Shift_Ins-Cp.P337fs
LGGTCGA-DU-6392-01exon_skip_454599
144086398144086935144086745144086746Frame_Shift_Ins-Cp.P337fs
HNSCTCGA-P3-A6T7-01exon_skip_454599
144086398144086935144086485144086485Nonsense_MutationCGp.S250*
THYMTCGA-X7-A8M1-01exon_skip_454599
144086398144086935144086578144086578Nonsense_MutationCAp.S292X
UCECTCGA-D1-A17Q-01exon_skip_454600
144093395144093594144093492144093492Nonsense_MutationGTp.E444*
HNSCTCGA-MZ-A7D7-01exon_skip_454600
144093395144093594144093548144093548Nonsense_MutationCAp.Y451*
UCECTCGA-BS-A0UF-01exon_skip_454590
exon_skip_454591
144070122144070202144070121144070121Splice_SiteGTe3-1

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description
PHACTR2_144074890_144075049_144081537_144081777_144086397_144086611_TCGA-AU-6004-01Sample: TCGA-AU-6004-01
Cancer type: COAD
ESID: exon_skip_454598
Skipped exon start: 144081538
Skipped exon end: 144081777
Mutation start: 144081695
Mutation end: 144081696
Mutation type: Frame_Shift_Ins
Reference seq: -
Mutation seq: A
AAchange: p.I193fs
exon_skip_121002_COAD_TCGA-AU-6004-01.png
boxplot
exon_skip_137953_COAD_TCGA-AU-6004-01.png
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exon_skip_300676_COAD_TCGA-AU-6004-01.png
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exon_skip_336630_COAD_TCGA-AU-6004-01.png
boxplot
exon_skip_422717_COAD_TCGA-AU-6004-01.png
boxplot
exon_skip_434040_COAD_TCGA-AU-6004-01.png
boxplot
exon_skip_454598_COAD_TCGA-AU-6004-01.png
boxplot
exon_skip_55853_COAD_TCGA-AU-6004-01.png
boxplot
PHACTR2_144074890_144075049_144081537_144081777_144086397_144086611_TCGA-HU-A4GQ-01Sample: TCGA-HU-A4GQ-01
Cancer type: STAD
ESID: exon_skip_454598
Skipped exon start: 144081538
Skipped exon end: 144081777
Mutation start: 144081696
Mutation end: 144081697
Mutation type: Frame_Shift_Ins
Reference seq: -
Mutation seq: A
AAchange: p.I204fs
exon_skip_102588_STAD_TCGA-HU-A4GQ-01.png
boxplot
exon_skip_137953_STAD_TCGA-HU-A4GQ-01.png
boxplot
exon_skip_28428_STAD_TCGA-HU-A4GQ-01.png
boxplot
exon_skip_298309_STAD_TCGA-HU-A4GQ-01.png
boxplot
exon_skip_299452_STAD_TCGA-HU-A4GQ-01.png
boxplot
exon_skip_3339_STAD_TCGA-HU-A4GQ-01.png
boxplot
exon_skip_454598_STAD_TCGA-HU-A4GQ-01.png
boxplot
exon_skip_473424_STAD_TCGA-HU-A4GQ-01.png
boxplot
PHACTR2_144074890_144075049_144081537_144081777_144086397_144086611_TCGA-EL-A3GX-01Sample: TCGA-EL-A3GX-01
Cancer type: THCA
ESID: exon_skip_454598
Skipped exon start: 144081538
Skipped exon end: 144081777
Mutation start: 144081695
Mutation end: 144081696
Mutation type: Frame_Shift_Ins
Reference seq: -
Mutation seq: A
AAchange: p.IK193fs
exon_skip_454598_THCA_TCGA-EL-A3GX-01.png
boxplot

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
IGROV1_OVARY144081538144081777144081696144081696Frame_Shift_DelA-p.K195fs
JHUEM1_ENDOMETRIUM144081538144081777144081696144081696Frame_Shift_DelA-p.K195fs
WSUNHL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE144086398144086935144086746144086746Frame_Shift_DelC-p.A337fs
HCC1419_BREAST144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
HEC251_ENDOMETRIUM144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
HLFA_FIBROBLAST144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
HS281T_FIBROBLAST144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
HS600T_FIBROBLAST144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
HS675T_FIBROBLAST144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
HS688AT_FIBROBLAST144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
JHH7_LIVER144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
KPL1_BREAST144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
LCLC103H_LUNG144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
LU99_LUNG144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
MFE319_ENDOMETRIUM144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
MKN74_STOMACH144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
NCCSTCK140_STOMACH144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
NCIH2004RT_SOFT_TISSUE144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
NCIH1568_LUNG144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
NCIH2106_LUNG144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
NH6_AUTONOMIC_GANGLIA144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
OAW28_OVARY144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
OAW42_OVARY144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
PLCPRF5_LIVER144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
PRECLH_PROSTATE144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
RERFLCKJ_LUNG144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
RS5_FIBROBLAST144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
SCABER_URINARY_TRACT144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
SNU119_OVARY144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
SNU520_STOMACH144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
SNU738_CENTRAL_NERVOUS_SYSTEM144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
SW1417_LARGE_INTESTINE144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
TE11_OESOPHAGUS144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
TTC549_SOFT_TISSUE144081538144081777144081623144081624Frame_Shift_Ins-Ap.K170fs
BT483_BREAST144081538144081777144081775144081776Frame_Shift_Ins-TGGTGp.A221fs
IGROV1_OVARY144086398144086935144086413144086414Frame_Shift_Ins-Ap.SK226fs
CW2_LARGE_INTESTINE144086398144086935144086413144086414Frame_Shift_Ins-Ap.SK226fs
EN_ENDOMETRIUM144086398144086935144086413144086414Frame_Shift_Ins-Ap.SK226fs
MDAMB330_BREAST144033153144033320144033306144033306Missense_MutationGCp.R56T
UACC62_SKIN144033153144033320144033317144033317Missense_MutationGAp.A60T
SW1783_CENTRAL_NERVOUS_SYSTEM144070122144070202144070146144070146Missense_MutationGAp.R69Q
BICR18_UPPER_AERODIGESTIVE_TRACT144070122144070202144070178144070178Missense_MutationGCp.V80L
BICR18_UPPER_AERODIGESTIVE_TRACT144074891144075049144074939144074939Missense_MutationCAp.P104H
SW982_SOFT_TISSUE144074891144075049144074960144074960Missense_MutationGAp.R111Q
SW982_SOFT_TISSUE144074891144075049144074989144074989Missense_MutationGAp.G121S
LK2_LUNG144081538144081777144081595144081595Missense_MutationCAp.P160H
HEC59_ENDOMETRIUM144081538144081777144081679144081679Missense_MutationAGp.D188G
TGBC11TKB_STOMACH144081538144081777144081687144081687Missense_MutationCTp.P191S
MDAMB134VI_BREAST144081538144081777144081714144081714Missense_MutationCTp.P200S
KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE144081538144081777144081735144081735Missense_MutationCGp.P207A
NCIH1304_LUNG144081538144081777144081747144081747Missense_MutationCAp.P211T
AM38_CENTRAL_NERVOUS_SYSTEM144086398144086935144086431144086431Missense_MutationCGp.S232C
RERFLCFM_LUNG144086398144086935144086446144086446Missense_MutationCTp.S237L
COLO741_SKIN144086398144086935144086563144086563Missense_MutationCGp.T276S
KYSE270_OESOPHAGUS144086398144086935144086664144086664Missense_MutationCTp.P310S
GMS10_CENTRAL_NERVOUS_SYSTEM144086398144086935144086809144086809Missense_MutationGAp.S358N
CAL33_UPPER_AERODIGESTIVE_TRACT144086398144086935144086829144086829Missense_MutationGAp.V365I
KYSE50_OESOPHAGUS144086398144086935144086872144086872Missense_MutationCGp.P379R
KARPAS231_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE144086398144086935144086875144086875Missense_MutationCTp.T380M
SW962_VULVA144086398144086935144086875144086875Missense_MutationCTp.T380M
HS229T_FIBROBLAST144093395144093594144093481144093481Missense_MutationCTp.A429V
SNU1079_BILIARY_TRACT144093395144093594144093498144093498Missense_MutationCTp.H435Y
ASPC1_PANCREAS144093395144093594144093510144093510Missense_MutationCAp.Q439K
SNU324_PANCREAS144086398144086935144086625144086625Nonsense_MutationGTp.E297*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PHACTR2

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value
exon_skip_4545996144074890:144075049:144086397:144086935:144093394:144093594144086397:144086935ENST00000305766.6,ENST00000367584.4,ENST00000367582.3HNSCrs9496767chr6:144086394C/T6.56e-04
exon_skip_4545996144074890:144075049:144086397:144086935:144093394:144093594144086397:144086935ENST00000305766.6,ENST00000367584.4,ENST00000367582.3HNSCrs9496767chr6:144086394C/T6.57e-04
exon_skip_4545996144074890:144075049:144086397:144086935:144093394:144093594144086397:144086935ENST00000305766.6,ENST00000367584.4,ENST00000367582.3KIRCrs9496767chr6:144086394C/T1.67e-03
exon_skip_4545996144074890:144075049:144086397:144086935:144093394:144093594144086397:144086935ENST00000305766.6,ENST00000367584.4,ENST00000367582.3KIRCrs9496767chr6:144086394C/T1.68e-03

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PHACTR2


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PHACTR2


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RelatedDrugs for PHACTR2

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 PHACTR2

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