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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 NRF1

check button Gene summary
Gene informationGene symbol

NRF1

Gene ID

4899

Gene namenuclear respiratory factor 1
SynonymsALPHA-PAL
Cytomap

7q32.2

Type of geneprotein-coding
Descriptionnuclear respiratory factor 1alpha palindromic-binding protein
Modification date20180523
UniProtAcc

Q16656

ContextPubMed: NRF1 [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 NRF1 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 NRF1

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 NRF1

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_4711997129251596:129251665:129281565:129281663:129297182:129297414129281565:129281663ENSG00000106459.10ENST00000454688.1
exon_skip_4712027129251596:129251665:129297182:129297414:129311268:129311383129297182:129297414ENSG00000106459.10ENST00000223190.4,ENST00000311967.2
exon_skip_4712037129251596:129251665:129297185:129297414:129311268:129311383129297185:129297414ENSG00000106459.10ENST00000353868.4
exon_skip_4712137129297190:129297414:129311268:129311383:129317471:129317598129311268:129311383ENSG00000106459.10ENST00000223190.4,ENST00000393231.3,ENST00000454688.1,ENST00000393230.2,ENST00000353868.4,ENST00000311967.2,ENST00000393232.1
exon_skip_4712147129317471:129317598:129330245:129330386:129348914:129348937129330245:129330386ENSG00000106459.10ENST00000223190.4,ENST00000393231.3,ENST00000454688.1,ENST00000393230.2,ENST00000539636.1,ENST00000353868.4,ENST00000311967.2,ENST00000393232.1
exon_skip_4712167129330245:129330386:129348914:129349073:129351314:129351416129348914:129349073ENSG00000106459.10ENST00000353868.4
exon_skip_4712187129348914:129349073:129350213:129350411:129351314:129351416129350213:129350411ENSG00000106459.10ENST00000223190.4,ENST00000393231.3,ENST00000393230.2,ENST00000539636.1,ENST00000311967.2,ENST00000393232.1
exon_skip_4712197129351314:129351416:129357058:129357216:129367080:129367205129357058:129357216ENSG00000106459.10ENST00000223190.4,ENST00000393231.3,ENST00000393230.2,ENST00000539636.1,ENST00000353868.4,ENST00000311967.2,ENST00000393232.1
exon_skip_4712237129367085:129367205:129384012:129384069:129394857:129395060129384012:129384069ENSG00000106459.10ENST00000393231.3,ENST00000311967.2

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

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Exon skipping events with PSIs in GTEx for NRF1

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_4711997129251596:129251665:129281565:129281663:129297182:129297414129281565:129281663ENSG00000106459.10ENST00000454688.1
exon_skip_4712027129251596:129251665:129297182:129297414:129311268:129311383129297182:129297414ENSG00000106459.10ENST00000223190.4,ENST00000311967.2
exon_skip_4712037129251596:129251665:129297185:129297414:129311268:129311383129297185:129297414ENSG00000106459.10ENST00000353868.4
exon_skip_4712137129297190:129297414:129311268:129311383:129317471:129317598129311268:129311383ENSG00000106459.10ENST00000393232.1,ENST00000353868.4,ENST00000454688.1,ENST00000223190.4,ENST00000311967.2,ENST00000393230.2,ENST00000393231.3
exon_skip_4712147129317471:129317598:129330245:129330386:129348914:129348937129330245:129330386ENSG00000106459.10ENST00000393232.1,ENST00000353868.4,ENST00000539636.1,ENST00000454688.1,ENST00000223190.4,ENST00000311967.2,ENST00000393230.2,ENST00000393231.3
exon_skip_4712157129330245:129330386:129348914:129349073:129350213:129350411129348914:129349073ENSG00000106459.10ENST00000393232.1,ENST00000539636.1,ENST00000223190.4,ENST00000311967.2,ENST00000393230.2,ENST00000393231.3
exon_skip_4712167129330245:129330386:129348914:129349073:129351314:129351416129348914:129349073ENSG00000106459.10ENST00000353868.4
exon_skip_4712187129348914:129349073:129350213:129350411:129351314:129351416129350213:129350411ENSG00000106459.10ENST00000393232.1,ENST00000539636.1,ENST00000223190.4,ENST00000311967.2,ENST00000393230.2,ENST00000393231.3
exon_skip_4712197129351314:129351416:129357058:129357216:129367080:129367205129357058:129357216ENSG00000106459.10ENST00000393232.1,ENST00000353868.4,ENST00000539636.1,ENST00000223190.4,ENST00000311967.2,ENST00000393230.2,ENST00000393231.3
exon_skip_4712237129367085:129367205:129384012:129384069:129394857:129395060129384012:129384069ENSG00000106459.10ENST00000311967.2,ENST00000393231.3

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 NRF1

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
ENST000002231901292971821292974145CDS-5UTR
ENST00000223190129311268129311383Frame-shift
ENST00000393230129311268129311383Frame-shift
ENST00000393232129311268129311383Frame-shift
ENST00000223190129357058129357216Frame-shift
ENST00000393230129357058129357216Frame-shift
ENST00000393232129357058129357216Frame-shift
ENST00000223190129330245129330386In-frame
ENST00000393230129330245129330386In-frame
ENST00000393232129330245129330386In-frame
ENST00000223190129350213129350411In-frame
ENST00000393230129350213129350411In-frame
ENST00000393232129350213129350411In-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
ENST000002231901292971821292974145CDS-5UTR
ENST00000223190129311268129311383Frame-shift
ENST00000393230129311268129311383Frame-shift
ENST00000393232129311268129311383Frame-shift
ENST00000223190129357058129357216Frame-shift
ENST00000393230129357058129357216Frame-shift
ENST00000393232129357058129357216Frame-shift
ENST00000223190129330245129330386In-frame
ENST00000393230129330245129330386In-frame
ENST00000393232129330245129330386In-frame
ENST00000223190129348914129349073In-frame
ENST00000393230129348914129349073In-frame
ENST00000393232129348914129349073In-frame
ENST00000223190129350213129350411In-frame
ENST00000393230129350213129350411In-frame
ENST00000393232129350213129350411In-frame

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Infer the effects of exon skipping event on protein functional features for NRF1

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
ENST000002231902441503129330245129330386544684155202
ENST000003932303540503129330245129330386576716155202
ENST000003932323545503129330245129330386583723155202
ENST0000022319024415031293502131293504118441041255321
ENST0000039323035405031293502131293504118761073255321
ENST0000039323235455031293502131293504118831080255321

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
ENST000002231902441503129330245129330386544684155202
ENST000003932303540503129330245129330386576716155202
ENST000003932323545503129330245129330386583723155202
ENST000002231902441503129348914129349073685843202255
ENST000003932303540503129348914129349073717875202255
ENST000003932323545503129348914129349073724882202255
ENST0000022319024415031293502131293504118441041255321
ENST0000039323035405031293502131293504118761073255321
ENST0000039323235455031293502131293504118831080255321

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
Q166561552021161Alternative sequenceID=VSP_054330;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q166561552021161Alternative sequenceID=VSP_054330;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q166561552021161Alternative sequenceID=VSP_054330;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q166561552021503ChainID=PRO_0000100208;Note=Nuclear respiratory factor 1
Q166561552021503ChainID=PRO_0000100208;Note=Nuclear respiratory factor 1
Q166561552021503ChainID=PRO_0000100208;Note=Nuclear respiratory factor 1
Q16656155202109305DNA binding.
Q16656155202109305DNA binding.
Q16656155202109305DNA binding.
Q16656255321256321Alternative sequenceID=VSP_003598;Note=In isoform Short. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q16656255321256321Alternative sequenceID=VSP_003598;Note=In isoform Short. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q16656255321256321Alternative sequenceID=VSP_003598;Note=In isoform Short. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q166562553211503ChainID=PRO_0000100208;Note=Nuclear respiratory factor 1
Q166562553211503ChainID=PRO_0000100208;Note=Nuclear respiratory factor 1
Q166562553211503ChainID=PRO_0000100208;Note=Nuclear respiratory factor 1
Q16656255321109305DNA binding.
Q16656255321109305DNA binding.
Q16656255321109305DNA binding.
Q16656255321301476RegionNote=Required for transcriptional activation
Q16656255321301476RegionNote=Required for transcriptional activation
Q16656255321301476RegionNote=Required for transcriptional activation


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
Q166561552021161Alternative sequenceID=VSP_054330;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q166561552021161Alternative sequenceID=VSP_054330;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q166561552021161Alternative sequenceID=VSP_054330;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q166561552021503ChainID=PRO_0000100208;Note=Nuclear respiratory factor 1
Q166561552021503ChainID=PRO_0000100208;Note=Nuclear respiratory factor 1
Q166561552021503ChainID=PRO_0000100208;Note=Nuclear respiratory factor 1
Q16656155202109305DNA binding.
Q16656155202109305DNA binding.
Q16656155202109305DNA binding.
Q166562022551503ChainID=PRO_0000100208;Note=Nuclear respiratory factor 1
Q166562022551503ChainID=PRO_0000100208;Note=Nuclear respiratory factor 1
Q166562022551503ChainID=PRO_0000100208;Note=Nuclear respiratory factor 1
Q16656202255109305DNA binding.
Q16656202255109305DNA binding.
Q16656202255109305DNA binding.
Q16656255321256321Alternative sequenceID=VSP_003598;Note=In isoform Short. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q16656255321256321Alternative sequenceID=VSP_003598;Note=In isoform Short. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q16656255321256321Alternative sequenceID=VSP_003598;Note=In isoform Short. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q166562553211503ChainID=PRO_0000100208;Note=Nuclear respiratory factor 1
Q166562553211503ChainID=PRO_0000100208;Note=Nuclear respiratory factor 1
Q166562553211503ChainID=PRO_0000100208;Note=Nuclear respiratory factor 1
Q16656255321109305DNA binding.
Q16656255321109305DNA binding.
Q16656255321109305DNA binding.
Q16656255321301476RegionNote=Required for transcriptional activation
Q16656255321301476RegionNote=Required for transcriptional activation
Q16656255321301476RegionNote=Required for transcriptional activation


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SNVs in the skipped exons for NRF1

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-A39Y-01exon_skip_471213
129311269129311383129311334129311334Frame_Shift_DelT-p.F97fs
HNSCTCGA-P3-A5Q6-01exon_skip_471218
129350214129350411129350403129350404Frame_Shift_Ins-Tp.Y319fs
LUADTCGA-75-5126-01exon_skip_471218
129350214129350411129350356129350356Nonsense_MutationCAp.S303*
LUADTCGA-62-A46P-01exon_skip_471219
129357059129357216129357122129357122Nonsense_MutationGTp.E377*

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
HCT116_LARGE_INTESTINE129311269129311383129311286129311288In_Frame_DelGCT-p.A84del
MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE129297186129297414129297229129297229Missense_MutationCTp.A13V
MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE129297183129297414129297229129297229Missense_MutationCTp.A13V
SBC3_LUNG129297186129297414129297342129297342Missense_MutationACp.T51P
SBC3_LUNG129297183129297414129297342129297342Missense_MutationACp.T51P
AN3CA_ENDOMETRIUM129297186129297414129297389129297389Missense_MutationGTp.E66D
AN3CA_ENDOMETRIUM129297183129297414129297389129297389Missense_MutationGTp.E66D
DU145_PROSTATE129297186129297414129297399129297399Missense_MutationCAp.H70N
DU145_PROSTATE129297183129297414129297399129297399Missense_MutationCAp.H70N
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE129311269129311383129311323129311323Missense_MutationGAp.R93Q
NCC021_KIDNEY129311269129311383129311359129311359Missense_MutationAGp.K105R
HEC151_ENDOMETRIUM129348915129349073129348971129348971Missense_MutationACp.K221N
HEC108_ENDOMETRIUM129350214129350411129350383129350383Missense_MutationAGp.N312S
NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE129357059129357216129357111129357111Missense_MutationCTp.T373M
A704_KIDNEY129357059129357216129357122129357122Missense_MutationGAp.E377K
YD38_UPPER_AERODIGESTIVE_TRACT129357059129357216129357124129357124Missense_MutationGTp.E377D
NCIH2110_LUNG129350214129350411129350411129350411Splice_SiteGCp.Q321H
SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE129357059129357216129357216129357216Splice_SiteGTp.S408I

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NRF1

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value
exon_skip_4711997129251596:129251665:129281565:129281663:129297182:129297414129281565:129281663ENST00000454688.1KIRCrs62489268chr7:129281590G/A2.10e-04
exon_skip_4712037129251596:129251665:129297185:129297414:129311268:129311383129297185:129297414ENST00000353868.4LGGrs1882094chr7:129297332G/T3.28e-06
exon_skip_4712037129251596:129251665:129297185:129297414:129311268:129311383129297185:129297414ENST00000353868.4LUSCrs1882094chr7:129297332G/T2.56e-04
exon_skip_4712037129251596:129251665:129297185:129297414:129311268:129311383129297185:129297414ENST00000353868.4LUSCrs1882094chr7:129297332G/T2.22e-03
exon_skip_4712027129251596:129251665:129297182:129297414:129311268:129311383129297182:129297414ENST00000223190.4,ENST00000311967.2LGGrs1882094chr7:129297332G/T3.28e-06
exon_skip_4712027129251596:129251665:129297182:129297414:129311268:129311383129297182:129297414ENST00000223190.4,ENST00000311967.2LUSCrs1882094chr7:129297332G/T2.56e-04
exon_skip_4712027129251596:129251665:129297182:129297414:129311268:129311383129297182:129297414ENST00000223190.4,ENST00000311967.2LUSCrs1882094chr7:129297332G/T2.22e-03

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NRF1


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NRF1


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RelatedDrugs for NRF1

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 NRF1

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
NRF1C0006079Bowen's Disease1CTD_human