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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:SMARCA1-ALG13 (FusionGDB2 ID:83278)

Fusion Gene Summary for SMARCA1-ALG13

check button Fusion gene summary
Fusion gene informationFusion gene name: SMARCA1-ALG13
Fusion gene ID: 83278
HgeneTgene
Gene symbol

SMARCA1

ALG13

Gene ID

6594

79868

Gene nameSWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1ALG13 UDP-N-acetylglucosaminyltransferase subunit
SynonymsISWI|NURF140|SNF2L|SNF2L1|SNF2LB|SNF2LT|SWI|SWI2|hSNF2LCDG1S|CXorf45|EIEE36|GLT28D1|MDS031|TDRD13|YGL047W
Cytomap

Xq25-q26.1

Xq23

Type of geneprotein-codingprotein-coding
Descriptionprobable global transcription activator SNF2L1ATP-dependent helicase SMARCA1SNF2-like 1global transcription activator homologous sequencenucleosome-remodeling factor subunit SNF2Lsucrose nonfermenting 2-like protein 1putative bifunctional UDP-N-acetylglucosamine transferase and deubiquitinase ALG13N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferaseUDP-N-acetylglucosamine transferase subunit ALG13 homologasparagine-linked glycosylation 13 homologg
Modification date2020032020200313
UniProtAcc.

Q9NP73

Ensembl transtripts involved in fusion geneENST00000371121, ENST00000371122, 
ENST00000371123, ENST00000478420, 
ENST00000371979, ENST00000251943, 
ENST00000394780, ENST00000470971, 
Fusion gene scores* DoF score5 X 5 X 3=754 X 4 X 4=64
# samples 54
** MAII scorelog2(5/75*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/64*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SMARCA1 [Title/Abstract] AND ALG13 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSMARCA1(128633709)-ALG13(110925464), # samples:1
Anticipated loss of major functional domain due to fusion event.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneSMARCA1

GO:0006338

chromatin remodeling

14609955

HgeneSMARCA1

GO:0043044

ATP-dependent chromatin remodeling

15640247


check buttonFusion gene breakpoints across SMARCA1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across ALG13 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4PRADTCGA-TK-A8OK-01ASMARCA1chrX

128633709

-ALG13chrX

110925464

+


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Fusion Gene ORF analysis for SMARCA1-ALG13

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
In-frameENST00000371121ENST00000371979SMARCA1chrX

128633709

-ALG13chrX

110925464

+
5CDS-5UTRENST00000371121ENST00000251943SMARCA1chrX

128633709

-ALG13chrX

110925464

+
5CDS-5UTRENST00000371121ENST00000394780SMARCA1chrX

128633709

-ALG13chrX

110925464

+
5CDS-intronENST00000371121ENST00000470971SMARCA1chrX

128633709

-ALG13chrX

110925464

+
In-frameENST00000371122ENST00000371979SMARCA1chrX

128633709

-ALG13chrX

110925464

+
5CDS-5UTRENST00000371122ENST00000251943SMARCA1chrX

128633709

-ALG13chrX

110925464

+
5CDS-5UTRENST00000371122ENST00000394780SMARCA1chrX

128633709

-ALG13chrX

110925464

+
5CDS-intronENST00000371122ENST00000470971SMARCA1chrX

128633709

-ALG13chrX

110925464

+
In-frameENST00000371123ENST00000371979SMARCA1chrX

128633709

-ALG13chrX

110925464

+
5CDS-5UTRENST00000371123ENST00000251943SMARCA1chrX

128633709

-ALG13chrX

110925464

+
5CDS-5UTRENST00000371123ENST00000394780SMARCA1chrX

128633709

-ALG13chrX

110925464

+
5CDS-intronENST00000371123ENST00000470971SMARCA1chrX

128633709

-ALG13chrX

110925464

+
intron-3CDSENST00000478420ENST00000371979SMARCA1chrX

128633709

-ALG13chrX

110925464

+
intron-5UTRENST00000478420ENST00000251943SMARCA1chrX

128633709

-ALG13chrX

110925464

+
intron-5UTRENST00000478420ENST00000394780SMARCA1chrX

128633709

-ALG13chrX

110925464

+
intron-intronENST00000478420ENST00000470971SMARCA1chrX

128633709

-ALG13chrX

110925464

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000371121SMARCA1chrX128633709-ENST00000371979ALG13chrX110925464+25011390501405451
ENST00000371122SMARCA1chrX128633709-ENST00000371979ALG13chrX110925464+25181407671422451
ENST00000371123SMARCA1chrX128633709-ENST00000371979ALG13chrX110925464+25181407671422451

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score
ENST00000371121ENST00000371979SMARCA1chrX128633709-ALG13chrX110925464+0.0001578240.99984217
ENST00000371122ENST00000371979SMARCA1chrX128633709-ALG13chrX110925464+0.0001592280.99984074
ENST00000371123ENST00000371979SMARCA1chrX128633709-ALG13chrX110925464+0.0001592280.99984074

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Fusion Genomic Features for SMARCA1-ALG13


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for SMARCA1-ALG13


check button Go to

FGviewer for the breakpoints of chrX:128633709-chrX:110925464

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.ALG13

Q9NP73

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: [Isoform 1]: Possible multifunctional enzyme with both glycosyltransferase and deubiquitinase activities.; FUNCTION: [Isoform 2]: May be involved in protein N-glycosylation, second step of the dolichol-linked oligosaccharide pathway.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page


* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSMARCA1chrX:128633709chrX:110925464ENST00000371121-1024195_360425.66666666666671232.0DomainHelicase ATP-binding
HgeneSMARCA1chrX:128633709chrX:110925464ENST00000371122-1025195_360425.66666666666671237.6666666666667DomainHelicase ATP-binding
HgeneSMARCA1chrX:128633709chrX:110925464ENST00000371123-1024195_360425.66666666666671203.0DomainHelicase ATP-binding
HgeneSMARCA1chrX:128633709chrX:110925464ENST00000371121-1024311_314425.66666666666671232.0MotifNote=DEAH box
HgeneSMARCA1chrX:128633709chrX:110925464ENST00000371122-1025311_314425.66666666666671237.6666666666667MotifNote=DEAH box
HgeneSMARCA1chrX:128633709chrX:110925464ENST00000371123-1024311_314425.66666666666671203.0MotifNote=DEAH box
HgeneSMARCA1chrX:128633709chrX:110925464ENST00000371121-1024208_215425.66666666666671232.0Nucleotide bindingATP
HgeneSMARCA1chrX:128633709chrX:110925464ENST00000371122-1025208_215425.66666666666671237.6666666666667Nucleotide bindingATP
HgeneSMARCA1chrX:128633709chrX:110925464ENST00000371123-1024208_215425.66666666666671203.0Nucleotide bindingATP
TgeneALG13chrX:128633709chrX:110925464ENST00000251943026887_9700955.0Compositional biasNote=Pro-rich
TgeneALG13chrX:128633709chrX:110925464ENST0000037197904887_9700166.0Compositional biasNote=Pro-rich
TgeneALG13chrX:128633709chrX:110925464ENST00000394780027887_97001138.0Compositional biasNote=Pro-rich
TgeneALG13chrX:128633709chrX:110925464ENST00000251943026231_3520955.0DomainOTU
TgeneALG13chrX:128633709chrX:110925464ENST00000251943026492_5520955.0DomainTudor
TgeneALG13chrX:128633709chrX:110925464ENST0000037197904231_3520166.0DomainOTU
TgeneALG13chrX:128633709chrX:110925464ENST0000037197904492_5520166.0DomainTudor
TgeneALG13chrX:128633709chrX:110925464ENST00000394780027231_35201138.0DomainOTU
TgeneALG13chrX:128633709chrX:110925464ENST00000394780027492_55201138.0DomainTudor
TgeneALG13chrX:128633709chrX:110925464ENST00000251943026126_4000955.0RegionNote=Deubiquitinase activity
TgeneALG13chrX:128633709chrX:110925464ENST000002519430261_1250955.0RegionNote=Glycosyltransferase activity
TgeneALG13chrX:128633709chrX:110925464ENST0000037197904126_4000166.0RegionNote=Deubiquitinase activity
TgeneALG13chrX:128633709chrX:110925464ENST00000371979041_1250166.0RegionNote=Glycosyltransferase activity
TgeneALG13chrX:128633709chrX:110925464ENST00000394780027126_40001138.0RegionNote=Deubiquitinase activity
TgeneALG13chrX:128633709chrX:110925464ENST000003947800271_12501138.0RegionNote=Glycosyltransferase activity

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSMARCA1chrX:128633709chrX:110925464ENST00000371121-1024490_653425.66666666666671232.0DomainHelicase C-terminal
HgeneSMARCA1chrX:128633709chrX:110925464ENST00000371121-1024855_907425.66666666666671232.0DomainSANT 1
HgeneSMARCA1chrX:128633709chrX:110925464ENST00000371121-1024958_1022425.66666666666671232.0DomainSANT 2
HgeneSMARCA1chrX:128633709chrX:110925464ENST00000371122-1025490_653425.66666666666671237.6666666666667DomainHelicase C-terminal
HgeneSMARCA1chrX:128633709chrX:110925464ENST00000371122-1025855_907425.66666666666671237.6666666666667DomainSANT 1
HgeneSMARCA1chrX:128633709chrX:110925464ENST00000371122-1025958_1022425.66666666666671237.6666666666667DomainSANT 2
HgeneSMARCA1chrX:128633709chrX:110925464ENST00000371123-1024490_653425.66666666666671203.0DomainHelicase C-terminal
HgeneSMARCA1chrX:128633709chrX:110925464ENST00000371123-1024855_907425.66666666666671203.0DomainSANT 1
HgeneSMARCA1chrX:128633709chrX:110925464ENST00000371123-1024958_1022425.66666666666671203.0DomainSANT 2


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Fusion Gene Sequence for SMARCA1-ALG13


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>In-frame_ENST00000371121_ENST00000371979_TCGA-TK-A8OK-01A_SMARCA1_chrX_128633709_-_ALG13_chrX_110925464_length(transcript)=2501nt_BP=1390nt
GCGGAGTGATTCCCCACCCCTGCTCCATCTAGCTCTTTCCAGTGCAGCCACTGCCGCCGCCCAGGAGCCCTCGTCCCCTGCCTTGTCCCC
CTACTCGTTCCCGCTCCCACGGCATGGAGCAGGACACTGCCGCAGTGGCAGCCACCGTGGCAGCCGCGGATGCGACCGCCACTATCGTGG
TCATAGAGGACGAGCAGCCCGGGCCGTCCACCTCTCAGGAGGAGGGAGCGGCCGCCGCGGCCACCGAAGCCACCGCGGCCACGGAGAAGG
GCGAGAAGAAGAAGGAGAAAAACGTTTCTTCATTTCAACTCAAACTTGCTGCTAAAGCGCCTAAATCTGAAAAGGAAATGGACCCAGAAT
ATGAAGAGAAAATGAAAGCCGACCGAGCAAAGAGATTTGAATTTTTACTGAAGCAGACAGAACTTTTTGCACATTTCATTCAGCCTTCAG
CACAGAAATCTCCAACATCTCCACTGAACATGAAATTGGGACGTCCCCGAATAAAGAAAGATGAAAAGCAGAGCTTAATTTCTGCTGGAG
ACTACCGCCATAGGCGCACAGAGCAAGAAGAAGATGAAGAGCTACTGTCTGAGAGTCGGAAAACATCTAATGTGTGTATTAGATTTGAGG
TGTCACCTTCATATGTGAAAGGGGGGCCACTGAGAGATTATCAGATTCGAGGACTGAATTGGTTGATCTCTTTATATGAAAATGGAGTCA
ATGGCATTTTGGCTGATGAAATGGGCCTTGGGAAAACTTTACAAACAATTGCTTTGCTTGGTTACCTGAAACACTACCGAAATATTCCTG
GACCTCACATGGTTTTAGTTCCAAAGTCTACTTTACACAACTGGATGAATGAATTTAAACGATGGGTCCCATCTCTCCGTGTCATTTGTT
TTGTCGGAGACAAGGATGCCAGAGCTGCTTTTATTCGTGATGAAATGATGCCAGGAGAGTGGGATGTTTGCGTTACTTCTTATGAGATGG
TAATTAAAGAAAAATCTGTATTCAAAAAGTTTCACTGGCGATACCTGGTCATTGATGAAGCTCACAGAATAAAGAATGAAAAATCTAAGC
TTTCAGAGATTGTTCGTGAGTTCAAGTCGACTAACCGCTTGCTCCTAACTGGAACACCTTTGCAGAATAACCTGCATGAACTGTGGGCCT
TACTCAACTTTTTATTGCCTGATGTCTTTAATTCTGCAGATGACTTTGATTCTTGGTTTGACACTAAAAATTGTCTTGGTGATCAAAAAC
TCGTGGAAAGACTTCATGCAGTTTTAAAACCATTTTTGTTACGCCGTATAAAAACTGATGTAGAGAAGAGTCTGCCACCTAAAAAGGAAA
TAAAGATTTACTTGGGGCTGAGTAAGATGCAACGAGAATGTACAAGGATTCCTTGAAAGAAGACATTCAGAAAGCAGATCTTGTTATTAG
TCACGCAGGTGCAGGAAGCTGTTTGGAGACTCTGGAAAAAGGAAAGCCACTCGTAGTGGTTATAAACGAAAAGTTGATGAACAATCATCA
GCTGGAACTGGCAAAGCAGCTACACAAAGAGGGTCATCTCTTCTATTGTACCTGCAGCACGCTTCCTGGGCTGTTACAGTCAATGGACTT
ATCAACACTGAAATGTTATCCTCCTGGCCAGCCAGAAAAATTTTCTGCATTTTTGGATAAAGTTGTTGGATTACAAAAATAAACACTAAA
CTCTCAACACTTTAAAAGCAACCCCCAAATTCAACCTATGTAATGTGATTAAATCAAATTAAATACATAATATATATTTACAAAATAATA
TAATTAATAAACTTCCTACATCTATAGAATGTATAGGAAATTTTATGTTGTGCACATTTGCATTGGGTCCAAATCCTAATTGCAGTTTAG
TGAAATTACTAGATTTTTTTCTAATCTTCAGTATGTAGTGAGCATTCACAGGTTTTCTCCTAGAATCTCAAGTGGAATTGGAATCATAAA
AATGAATGAGATTTGAAAACTTTCACAAAGATTATAAATGTAGTTAGTTTGATACTCCTTAGAATAAAAAAATGAAACAGTAACAACTTT
TATGTAAAAAAATTTTACATAAGAGTTAGCATCTTTAGCTTTATAATCTAAGGAACCAAATTTAAAAAATGATGGATTATGCTCTGTGAA
ATGAAAAGTTCAATCATTGCCTAAAAAAGATGATCAAGTTAGTTGATCTCTTGTACTTGGAAAAGCTACTTTTTTCCTAAAGAACAGAGT
GGAGTGGATATATTCACTTTTTTTTTCTAAAACATACAAAGTGATAAAATAATCGTGCCTAATGTCAAAACTTTACTGGTTTGAGAAGAA
TAATCAAAAAGGACTTATACCAATAGGACTTACTATTGTTTTTTAAGGATCTCCTCTCACAGTGGTAATGAAACATTAACTGTAACAGAA

>In-frame_ENST00000371121_ENST00000371979_TCGA-TK-A8OK-01A_SMARCA1_chrX_128633709_-_ALG13_chrX_110925464_length(amino acids)=451AA_start in transcript=50_stop in transcript=1405
MPPPRSPRPLPCPPTRSRSHGMEQDTAAVAATVAAADATATIVVIEDEQPGPSTSQEEGAAAAATEATAATEKGEKKKEKNVSSFQLKLA
AKAPKSEKEMDPEYEEKMKADRAKRFEFLLKQTELFAHFIQPSAQKSPTSPLNMKLGRPRIKKDEKQSLISAGDYRHRRTEQEEDEELLS
ESRKTSNVCIRFEVSPSYVKGGPLRDYQIRGLNWLISLYENGVNGILADEMGLGKTLQTIALLGYLKHYRNIPGPHMVLVPKSTLHNWMN
EFKRWVPSLRVICFVGDKDARAAFIRDEMMPGEWDVCVTSYEMVIKEKSVFKKFHWRYLVIDEAHRIKNEKSKLSEIVREFKSTNRLLLT
GTPLQNNLHELWALLNFLLPDVFNSADDFDSWFDTKNCLGDQKLVERLHAVLKPFLLRRIKTDVEKSLPPKKEIKIYLGLSKMQRECTRI

--------------------------------------------------------------
>In-frame_ENST00000371122_ENST00000371979_TCGA-TK-A8OK-01A_SMARCA1_chrX_128633709_-_ALG13_chrX_110925464_length(transcript)=2518nt_BP=1407nt
GAGCGAAGGGGTTGGAAGCGGAGTGATTCCCCACCCCTGCTCCATCTAGCTCTTTCCAGTGCAGCCACTGCCGCCGCCCAGGAGCCCTCG
TCCCCTGCCTTGTCCCCCTACTCGTTCCCGCTCCCACGGCATGGAGCAGGACACTGCCGCAGTGGCAGCCACCGTGGCAGCCGCGGATGC
GACCGCCACTATCGTGGTCATAGAGGACGAGCAGCCCGGGCCGTCCACCTCTCAGGAGGAGGGAGCGGCCGCCGCGGCCACCGAAGCCAC
CGCGGCCACGGAGAAGGGCGAGAAGAAGAAGGAGAAAAACGTTTCTTCATTTCAACTCAAACTTGCTGCTAAAGCGCCTAAATCTGAAAA
GGAAATGGACCCAGAATATGAAGAGAAAATGAAAGCCGACCGAGCAAAGAGATTTGAATTTTTACTGAAGCAGACAGAACTTTTTGCACA
TTTCATTCAGCCTTCAGCACAGAAATCTCCAACATCTCCACTGAACATGAAATTGGGACGTCCCCGAATAAAGAAAGATGAAAAGCAGAG
CTTAATTTCTGCTGGAGACTACCGCCATAGGCGCACAGAGCAAGAAGAAGATGAAGAGCTACTGTCTGAGAGTCGGAAAACATCTAATGT
GTGTATTAGATTTGAGGTGTCACCTTCATATGTGAAAGGGGGGCCACTGAGAGATTATCAGATTCGAGGACTGAATTGGTTGATCTCTTT
ATATGAAAATGGAGTCAATGGCATTTTGGCTGATGAAATGGGCCTTGGGAAAACTTTACAAACAATTGCTTTGCTTGGTTACCTGAAACA
CTACCGAAATATTCCTGGACCTCACATGGTTTTAGTTCCAAAGTCTACTTTACACAACTGGATGAATGAATTTAAACGATGGGTCCCATC
TCTCCGTGTCATTTGTTTTGTCGGAGACAAGGATGCCAGAGCTGCTTTTATTCGTGATGAAATGATGCCAGGAGAGTGGGATGTTTGCGT
TACTTCTTATGAGATGGTAATTAAAGAAAAATCTGTATTCAAAAAGTTTCACTGGCGATACCTGGTCATTGATGAAGCTCACAGAATAAA
GAATGAAAAATCTAAGCTTTCAGAGATTGTTCGTGAGTTCAAGTCGACTAACCGCTTGCTCCTAACTGGAACACCTTTGCAGAATAACCT
GCATGAACTGTGGGCCTTACTCAACTTTTTATTGCCTGATGTCTTTAATTCTGCAGATGACTTTGATTCTTGGTTTGACACTAAAAATTG
TCTTGGTGATCAAAAACTCGTGGAAAGACTTCATGCAGTTTTAAAACCATTTTTGTTACGCCGTATAAAAACTGATGTAGAGAAGAGTCT
GCCACCTAAAAAGGAAATAAAGATTTACTTGGGGCTGAGTAAGATGCAACGAGAATGTACAAGGATTCCTTGAAAGAAGACATTCAGAAA
GCAGATCTTGTTATTAGTCACGCAGGTGCAGGAAGCTGTTTGGAGACTCTGGAAAAAGGAAAGCCACTCGTAGTGGTTATAAACGAAAAG
TTGATGAACAATCATCAGCTGGAACTGGCAAAGCAGCTACACAAAGAGGGTCATCTCTTCTATTGTACCTGCAGCACGCTTCCTGGGCTG
TTACAGTCAATGGACTTATCAACACTGAAATGTTATCCTCCTGGCCAGCCAGAAAAATTTTCTGCATTTTTGGATAAAGTTGTTGGATTA
CAAAAATAAACACTAAACTCTCAACACTTTAAAAGCAACCCCCAAATTCAACCTATGTAATGTGATTAAATCAAATTAAATACATAATAT
ATATTTACAAAATAATATAATTAATAAACTTCCTACATCTATAGAATGTATAGGAAATTTTATGTTGTGCACATTTGCATTGGGTCCAAA
TCCTAATTGCAGTTTAGTGAAATTACTAGATTTTTTTCTAATCTTCAGTATGTAGTGAGCATTCACAGGTTTTCTCCTAGAATCTCAAGT
GGAATTGGAATCATAAAAATGAATGAGATTTGAAAACTTTCACAAAGATTATAAATGTAGTTAGTTTGATACTCCTTAGAATAAAAAAAT
GAAACAGTAACAACTTTTATGTAAAAAAATTTTACATAAGAGTTAGCATCTTTAGCTTTATAATCTAAGGAACCAAATTTAAAAAATGAT
GGATTATGCTCTGTGAAATGAAAAGTTCAATCATTGCCTAAAAAAGATGATCAAGTTAGTTGATCTCTTGTACTTGGAAAAGCTACTTTT
TTCCTAAAGAACAGAGTGGAGTGGATATATTCACTTTTTTTTTCTAAAACATACAAAGTGATAAAATAATCGTGCCTAATGTCAAAACTT
TACTGGTTTGAGAAGAATAATCAAAAAGGACTTATACCAATAGGACTTACTATTGTTTTTTAAGGATCTCCTCTCACAGTGGTAATGAAA

>In-frame_ENST00000371122_ENST00000371979_TCGA-TK-A8OK-01A_SMARCA1_chrX_128633709_-_ALG13_chrX_110925464_length(amino acids)=451AA_start in transcript=67_stop in transcript=1422
MPPPRSPRPLPCPPTRSRSHGMEQDTAAVAATVAAADATATIVVIEDEQPGPSTSQEEGAAAAATEATAATEKGEKKKEKNVSSFQLKLA
AKAPKSEKEMDPEYEEKMKADRAKRFEFLLKQTELFAHFIQPSAQKSPTSPLNMKLGRPRIKKDEKQSLISAGDYRHRRTEQEEDEELLS
ESRKTSNVCIRFEVSPSYVKGGPLRDYQIRGLNWLISLYENGVNGILADEMGLGKTLQTIALLGYLKHYRNIPGPHMVLVPKSTLHNWMN
EFKRWVPSLRVICFVGDKDARAAFIRDEMMPGEWDVCVTSYEMVIKEKSVFKKFHWRYLVIDEAHRIKNEKSKLSEIVREFKSTNRLLLT
GTPLQNNLHELWALLNFLLPDVFNSADDFDSWFDTKNCLGDQKLVERLHAVLKPFLLRRIKTDVEKSLPPKKEIKIYLGLSKMQRECTRI

--------------------------------------------------------------
>In-frame_ENST00000371123_ENST00000371979_TCGA-TK-A8OK-01A_SMARCA1_chrX_128633709_-_ALG13_chrX_110925464_length(transcript)=2518nt_BP=1407nt
GAGCGAAGGGGTTGGAAGCGGAGTGATTCCCCACCCCTGCTCCATCTAGCTCTTTCCAGTGCAGCCACTGCCGCCGCCCAGGAGCCCTCG
TCCCCTGCCTTGTCCCCCTACTCGTTCCCGCTCCCACGGCATGGAGCAGGACACTGCCGCAGTGGCAGCCACCGTGGCAGCCGCGGATGC
GACCGCCACTATCGTGGTCATAGAGGACGAGCAGCCCGGGCCGTCCACCTCTCAGGAGGAGGGAGCGGCCGCCGCGGCCACCGAAGCCAC
CGCGGCCACGGAGAAGGGCGAGAAGAAGAAGGAGAAAAACGTTTCTTCATTTCAACTCAAACTTGCTGCTAAAGCGCCTAAATCTGAAAA
GGAAATGGACCCAGAATATGAAGAGAAAATGAAAGCCGACCGAGCAAAGAGATTTGAATTTTTACTGAAGCAGACAGAACTTTTTGCACA
TTTCATTCAGCCTTCAGCACAGAAATCTCCAACATCTCCACTGAACATGAAATTGGGACGTCCCCGAATAAAGAAAGATGAAAAGCAGAG
CTTAATTTCTGCTGGAGACTACCGCCATAGGCGCACAGAGCAAGAAGAAGATGAAGAGCTACTGTCTGAGAGTCGGAAAACATCTAATGT
GTGTATTAGATTTGAGGTGTCACCTTCATATGTGAAAGGGGGGCCACTGAGAGATTATCAGATTCGAGGACTGAATTGGTTGATCTCTTT
ATATGAAAATGGAGTCAATGGCATTTTGGCTGATGAAATGGGCCTTGGGAAAACTTTACAAACAATTGCTTTGCTTGGTTACCTGAAACA
CTACCGAAATATTCCTGGACCTCACATGGTTTTAGTTCCAAAGTCTACTTTACACAACTGGATGAATGAATTTAAACGATGGGTCCCATC
TCTCCGTGTCATTTGTTTTGTCGGAGACAAGGATGCCAGAGCTGCTTTTATTCGTGATGAAATGATGCCAGGAGAGTGGGATGTTTGCGT
TACTTCTTATGAGATGGTAATTAAAGAAAAATCTGTATTCAAAAAGTTTCACTGGCGATACCTGGTCATTGATGAAGCTCACAGAATAAA
GAATGAAAAATCTAAGCTTTCAGAGATTGTTCGTGAGTTCAAGTCGACTAACCGCTTGCTCCTAACTGGAACACCTTTGCAGAATAACCT
GCATGAACTGTGGGCCTTACTCAACTTTTTATTGCCTGATGTCTTTAATTCTGCAGATGACTTTGATTCTTGGTTTGACACTAAAAATTG
TCTTGGTGATCAAAAACTCGTGGAAAGACTTCATGCAGTTTTAAAACCATTTTTGTTACGCCGTATAAAAACTGATGTAGAGAAGAGTCT
GCCACCTAAAAAGGAAATAAAGATTTACTTGGGGCTGAGTAAGATGCAACGAGAATGTACAAGGATTCCTTGAAAGAAGACATTCAGAAA
GCAGATCTTGTTATTAGTCACGCAGGTGCAGGAAGCTGTTTGGAGACTCTGGAAAAAGGAAAGCCACTCGTAGTGGTTATAAACGAAAAG
TTGATGAACAATCATCAGCTGGAACTGGCAAAGCAGCTACACAAAGAGGGTCATCTCTTCTATTGTACCTGCAGCACGCTTCCTGGGCTG
TTACAGTCAATGGACTTATCAACACTGAAATGTTATCCTCCTGGCCAGCCAGAAAAATTTTCTGCATTTTTGGATAAAGTTGTTGGATTA
CAAAAATAAACACTAAACTCTCAACACTTTAAAAGCAACCCCCAAATTCAACCTATGTAATGTGATTAAATCAAATTAAATACATAATAT
ATATTTACAAAATAATATAATTAATAAACTTCCTACATCTATAGAATGTATAGGAAATTTTATGTTGTGCACATTTGCATTGGGTCCAAA
TCCTAATTGCAGTTTAGTGAAATTACTAGATTTTTTTCTAATCTTCAGTATGTAGTGAGCATTCACAGGTTTTCTCCTAGAATCTCAAGT
GGAATTGGAATCATAAAAATGAATGAGATTTGAAAACTTTCACAAAGATTATAAATGTAGTTAGTTTGATACTCCTTAGAATAAAAAAAT
GAAACAGTAACAACTTTTATGTAAAAAAATTTTACATAAGAGTTAGCATCTTTAGCTTTATAATCTAAGGAACCAAATTTAAAAAATGAT
GGATTATGCTCTGTGAAATGAAAAGTTCAATCATTGCCTAAAAAAGATGATCAAGTTAGTTGATCTCTTGTACTTGGAAAAGCTACTTTT
TTCCTAAAGAACAGAGTGGAGTGGATATATTCACTTTTTTTTTCTAAAACATACAAAGTGATAAAATAATCGTGCCTAATGTCAAAACTT
TACTGGTTTGAGAAGAATAATCAAAAAGGACTTATACCAATAGGACTTACTATTGTTTTTTAAGGATCTCCTCTCACAGTGGTAATGAAA

>In-frame_ENST00000371123_ENST00000371979_TCGA-TK-A8OK-01A_SMARCA1_chrX_128633709_-_ALG13_chrX_110925464_length(amino acids)=451AA_start in transcript=67_stop in transcript=1422
MPPPRSPRPLPCPPTRSRSHGMEQDTAAVAATVAAADATATIVVIEDEQPGPSTSQEEGAAAAATEATAATEKGEKKKEKNVSSFQLKLA
AKAPKSEKEMDPEYEEKMKADRAKRFEFLLKQTELFAHFIQPSAQKSPTSPLNMKLGRPRIKKDEKQSLISAGDYRHRRTEQEEDEELLS
ESRKTSNVCIRFEVSPSYVKGGPLRDYQIRGLNWLISLYENGVNGILADEMGLGKTLQTIALLGYLKHYRNIPGPHMVLVPKSTLHNWMN
EFKRWVPSLRVICFVGDKDARAAFIRDEMMPGEWDVCVTSYEMVIKEKSVFKKFHWRYLVIDEAHRIKNEKSKLSEIVREFKSTNRLLLT
GTPLQNNLHELWALLNFLLPDVFNSADDFDSWFDTKNCLGDQKLVERLHAVLKPFLLRRIKTDVEKSLPPKKEIKIYLGLSKMQRECTRI

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Fusion Gene PPI Analysis for SMARCA1-ALG13


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for SMARCA1-ALG13


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for SMARCA1-ALG13


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSMARCA1C0265338Coffin-Siris syndrome2CLINGEN;GENOMICS_ENGLAND
HgeneSMARCA1C0033578Prostatic Neoplasms1CTD_human
HgeneSMARCA1C0376358Malignant neoplasm of prostate1CTD_human
TgeneALG13C3550904EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 366CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneALG13C0543888Epileptic encephalopathy2GENOMICS_ENGLAND
TgeneALG13C0014544Epilepsy1CTD_human
TgeneALG13C0086237Epilepsy, Cryptogenic1CTD_human
TgeneALG13C0236018Aura1CTD_human
TgeneALG13C0751111Awakening Epilepsy1CTD_human
TgeneALG13C1535926Neurodevelopmental Disorders1CTD_human
TgeneALG13C2931498Mental Retardation, X-Linked 11ORPHANET
TgeneALG13C3714756Intellectual Disability1GENOMICS_ENGLAND
TgeneALG13C4317295Congenital disorder of glycosylation type 1s1GENOMICS_ENGLAND