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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:SIK2-ALG9 (FusionGDB2 ID:81272)

Fusion Gene Summary for SIK2-ALG9

check button Fusion gene summary
Fusion gene informationFusion gene name: SIK2-ALG9
Fusion gene ID: 81272
HgeneTgene
Gene symbol

SIK2

ALG9

Gene ID

23235

79796

Gene namesalt inducible kinase 2ALG9 alpha-1,2-mannosyltransferase
SynonymsLOH11CR1I|QIK|SIK-2|SNF1LK2CDG1L|DIBD1|GIKANIS|LOH11CR1J
Cytomap

11q23.1

11q23.1

Type of geneprotein-codingprotein-coding
Descriptionserine/threonine-protein kinase SIK2SNF1-like kinase 2qin-induced kinasesalt-inducible protein kinase 2salt-inducible serine/threonine kinase 2serine/threonine-protein kinase SNF1-like kinase 2alpha-1,2-mannosyltransferase ALG9asparagine-linked glycosylation 9 alpha-12-mannosyltransferase-like proteinasparagine-linked glycosylation 9 homolog (S. cerevisiae, alpha- 1,2-mannosyltransferase)asparagine-linked glycosylation 9 homolog (yeast, alph
Modification date2020031320200313
UniProtAcc.

Q9H6U8

Ensembl transtripts involved in fusion geneENST00000304987, ENST00000533868, 
ENST00000531154, ENST00000398006, 
ENST00000527228, ENST00000524880, 
ENST00000527377, 
Fusion gene scores* DoF score13 X 7 X 10=9104 X 3 X 4=48
# samples 135
** MAII scorelog2(13/910*10)=-2.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/48*10)=0.0588936890535686
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: SIK2 [Title/Abstract] AND ALG9 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSIK2(111473422)-ALG9(111680497), # 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
HgeneSIK2

GO:0006468

protein phosphorylation

14976552

HgeneSIK2

GO:0035556

intracellular signal transduction

14976552

HgeneSIK2

GO:0046777

protein autophosphorylation

18348280


check buttonFusion gene breakpoints across SIK2 (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 ALG9 (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
ChimerDB4Non-CancerTCGA-HC-7747-11ASIK2chr11

111473422

+ALG9chr11

111680497

-


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Fusion Gene ORF analysis for SIK2-ALG9

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-frameENST00000304987ENST00000531154SIK2chr11

111473422

+ALG9chr11

111680497

-
In-frameENST00000304987ENST00000398006SIK2chr11

111473422

+ALG9chr11

111680497

-
5CDS-5UTRENST00000304987ENST00000527228SIK2chr11

111473422

+ALG9chr11

111680497

-
5CDS-3UTRENST00000304987ENST00000524880SIK2chr11

111473422

+ALG9chr11

111680497

-
5CDS-intronENST00000304987ENST00000527377SIK2chr11

111473422

+ALG9chr11

111680497

-
intron-3CDSENST00000533868ENST00000531154SIK2chr11

111473422

+ALG9chr11

111680497

-
intron-3CDSENST00000533868ENST00000398006SIK2chr11

111473422

+ALG9chr11

111680497

-
intron-5UTRENST00000533868ENST00000527228SIK2chr11

111473422

+ALG9chr11

111680497

-
intron-3UTRENST00000533868ENST00000524880SIK2chr11

111473422

+ALG9chr11

111680497

-
intron-intronENST00000533868ENST00000527377SIK2chr11

111473422

+ALG9chr11

111680497

-

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)
ENST00000304987SIK2chr11111473422+ENST00000531154ALG9chr11111680497-67630835562175
ENST00000304987SIK2chr11111473422+ENST00000398006ALG9chr11111680497-67630835562175

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
ENST00000304987ENST00000531154SIK2chr11111473422+ALG9chr11111680497-0.0338979140.96610206
ENST00000304987ENST00000398006SIK2chr11111473422+ALG9chr11111680497-0.0338979140.96610206

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Fusion Genomic Features for SIK2-ALG9


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 SIK2-ALG9


check button Go to

FGviewer for the breakpoints of chr11:111473422-chr11:111680497

.
- 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
.ALG9

Q9H6U8

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: Catalyzes the transfer of mannose from Dol-P-Man to lipid-linked oligosaccharides. {ECO:0000269|PubMed:15148656, ECO:0000269|PubMed:15945070}.

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
HgeneSIK2chr11:111473422chr11:111680497ENST00000304987+11526_3445.0927.0Nucleotide bindingATP
TgeneALG9chr11:111473422chr11:111680497ENST000003980061215364_370356.0441.0Topological domainLumenal
TgeneALG9chr11:111473422chr11:111680497ENST000003980061215392_405356.0441.0Topological domainCytoplasmic
TgeneALG9chr11:111473422chr11:111680497ENST000003980061215427_611356.0441.0Topological domainLumenal
TgeneALG9chr11:111473422chr11:111680497ENST000005311541215364_370363.0448.0Topological domainLumenal
TgeneALG9chr11:111473422chr11:111680497ENST000005311541215392_405363.0448.0Topological domainCytoplasmic
TgeneALG9chr11:111473422chr11:111680497ENST000005311541215427_611363.0448.0Topological domainLumenal
TgeneALG9chr11:111473422chr11:111680497ENST000003980061215371_391356.0441.0TransmembraneHelical
TgeneALG9chr11:111473422chr11:111680497ENST000003980061215406_426356.0441.0TransmembraneHelical
TgeneALG9chr11:111473422chr11:111680497ENST000005311541215371_391363.0448.0TransmembraneHelical
TgeneALG9chr11:111473422chr11:111680497ENST000005311541215406_426363.0448.0TransmembraneHelical

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSIK2chr11:111473422chr11:111680497ENST00000304987+11520_27145.0927.0DomainProtein kinase
HgeneSIK2chr11:111473422chr11:111680497ENST00000304987+115295_33545.0927.0DomainUBA
TgeneALG9chr11:111473422chr11:111680497ENST000003980061215157_171356.0441.0Topological domainCytoplasmic
TgeneALG9chr11:111473422chr11:111680497ENST000003980061215193_213356.0441.0Topological domainLumenal
TgeneALG9chr11:111473422chr11:111680497ENST0000039800612151_135356.0441.0Topological domainLumenal
TgeneALG9chr11:111473422chr11:111680497ENST000003980061215235_249356.0441.0Topological domainCytoplasmic
TgeneALG9chr11:111473422chr11:111680497ENST000003980061215271_304356.0441.0Topological domainLumenal
TgeneALG9chr11:111473422chr11:111680497ENST000003980061215326_342356.0441.0Topological domainCytoplasmic
TgeneALG9chr11:111473422chr11:111680497ENST000005311541215157_171363.0448.0Topological domainCytoplasmic
TgeneALG9chr11:111473422chr11:111680497ENST000005311541215193_213363.0448.0Topological domainLumenal
TgeneALG9chr11:111473422chr11:111680497ENST0000053115412151_135363.0448.0Topological domainLumenal
TgeneALG9chr11:111473422chr11:111680497ENST000005311541215235_249363.0448.0Topological domainCytoplasmic
TgeneALG9chr11:111473422chr11:111680497ENST000005311541215271_304363.0448.0Topological domainLumenal
TgeneALG9chr11:111473422chr11:111680497ENST000005311541215326_342363.0448.0Topological domainCytoplasmic
TgeneALG9chr11:111473422chr11:111680497ENST000003980061215136_156356.0441.0TransmembraneHelical
TgeneALG9chr11:111473422chr11:111680497ENST000003980061215172_192356.0441.0TransmembraneHelical
TgeneALG9chr11:111473422chr11:111680497ENST000003980061215214_234356.0441.0TransmembraneHelical
TgeneALG9chr11:111473422chr11:111680497ENST000003980061215250_270356.0441.0TransmembraneHelical
TgeneALG9chr11:111473422chr11:111680497ENST000003980061215305_325356.0441.0TransmembraneHelical
TgeneALG9chr11:111473422chr11:111680497ENST000003980061215343_363356.0441.0TransmembraneHelical
TgeneALG9chr11:111473422chr11:111680497ENST000005311541215136_156363.0448.0TransmembraneHelical
TgeneALG9chr11:111473422chr11:111680497ENST000005311541215172_192363.0448.0TransmembraneHelical
TgeneALG9chr11:111473422chr11:111680497ENST000005311541215214_234363.0448.0TransmembraneHelical
TgeneALG9chr11:111473422chr11:111680497ENST000005311541215250_270363.0448.0TransmembraneHelical
TgeneALG9chr11:111473422chr11:111680497ENST000005311541215305_325363.0448.0TransmembraneHelical
TgeneALG9chr11:111473422chr11:111680497ENST000005311541215343_363363.0448.0TransmembraneHelical


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Fusion Gene Sequence for SIK2-ALG9


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_ENST00000304987_ENST00000531154_TCGA-HC-7747-11A_SIK2_chr11_111473422_+_ALG9_chr11_111680497_length(transcript)=676nt_BP=308nt
GACGTCGGCGCACGTCAGCGGCGGCGCGCGCCTGGCTGGGCCCTGGGGAGCGGGAGGGAAGGAGCGAAGGAGCGAAGGAGCAAGCGGAGC
GGCCGTCGCCCAAGCCAAGCCGCGCTGCCAACCCTCCCGCCCGCCCGCGCTCCTGTCCGCCGTGTCTAGCAGCGGGGCCCAGCATGGTCA
TGGCGGATGGCCCGAGGCACTTGCAGCGCGGGCCGGTCCGGGTGGGGTTCTACGACATCGAGGGCACGCTGGGCAAGGGCAACTTCGCTG
TGGTGAAGCTGGGGCGGCACCGGATCACCAAGACGGAGATTGATATCAGTAAATGCCATTATTTAGTGGATTTGGACACCATGAGAGAAA
CACCCCGGGAGCCAAAATATTCATCCAATAAAGAAGAATGGATCAGCTTGGCCTATAGACCATTCCTTGATGCTTCTAGATCTTCAAAGC
TGCTGCGGGCATTCTATGTCCCCTTCCTGTCAGATCAGTATACAGTGTACGTAAACTACACCATCCTCAAACCCCGGAAAGCAAAGCAAA
TCAGGAAGAAAAGTGGAGGTTAGCAACACACCTGTGGCCCCAAAGGACAACCATCTTGTTAACTATTGATTCCAGTGACCTGACTCCCTG

>In-frame_ENST00000304987_ENST00000531154_TCGA-HC-7747-11A_SIK2_chr11_111473422_+_ALG9_chr11_111680497_length(amino acids)=175AA_start in transcript=35_stop in transcript=562
MGPGEREGRSEGAKEQAERPSPKPSRAANPPARPRSCPPCLAAGPSMVMADGPRHLQRGPVRVGFYDIEGTLGKGNFAVVKLGRHRITKT

--------------------------------------------------------------
>In-frame_ENST00000304987_ENST00000398006_TCGA-HC-7747-11A_SIK2_chr11_111473422_+_ALG9_chr11_111680497_length(transcript)=676nt_BP=308nt
GACGTCGGCGCACGTCAGCGGCGGCGCGCGCCTGGCTGGGCCCTGGGGAGCGGGAGGGAAGGAGCGAAGGAGCGAAGGAGCAAGCGGAGC
GGCCGTCGCCCAAGCCAAGCCGCGCTGCCAACCCTCCCGCCCGCCCGCGCTCCTGTCCGCCGTGTCTAGCAGCGGGGCCCAGCATGGTCA
TGGCGGATGGCCCGAGGCACTTGCAGCGCGGGCCGGTCCGGGTGGGGTTCTACGACATCGAGGGCACGCTGGGCAAGGGCAACTTCGCTG
TGGTGAAGCTGGGGCGGCACCGGATCACCAAGACGGAGATTGATATCAGTAAATGCCATTATTTAGTGGATTTGGACACCATGAGAGAAA
CACCCCGGGAGCCAAAATATTCATCCAATAAAGAAGAATGGATCAGCTTGGCCTATAGACCATTCCTTGATGCTTCTAGATCTTCAAAGC
TGCTGCGGGCATTCTATGTCCCCTTCCTGTCAGATCAGTATACAGTGTACGTAAACTACACCATCCTCAAACCCCGGAAAGCAAAGCAAA
TCAGGAAGAAAAGTGGAGGTTAGCAACACACCTGTGGCCCCAAAGGACAACCATCTTGTTAACTATTGATTCCAGTGACCTGACTCCCTG

>In-frame_ENST00000304987_ENST00000398006_TCGA-HC-7747-11A_SIK2_chr11_111473422_+_ALG9_chr11_111680497_length(amino acids)=175AA_start in transcript=35_stop in transcript=562
MGPGEREGRSEGAKEQAERPSPKPSRAANPPARPRSCPPCLAAGPSMVMADGPRHLQRGPVRVGFYDIEGTLGKGNFAVVKLGRHRITKT

--------------------------------------------------------------

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Fusion Gene PPI Analysis for SIK2-ALG9


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 SIK2-ALG9


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 SIK2-ALG9


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneALG9C2931006Congenital disorder of glycosylation type 1L5CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneALG9C1849762Polycystic Kidney Disease, Potter Type I, with Microbrachycephaly, Hypertelorism, and Brachymelia2CTD_human;GENOMICS_ENGLAND
TgeneALG9C0085413Polycystic Kidney, Autosomal Dominant1GENOMICS_ENGLAND
TgeneALG9C0158683Polycystic liver disease1GENOMICS_ENGLAND
TgeneALG9C1691228Cystic Kidney Diseases1GENOMICS_ENGLAND
TgeneALG9C4551631Cystic liver disease1GENOMICS_ENGLAND