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Center for Computational Systems Medicine level2
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein Structure

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pLDDT scores

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Ramachandran Plot of Fusion Protein Structure

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:ITGA9-SEC13

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ITGA9-SEC13
FusionPDB ID: 40472
FusionGDB2.0 ID: 40472
HgeneTgene
Gene symbol

ITGA9

SEC13

Gene ID

3680

6396

Gene nameintegrin subunit alpha 9SEC13 homolog, nuclear pore and COPII coat complex component
SynonymsALPHA-RLC|ITGA4L|RLCD3S1231E|SEC13L1|SEC13R|npp-20
Cytomap

3p22.2

3p25.3

Type of geneprotein-codingprotein-coding
Descriptionintegrin alpha-9integrin alpha-RLCprotein SEC13 homologGATOR complex protein SEC13SEC13 homolog, nuclear pore and COPII coating complex componentSEC13-like 1 isoformSEC13-like protein 1SEC13-related protein
Modification date2020031320200320
UniProtAcc

Q13797

.
Ensembl transtripts involved in fusion geneENST idsENST00000264741, ENST00000422441, 
ENST00000492602, ENST00000337354, 
ENST00000350697, ENST00000383801, 
ENST00000397109, ENST00000397117, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score12 X 8 X 10=9609 X 8 X 4=288
# samples 138
** MAII scorelog2(13/960*10)=-2.88452278258006
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/288*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: ITGA9 [Title/Abstract] AND SEC13 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ITGA9(37792060)-SEC13(10347376), # samples:4
Anticipated loss of major functional domain due to fusion event.ITGA9-SEC13 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
ITGA9-SEC13 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
* 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
TgeneSEC13

GO:0090110

cargo loading into COPII-coated vesicle

17499046|18843296


check buttonFusion gene breakpoints across ITGA9 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across SEC13 (3'-gene)
* 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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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4LUADTCGA-MP-A4TK-01AITGA9chr3

37792059

+SEC13chr3

10347375

-
ChimerDB4LUADTCGA-MP-A4TK-01AITGA9chr3

37792060

-SEC13chr3

10347376

-
ChimerDB4LUADTCGA-MP-A4TK-01AITGA9chr3

37792060

+SEC13chr3

10347376

-
ChimerDB4LUADTCGA-MP-A4TKITGA9chr3

37792060

+SEC13chr3

10347376

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000264741ITGA9chr337792060+ENST00000397109SEC13chr310347376-3646279725033151021
ENST00000264741ITGA9chr337792060+ENST00000337354SEC13chr310347376-3646279725033151021
ENST00000264741ITGA9chr337792060+ENST00000350697SEC13chr310347376-3646279725033151021
ENST00000264741ITGA9chr337792060+ENST00000397117SEC13chr310347376-340027972503243997
ENST00000264741ITGA9chr337792060+ENST00000383801SEC13chr310347376-3616279725033151021
ENST00000264741ITGA9chr337792059+ENST00000397109SEC13chr310347375-3646279725033151021
ENST00000264741ITGA9chr337792059+ENST00000337354SEC13chr310347375-3646279725033151021
ENST00000264741ITGA9chr337792059+ENST00000350697SEC13chr310347375-3646279725033151021
ENST00000264741ITGA9chr337792059+ENST00000397117SEC13chr310347375-340027972503243997
ENST00000264741ITGA9chr337792059+ENST00000383801SEC13chr310347375-3616279725033151021

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
ENST00000264741ENST00000397109ITGA9chr337792060+SEC13chr310347376-0.0021382760.9978617
ENST00000264741ENST00000337354ITGA9chr337792060+SEC13chr310347376-0.0021382760.9978617
ENST00000264741ENST00000350697ITGA9chr337792060+SEC13chr310347376-0.0021382760.9978617
ENST00000264741ENST00000397117ITGA9chr337792060+SEC13chr310347376-0.0012426680.99875736
ENST00000264741ENST00000383801ITGA9chr337792060+SEC13chr310347376-0.0022149990.997785
ENST00000264741ENST00000397109ITGA9chr337792059+SEC13chr310347375-0.0021382760.9978617
ENST00000264741ENST00000337354ITGA9chr337792059+SEC13chr310347375-0.0021382760.9978617
ENST00000264741ENST00000350697ITGA9chr337792059+SEC13chr310347375-0.0021382760.9978617
ENST00000264741ENST00000397117ITGA9chr337792059+SEC13chr310347375-0.0012426680.99875736
ENST00000264741ENST00000383801ITGA9chr337792059+SEC13chr310347375-0.0022149990.997785

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>40472_40472_1_ITGA9-SEC13_ITGA9_chr3_37792059_ENST00000264741_SEC13_chr3_10347375_ENST00000337354_length(amino acids)=1021AA_BP=849
MGMGGPAAPRGAGRLRALLLALVVAGIPAGAYNLDPQRPVHFQGPADSFFGYAVLEHFHDNTRWVLVGAPKADSKYSPSVKSPGAVFKCR
VHTNPDRRCTELDMARGKNRGTSCGKTCREDRDDEWMGVSLARQPKADGRVLACAHRWKNIYYEADHILPHGFCYIIPSNLQAKGRTLIP
CYEEYKKKYGEEHGSCQAGIAGFFTEELVVMGAPGSFYWAGTIKVLNLTDNTYLKLNDEVIMNRRYTYLGYAVTAGHFSHPSTIDVVGGA
PQDKGIGKVYIFRADRRSGTLIKIFQASGKKMGSYFGSSLCAVDLNGDGLSDLLVGAPMFSEIRDEGQVTVYINRGNGALEEQLALTGDG
AYNAHFGESIASLDDLDNDGFPDVAIGAPKEDDFAGAVYIYHGDAGGIVPQYSMKLSGQKINPVLRMFGQSISGGIDMDGNGYPDVTVGA
FMSDSVVLLRARPVITVDVSIFLPGSINITAPQCHDGQQPVNCLNVTTCFSFHGKHVPGEIGLNYVLMADVAKKEKGQMPRVYFVLLGET
MGQVTEKLQLTYMEETCRHYVAHVKRRVQDVISPIVFEAAYSLSEHVTGEEERELPPLTPVLRWKKGQKIAQKNQTVFERNCRSEDCAAD
LQLQGKLLLSSMDEKTLYLALGAVKNISLNISISNLGDDAYDANVSFNVSRELFFINMWQKEEMGISCELLESDFLKCSVGFPFMRSKSK
YEFSVIFDTSHLSGEEEVLSFIVTAQSGNTERSESLHDNTLVLMVPLMHEVDTSITGIMSPTSFVYGESVDAANFIQLDDLECHFQPINI
TLQVYNTGPSTLPGSSVSISFPNRLSSGGAEMFHVQEMVIGCNAVSWAPAVVPGSLIDHPSGQKPNYIKRFASGGCDNLIKLWKEEEDGQ
WKEEQKLEAHSDWVRDVAWAPSIGLPTSTIASCSQDGRVFIWTCDDASSNTWSPKLLHKFNDVVWHVSWSITANILAVSGGDNKVTLWKE

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

>40472_40472_2_ITGA9-SEC13_ITGA9_chr3_37792059_ENST00000264741_SEC13_chr3_10347375_ENST00000350697_length(amino acids)=1021AA_BP=849
MGMGGPAAPRGAGRLRALLLALVVAGIPAGAYNLDPQRPVHFQGPADSFFGYAVLEHFHDNTRWVLVGAPKADSKYSPSVKSPGAVFKCR
VHTNPDRRCTELDMARGKNRGTSCGKTCREDRDDEWMGVSLARQPKADGRVLACAHRWKNIYYEADHILPHGFCYIIPSNLQAKGRTLIP
CYEEYKKKYGEEHGSCQAGIAGFFTEELVVMGAPGSFYWAGTIKVLNLTDNTYLKLNDEVIMNRRYTYLGYAVTAGHFSHPSTIDVVGGA
PQDKGIGKVYIFRADRRSGTLIKIFQASGKKMGSYFGSSLCAVDLNGDGLSDLLVGAPMFSEIRDEGQVTVYINRGNGALEEQLALTGDG
AYNAHFGESIASLDDLDNDGFPDVAIGAPKEDDFAGAVYIYHGDAGGIVPQYSMKLSGQKINPVLRMFGQSISGGIDMDGNGYPDVTVGA
FMSDSVVLLRARPVITVDVSIFLPGSINITAPQCHDGQQPVNCLNVTTCFSFHGKHVPGEIGLNYVLMADVAKKEKGQMPRVYFVLLGET
MGQVTEKLQLTYMEETCRHYVAHVKRRVQDVISPIVFEAAYSLSEHVTGEEERELPPLTPVLRWKKGQKIAQKNQTVFERNCRSEDCAAD
LQLQGKLLLSSMDEKTLYLALGAVKNISLNISISNLGDDAYDANVSFNVSRELFFINMWQKEEMGISCELLESDFLKCSVGFPFMRSKSK
YEFSVIFDTSHLSGEEEVLSFIVTAQSGNTERSESLHDNTLVLMVPLMHEVDTSITGIMSPTSFVYGESVDAANFIQLDDLECHFQPINI
TLQVYNTGPSTLPGSSVSISFPNRLSSGGAEMFHVQEMVIGCNAVSWAPAVVPGSLIDHPSGQKPNYIKRFASGGCDNLIKLWKEEEDGQ
WKEEQKLEAHSDWVRDVAWAPSIGLPTSTIASCSQDGRVFIWTCDDASSNTWSPKLLHKFNDVVWHVSWSITANILAVSGGDNKVTLWKE

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

>40472_40472_3_ITGA9-SEC13_ITGA9_chr3_37792059_ENST00000264741_SEC13_chr3_10347375_ENST00000383801_length(amino acids)=1021AA_BP=849
MGMGGPAAPRGAGRLRALLLALVVAGIPAGAYNLDPQRPVHFQGPADSFFGYAVLEHFHDNTRWVLVGAPKADSKYSPSVKSPGAVFKCR
VHTNPDRRCTELDMARGKNRGTSCGKTCREDRDDEWMGVSLARQPKADGRVLACAHRWKNIYYEADHILPHGFCYIIPSNLQAKGRTLIP
CYEEYKKKYGEEHGSCQAGIAGFFTEELVVMGAPGSFYWAGTIKVLNLTDNTYLKLNDEVIMNRRYTYLGYAVTAGHFSHPSTIDVVGGA
PQDKGIGKVYIFRADRRSGTLIKIFQASGKKMGSYFGSSLCAVDLNGDGLSDLLVGAPMFSEIRDEGQVTVYINRGNGALEEQLALTGDG
AYNAHFGESIASLDDLDNDGFPDVAIGAPKEDDFAGAVYIYHGDAGGIVPQYSMKLSGQKINPVLRMFGQSISGGIDMDGNGYPDVTVGA
FMSDSVVLLRARPVITVDVSIFLPGSINITAPQCHDGQQPVNCLNVTTCFSFHGKHVPGEIGLNYVLMADVAKKEKGQMPRVYFVLLGET
MGQVTEKLQLTYMEETCRHYVAHVKRRVQDVISPIVFEAAYSLSEHVTGEEERELPPLTPVLRWKKGQKIAQKNQTVFERNCRSEDCAAD
LQLQGKLLLSSMDEKTLYLALGAVKNISLNISISNLGDDAYDANVSFNVSRELFFINMWQKEEMGISCELLESDFLKCSVGFPFMRSKSK
YEFSVIFDTSHLSGEEEVLSFIVTAQSGNTERSESLHDNTLVLMVPLMHEVDTSITGIMSPTSFVYGESVDAANFIQLDDLECHFQPINI
TLQVYNTGPSTLPGSSVSISFPNRLSSGGAEMFHVQEMVIGCNAVSWAPAVVPGSLIDHPSGQKPNYIKRFASGGCDNLIKLWKEEEDGQ
WKEEQKLEAHSDWVRDVAWAPSIGLPTSTIASCSQDGRVFIWTCDDASSNTWSPKLLHKFNDVVWHVSWSITANILAVSGGDNKVTLWKE

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

>40472_40472_4_ITGA9-SEC13_ITGA9_chr3_37792059_ENST00000264741_SEC13_chr3_10347375_ENST00000397109_length(amino acids)=1021AA_BP=849
MGMGGPAAPRGAGRLRALLLALVVAGIPAGAYNLDPQRPVHFQGPADSFFGYAVLEHFHDNTRWVLVGAPKADSKYSPSVKSPGAVFKCR
VHTNPDRRCTELDMARGKNRGTSCGKTCREDRDDEWMGVSLARQPKADGRVLACAHRWKNIYYEADHILPHGFCYIIPSNLQAKGRTLIP
CYEEYKKKYGEEHGSCQAGIAGFFTEELVVMGAPGSFYWAGTIKVLNLTDNTYLKLNDEVIMNRRYTYLGYAVTAGHFSHPSTIDVVGGA
PQDKGIGKVYIFRADRRSGTLIKIFQASGKKMGSYFGSSLCAVDLNGDGLSDLLVGAPMFSEIRDEGQVTVYINRGNGALEEQLALTGDG
AYNAHFGESIASLDDLDNDGFPDVAIGAPKEDDFAGAVYIYHGDAGGIVPQYSMKLSGQKINPVLRMFGQSISGGIDMDGNGYPDVTVGA
FMSDSVVLLRARPVITVDVSIFLPGSINITAPQCHDGQQPVNCLNVTTCFSFHGKHVPGEIGLNYVLMADVAKKEKGQMPRVYFVLLGET
MGQVTEKLQLTYMEETCRHYVAHVKRRVQDVISPIVFEAAYSLSEHVTGEEERELPPLTPVLRWKKGQKIAQKNQTVFERNCRSEDCAAD
LQLQGKLLLSSMDEKTLYLALGAVKNISLNISISNLGDDAYDANVSFNVSRELFFINMWQKEEMGISCELLESDFLKCSVGFPFMRSKSK
YEFSVIFDTSHLSGEEEVLSFIVTAQSGNTERSESLHDNTLVLMVPLMHEVDTSITGIMSPTSFVYGESVDAANFIQLDDLECHFQPINI
TLQVYNTGPSTLPGSSVSISFPNRLSSGGAEMFHVQEMVIGCNAVSWAPAVVPGSLIDHPSGQKPNYIKRFASGGCDNLIKLWKEEEDGQ
WKEEQKLEAHSDWVRDVAWAPSIGLPTSTIASCSQDGRVFIWTCDDASSNTWSPKLLHKFNDVVWHVSWSITANILAVSGGDNKVTLWKE

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

>40472_40472_5_ITGA9-SEC13_ITGA9_chr3_37792059_ENST00000264741_SEC13_chr3_10347375_ENST00000397117_length(amino acids)=997AA_BP=849
MGMGGPAAPRGAGRLRALLLALVVAGIPAGAYNLDPQRPVHFQGPADSFFGYAVLEHFHDNTRWVLVGAPKADSKYSPSVKSPGAVFKCR
VHTNPDRRCTELDMARGKNRGTSCGKTCREDRDDEWMGVSLARQPKADGRVLACAHRWKNIYYEADHILPHGFCYIIPSNLQAKGRTLIP
CYEEYKKKYGEEHGSCQAGIAGFFTEELVVMGAPGSFYWAGTIKVLNLTDNTYLKLNDEVIMNRRYTYLGYAVTAGHFSHPSTIDVVGGA
PQDKGIGKVYIFRADRRSGTLIKIFQASGKKMGSYFGSSLCAVDLNGDGLSDLLVGAPMFSEIRDEGQVTVYINRGNGALEEQLALTGDG
AYNAHFGESIASLDDLDNDGFPDVAIGAPKEDDFAGAVYIYHGDAGGIVPQYSMKLSGQKINPVLRMFGQSISGGIDMDGNGYPDVTVGA
FMSDSVVLLRARPVITVDVSIFLPGSINITAPQCHDGQQPVNCLNVTTCFSFHGKHVPGEIGLNYVLMADVAKKEKGQMPRVYFVLLGET
MGQVTEKLQLTYMEETCRHYVAHVKRRVQDVISPIVFEAAYSLSEHVTGEEERELPPLTPVLRWKKGQKIAQKNQTVFERNCRSEDCAAD
LQLQGKLLLSSMDEKTLYLALGAVKNISLNISISNLGDDAYDANVSFNVSRELFFINMWQKEEMGISCELLESDFLKCSVGFPFMRSKSK
YEFSVIFDTSHLSGEEEVLSFIVTAQSGNTERSESLHDNTLVLMVPLMHEVDTSITGIMSPTSFVYGESVDAANFIQLDDLECHFQPINI
TLQVYNTGPSTLPGSSVSISFPNRLSSGGAEMFHVQEMVIGCNAVSWAPAVVPGSLIDHPSGQKPNYIKRFASGGCDNLIKLWKEEEDGQ
WKEEQKLEAHSDWVRDVAWAPSIGLPTSTIASCSQDGRVFIWTCDDASSNTWSPKLLHKFNDVVWHVSWSITANILAVSGGDNKEELQMQ

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

>40472_40472_6_ITGA9-SEC13_ITGA9_chr3_37792060_ENST00000264741_SEC13_chr3_10347376_ENST00000337354_length(amino acids)=1021AA_BP=849
MGMGGPAAPRGAGRLRALLLALVVAGIPAGAYNLDPQRPVHFQGPADSFFGYAVLEHFHDNTRWVLVGAPKADSKYSPSVKSPGAVFKCR
VHTNPDRRCTELDMARGKNRGTSCGKTCREDRDDEWMGVSLARQPKADGRVLACAHRWKNIYYEADHILPHGFCYIIPSNLQAKGRTLIP
CYEEYKKKYGEEHGSCQAGIAGFFTEELVVMGAPGSFYWAGTIKVLNLTDNTYLKLNDEVIMNRRYTYLGYAVTAGHFSHPSTIDVVGGA
PQDKGIGKVYIFRADRRSGTLIKIFQASGKKMGSYFGSSLCAVDLNGDGLSDLLVGAPMFSEIRDEGQVTVYINRGNGALEEQLALTGDG
AYNAHFGESIASLDDLDNDGFPDVAIGAPKEDDFAGAVYIYHGDAGGIVPQYSMKLSGQKINPVLRMFGQSISGGIDMDGNGYPDVTVGA
FMSDSVVLLRARPVITVDVSIFLPGSINITAPQCHDGQQPVNCLNVTTCFSFHGKHVPGEIGLNYVLMADVAKKEKGQMPRVYFVLLGET
MGQVTEKLQLTYMEETCRHYVAHVKRRVQDVISPIVFEAAYSLSEHVTGEEERELPPLTPVLRWKKGQKIAQKNQTVFERNCRSEDCAAD
LQLQGKLLLSSMDEKTLYLALGAVKNISLNISISNLGDDAYDANVSFNVSRELFFINMWQKEEMGISCELLESDFLKCSVGFPFMRSKSK
YEFSVIFDTSHLSGEEEVLSFIVTAQSGNTERSESLHDNTLVLMVPLMHEVDTSITGIMSPTSFVYGESVDAANFIQLDDLECHFQPINI
TLQVYNTGPSTLPGSSVSISFPNRLSSGGAEMFHVQEMVIGCNAVSWAPAVVPGSLIDHPSGQKPNYIKRFASGGCDNLIKLWKEEEDGQ
WKEEQKLEAHSDWVRDVAWAPSIGLPTSTIASCSQDGRVFIWTCDDASSNTWSPKLLHKFNDVVWHVSWSITANILAVSGGDNKVTLWKE

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

>40472_40472_7_ITGA9-SEC13_ITGA9_chr3_37792060_ENST00000264741_SEC13_chr3_10347376_ENST00000350697_length(amino acids)=1021AA_BP=849
MGMGGPAAPRGAGRLRALLLALVVAGIPAGAYNLDPQRPVHFQGPADSFFGYAVLEHFHDNTRWVLVGAPKADSKYSPSVKSPGAVFKCR
VHTNPDRRCTELDMARGKNRGTSCGKTCREDRDDEWMGVSLARQPKADGRVLACAHRWKNIYYEADHILPHGFCYIIPSNLQAKGRTLIP
CYEEYKKKYGEEHGSCQAGIAGFFTEELVVMGAPGSFYWAGTIKVLNLTDNTYLKLNDEVIMNRRYTYLGYAVTAGHFSHPSTIDVVGGA
PQDKGIGKVYIFRADRRSGTLIKIFQASGKKMGSYFGSSLCAVDLNGDGLSDLLVGAPMFSEIRDEGQVTVYINRGNGALEEQLALTGDG
AYNAHFGESIASLDDLDNDGFPDVAIGAPKEDDFAGAVYIYHGDAGGIVPQYSMKLSGQKINPVLRMFGQSISGGIDMDGNGYPDVTVGA
FMSDSVVLLRARPVITVDVSIFLPGSINITAPQCHDGQQPVNCLNVTTCFSFHGKHVPGEIGLNYVLMADVAKKEKGQMPRVYFVLLGET
MGQVTEKLQLTYMEETCRHYVAHVKRRVQDVISPIVFEAAYSLSEHVTGEEERELPPLTPVLRWKKGQKIAQKNQTVFERNCRSEDCAAD
LQLQGKLLLSSMDEKTLYLALGAVKNISLNISISNLGDDAYDANVSFNVSRELFFINMWQKEEMGISCELLESDFLKCSVGFPFMRSKSK
YEFSVIFDTSHLSGEEEVLSFIVTAQSGNTERSESLHDNTLVLMVPLMHEVDTSITGIMSPTSFVYGESVDAANFIQLDDLECHFQPINI
TLQVYNTGPSTLPGSSVSISFPNRLSSGGAEMFHVQEMVIGCNAVSWAPAVVPGSLIDHPSGQKPNYIKRFASGGCDNLIKLWKEEEDGQ
WKEEQKLEAHSDWVRDVAWAPSIGLPTSTIASCSQDGRVFIWTCDDASSNTWSPKLLHKFNDVVWHVSWSITANILAVSGGDNKVTLWKE

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

>40472_40472_8_ITGA9-SEC13_ITGA9_chr3_37792060_ENST00000264741_SEC13_chr3_10347376_ENST00000383801_length(amino acids)=1021AA_BP=849
MGMGGPAAPRGAGRLRALLLALVVAGIPAGAYNLDPQRPVHFQGPADSFFGYAVLEHFHDNTRWVLVGAPKADSKYSPSVKSPGAVFKCR
VHTNPDRRCTELDMARGKNRGTSCGKTCREDRDDEWMGVSLARQPKADGRVLACAHRWKNIYYEADHILPHGFCYIIPSNLQAKGRTLIP
CYEEYKKKYGEEHGSCQAGIAGFFTEELVVMGAPGSFYWAGTIKVLNLTDNTYLKLNDEVIMNRRYTYLGYAVTAGHFSHPSTIDVVGGA
PQDKGIGKVYIFRADRRSGTLIKIFQASGKKMGSYFGSSLCAVDLNGDGLSDLLVGAPMFSEIRDEGQVTVYINRGNGALEEQLALTGDG
AYNAHFGESIASLDDLDNDGFPDVAIGAPKEDDFAGAVYIYHGDAGGIVPQYSMKLSGQKINPVLRMFGQSISGGIDMDGNGYPDVTVGA
FMSDSVVLLRARPVITVDVSIFLPGSINITAPQCHDGQQPVNCLNVTTCFSFHGKHVPGEIGLNYVLMADVAKKEKGQMPRVYFVLLGET
MGQVTEKLQLTYMEETCRHYVAHVKRRVQDVISPIVFEAAYSLSEHVTGEEERELPPLTPVLRWKKGQKIAQKNQTVFERNCRSEDCAAD
LQLQGKLLLSSMDEKTLYLALGAVKNISLNISISNLGDDAYDANVSFNVSRELFFINMWQKEEMGISCELLESDFLKCSVGFPFMRSKSK
YEFSVIFDTSHLSGEEEVLSFIVTAQSGNTERSESLHDNTLVLMVPLMHEVDTSITGIMSPTSFVYGESVDAANFIQLDDLECHFQPINI
TLQVYNTGPSTLPGSSVSISFPNRLSSGGAEMFHVQEMVIGCNAVSWAPAVVPGSLIDHPSGQKPNYIKRFASGGCDNLIKLWKEEEDGQ
WKEEQKLEAHSDWVRDVAWAPSIGLPTSTIASCSQDGRVFIWTCDDASSNTWSPKLLHKFNDVVWHVSWSITANILAVSGGDNKVTLWKE

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

>40472_40472_9_ITGA9-SEC13_ITGA9_chr3_37792060_ENST00000264741_SEC13_chr3_10347376_ENST00000397109_length(amino acids)=1021AA_BP=849
MGMGGPAAPRGAGRLRALLLALVVAGIPAGAYNLDPQRPVHFQGPADSFFGYAVLEHFHDNTRWVLVGAPKADSKYSPSVKSPGAVFKCR
VHTNPDRRCTELDMARGKNRGTSCGKTCREDRDDEWMGVSLARQPKADGRVLACAHRWKNIYYEADHILPHGFCYIIPSNLQAKGRTLIP
CYEEYKKKYGEEHGSCQAGIAGFFTEELVVMGAPGSFYWAGTIKVLNLTDNTYLKLNDEVIMNRRYTYLGYAVTAGHFSHPSTIDVVGGA
PQDKGIGKVYIFRADRRSGTLIKIFQASGKKMGSYFGSSLCAVDLNGDGLSDLLVGAPMFSEIRDEGQVTVYINRGNGALEEQLALTGDG
AYNAHFGESIASLDDLDNDGFPDVAIGAPKEDDFAGAVYIYHGDAGGIVPQYSMKLSGQKINPVLRMFGQSISGGIDMDGNGYPDVTVGA
FMSDSVVLLRARPVITVDVSIFLPGSINITAPQCHDGQQPVNCLNVTTCFSFHGKHVPGEIGLNYVLMADVAKKEKGQMPRVYFVLLGET
MGQVTEKLQLTYMEETCRHYVAHVKRRVQDVISPIVFEAAYSLSEHVTGEEERELPPLTPVLRWKKGQKIAQKNQTVFERNCRSEDCAAD
LQLQGKLLLSSMDEKTLYLALGAVKNISLNISISNLGDDAYDANVSFNVSRELFFINMWQKEEMGISCELLESDFLKCSVGFPFMRSKSK
YEFSVIFDTSHLSGEEEVLSFIVTAQSGNTERSESLHDNTLVLMVPLMHEVDTSITGIMSPTSFVYGESVDAANFIQLDDLECHFQPINI
TLQVYNTGPSTLPGSSVSISFPNRLSSGGAEMFHVQEMVIGCNAVSWAPAVVPGSLIDHPSGQKPNYIKRFASGGCDNLIKLWKEEEDGQ
WKEEQKLEAHSDWVRDVAWAPSIGLPTSTIASCSQDGRVFIWTCDDASSNTWSPKLLHKFNDVVWHVSWSITANILAVSGGDNKVTLWKE

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

>40472_40472_10_ITGA9-SEC13_ITGA9_chr3_37792060_ENST00000264741_SEC13_chr3_10347376_ENST00000397117_length(amino acids)=997AA_BP=849
MGMGGPAAPRGAGRLRALLLALVVAGIPAGAYNLDPQRPVHFQGPADSFFGYAVLEHFHDNTRWVLVGAPKADSKYSPSVKSPGAVFKCR
VHTNPDRRCTELDMARGKNRGTSCGKTCREDRDDEWMGVSLARQPKADGRVLACAHRWKNIYYEADHILPHGFCYIIPSNLQAKGRTLIP
CYEEYKKKYGEEHGSCQAGIAGFFTEELVVMGAPGSFYWAGTIKVLNLTDNTYLKLNDEVIMNRRYTYLGYAVTAGHFSHPSTIDVVGGA
PQDKGIGKVYIFRADRRSGTLIKIFQASGKKMGSYFGSSLCAVDLNGDGLSDLLVGAPMFSEIRDEGQVTVYINRGNGALEEQLALTGDG
AYNAHFGESIASLDDLDNDGFPDVAIGAPKEDDFAGAVYIYHGDAGGIVPQYSMKLSGQKINPVLRMFGQSISGGIDMDGNGYPDVTVGA
FMSDSVVLLRARPVITVDVSIFLPGSINITAPQCHDGQQPVNCLNVTTCFSFHGKHVPGEIGLNYVLMADVAKKEKGQMPRVYFVLLGET
MGQVTEKLQLTYMEETCRHYVAHVKRRVQDVISPIVFEAAYSLSEHVTGEEERELPPLTPVLRWKKGQKIAQKNQTVFERNCRSEDCAAD
LQLQGKLLLSSMDEKTLYLALGAVKNISLNISISNLGDDAYDANVSFNVSRELFFINMWQKEEMGISCELLESDFLKCSVGFPFMRSKSK
YEFSVIFDTSHLSGEEEVLSFIVTAQSGNTERSESLHDNTLVLMVPLMHEVDTSITGIMSPTSFVYGESVDAANFIQLDDLECHFQPINI
TLQVYNTGPSTLPGSSVSISFPNRLSSGGAEMFHVQEMVIGCNAVSWAPAVVPGSLIDHPSGQKPNYIKRFASGGCDNLIKLWKEEEDGQ
WKEEQKLEAHSDWVRDVAWAPSIGLPTSTIASCSQDGRVFIWTCDDASSNTWSPKLLHKFNDVVWHVSWSITANILAVSGGDNKEELQMQ

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Fusion Protein Functional Features


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr3:37792060/chr3:10347376)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
ITGA9

Q13797

.
FUNCTION: Integrin alpha-9/beta-1 (ITGA9:ITGB1) is a receptor for VCAM1, cytotactin and osteopontin. It recognizes the sequence A-E-I-D-G-I-E-L in cytotactin. {ECO:0000250}.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.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneITGA9chr3:37792059chr3:10347375ENST00000264741+2328312_320847.01036.0Calcium bindingOntology_term=ECO:0000255
HgeneITGA9chr3:37792059chr3:10347375ENST00000264741+2328373_381847.01036.0Calcium bindingOntology_term=ECO:0000255
HgeneITGA9chr3:37792059chr3:10347375ENST00000264741+2328435_443847.01036.0Calcium bindingOntology_term=ECO:0000255
HgeneITGA9chr3:37792060chr3:10347376ENST00000264741+2328312_320847.01036.0Calcium bindingOntology_term=ECO:0000255
HgeneITGA9chr3:37792060chr3:10347376ENST00000264741+2328373_381847.01036.0Calcium bindingOntology_term=ECO:0000255
HgeneITGA9chr3:37792060chr3:10347376ENST00000264741+2328435_443847.01036.0Calcium bindingOntology_term=ECO:0000255
HgeneITGA9chr3:37792059chr3:10347375ENST00000264741+2328111_174847.01036.0RepeatFG-GAP 2
HgeneITGA9chr3:37792059chr3:10347375ENST00000264741+2328182_232847.01036.0RepeatFG-GAP 3
HgeneITGA9chr3:37792059chr3:10347375ENST00000264741+2328233_289847.01036.0RepeatFG-GAP 4
HgeneITGA9chr3:37792059chr3:10347375ENST00000264741+2328290_349847.01036.0RepeatFG-GAP 5
HgeneITGA9chr3:37792059chr3:10347375ENST00000264741+2328351_408847.01036.0RepeatFG-GAP 6
HgeneITGA9chr3:37792059chr3:10347375ENST00000264741+232835_96847.01036.0RepeatFG-GAP 1
HgeneITGA9chr3:37792059chr3:10347375ENST00000264741+2328411_474847.01036.0RepeatFG-GAP 7
HgeneITGA9chr3:37792060chr3:10347376ENST00000264741+2328111_174847.01036.0RepeatFG-GAP 2
HgeneITGA9chr3:37792060chr3:10347376ENST00000264741+2328182_232847.01036.0RepeatFG-GAP 3
HgeneITGA9chr3:37792060chr3:10347376ENST00000264741+2328233_289847.01036.0RepeatFG-GAP 4
HgeneITGA9chr3:37792060chr3:10347376ENST00000264741+2328290_349847.01036.0RepeatFG-GAP 5
HgeneITGA9chr3:37792060chr3:10347376ENST00000264741+2328351_408847.01036.0RepeatFG-GAP 6
HgeneITGA9chr3:37792060chr3:10347376ENST00000264741+232835_96847.01036.0RepeatFG-GAP 1
HgeneITGA9chr3:37792060chr3:10347376ENST00000264741+2328411_474847.01036.0RepeatFG-GAP 7
TgeneSEC13chr3:37792059chr3:10347375ENST00000337354510210_253153.0326.0RepeatNote=WD 5
TgeneSEC13chr3:37792059chr3:10347375ENST00000337354510260_299153.0326.0RepeatNote=WD 6
TgeneSEC13chr3:37792059chr3:10347375ENST0000035069749148_204150.0323.0RepeatNote=WD 4
TgeneSEC13chr3:37792059chr3:10347375ENST0000035069749210_253150.0323.0RepeatNote=WD 5
TgeneSEC13chr3:37792059chr3:10347375ENST0000035069749260_299150.0323.0RepeatNote=WD 6
TgeneSEC13chr3:37792059chr3:10347375ENST0000039710949148_204136.0309.0RepeatNote=WD 4
TgeneSEC13chr3:37792059chr3:10347375ENST0000039710949210_253136.0309.0RepeatNote=WD 5
TgeneSEC13chr3:37792059chr3:10347375ENST0000039710949260_299136.0309.0RepeatNote=WD 6
TgeneSEC13chr3:37792060chr3:10347376ENST00000337354510210_253153.0326.0RepeatNote=WD 5
TgeneSEC13chr3:37792060chr3:10347376ENST00000337354510260_299153.0326.0RepeatNote=WD 6
TgeneSEC13chr3:37792060chr3:10347376ENST0000035069749148_204150.0323.0RepeatNote=WD 4
TgeneSEC13chr3:37792060chr3:10347376ENST0000035069749210_253150.0323.0RepeatNote=WD 5
TgeneSEC13chr3:37792060chr3:10347376ENST0000035069749260_299150.0323.0RepeatNote=WD 6
TgeneSEC13chr3:37792060chr3:10347376ENST0000039710949148_204136.0309.0RepeatNote=WD 4
TgeneSEC13chr3:37792060chr3:10347376ENST0000039710949210_253136.0309.0RepeatNote=WD 5
TgeneSEC13chr3:37792060chr3:10347376ENST0000039710949260_299136.0309.0RepeatNote=WD 6

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneITGA9chr3:37792059chr3:10347375ENST00000264741+23281005_1009847.01036.0MotifNote=GFFKR motif
HgeneITGA9chr3:37792060chr3:10347376ENST00000264741+23281005_1009847.01036.0MotifNote=GFFKR motif
HgeneITGA9chr3:37792059chr3:10347375ENST00000264741+23281003_1035847.01036.0Topological domainCytoplasmic
HgeneITGA9chr3:37792059chr3:10347375ENST00000264741+232830_981847.01036.0Topological domainExtracellular
HgeneITGA9chr3:37792060chr3:10347376ENST00000264741+23281003_1035847.01036.0Topological domainCytoplasmic
HgeneITGA9chr3:37792060chr3:10347376ENST00000264741+232830_981847.01036.0Topological domainExtracellular
HgeneITGA9chr3:37792059chr3:10347375ENST00000264741+2328982_1002847.01036.0TransmembraneHelical
HgeneITGA9chr3:37792060chr3:10347376ENST00000264741+2328982_1002847.01036.0TransmembraneHelical
TgeneSEC13chr3:37792059chr3:10347375ENST00000337354510101_144153.0326.0RepeatNote=WD 3
TgeneSEC13chr3:37792059chr3:10347375ENST0000033735451011_50153.0326.0RepeatNote=WD 1
TgeneSEC13chr3:37792059chr3:10347375ENST00000337354510148_204153.0326.0RepeatNote=WD 4
TgeneSEC13chr3:37792059chr3:10347375ENST0000033735451055_96153.0326.0RepeatNote=WD 2
TgeneSEC13chr3:37792059chr3:10347375ENST0000035069749101_144150.0323.0RepeatNote=WD 3
TgeneSEC13chr3:37792059chr3:10347375ENST000003506974911_50150.0323.0RepeatNote=WD 1
TgeneSEC13chr3:37792059chr3:10347375ENST000003506974955_96150.0323.0RepeatNote=WD 2
TgeneSEC13chr3:37792059chr3:10347375ENST0000039710949101_144136.0309.0RepeatNote=WD 3
TgeneSEC13chr3:37792059chr3:10347375ENST000003971094911_50136.0309.0RepeatNote=WD 1
TgeneSEC13chr3:37792059chr3:10347375ENST000003971094955_96136.0309.0RepeatNote=WD 2
TgeneSEC13chr3:37792060chr3:10347376ENST00000337354510101_144153.0326.0RepeatNote=WD 3
TgeneSEC13chr3:37792060chr3:10347376ENST0000033735451011_50153.0326.0RepeatNote=WD 1
TgeneSEC13chr3:37792060chr3:10347376ENST00000337354510148_204153.0326.0RepeatNote=WD 4
TgeneSEC13chr3:37792060chr3:10347376ENST0000033735451055_96153.0326.0RepeatNote=WD 2
TgeneSEC13chr3:37792060chr3:10347376ENST0000035069749101_144150.0323.0RepeatNote=WD 3
TgeneSEC13chr3:37792060chr3:10347376ENST000003506974911_50150.0323.0RepeatNote=WD 1
TgeneSEC13chr3:37792060chr3:10347376ENST000003506974955_96150.0323.0RepeatNote=WD 2
TgeneSEC13chr3:37792060chr3:10347376ENST0000039710949101_144136.0309.0RepeatNote=WD 3
TgeneSEC13chr3:37792060chr3:10347376ENST000003971094911_50136.0309.0RepeatNote=WD 1
TgeneSEC13chr3:37792060chr3:10347376ENST000003971094955_96136.0309.0RepeatNote=WD 2


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Fusion Protein Structures

check button PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Fusion protein PDB link (fusion AA seq ID in FusionPDB)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)
PDB file >>>1802_ITGA9_37792060_SEC13_10347376_ranked_0.pdbITGA93779205937792060ENST00000383801SEC13chr310347376-
MGMGGPAAPRGAGRLRALLLALVVAGIPAGAYNLDPQRPVHFQGPADSFFGYAVLEHFHDNTRWVLVGAPKADSKYSPSVKSPGAVFKCR
VHTNPDRRCTELDMARGKNRGTSCGKTCREDRDDEWMGVSLARQPKADGRVLACAHRWKNIYYEADHILPHGFCYIIPSNLQAKGRTLIP
CYEEYKKKYGEEHGSCQAGIAGFFTEELVVMGAPGSFYWAGTIKVLNLTDNTYLKLNDEVIMNRRYTYLGYAVTAGHFSHPSTIDVVGGA
PQDKGIGKVYIFRADRRSGTLIKIFQASGKKMGSYFGSSLCAVDLNGDGLSDLLVGAPMFSEIRDEGQVTVYINRGNGALEEQLALTGDG
AYNAHFGESIASLDDLDNDGFPDVAIGAPKEDDFAGAVYIYHGDAGGIVPQYSMKLSGQKINPVLRMFGQSISGGIDMDGNGYPDVTVGA
FMSDSVVLLRARPVITVDVSIFLPGSINITAPQCHDGQQPVNCLNVTTCFSFHGKHVPGEIGLNYVLMADVAKKEKGQMPRVYFVLLGET
MGQVTEKLQLTYMEETCRHYVAHVKRRVQDVISPIVFEAAYSLSEHVTGEEERELPPLTPVLRWKKGQKIAQKNQTVFERNCRSEDCAAD
LQLQGKLLLSSMDEKTLYLALGAVKNISLNISISNLGDDAYDANVSFNVSRELFFINMWQKEEMGISCELLESDFLKCSVGFPFMRSKSK
YEFSVIFDTSHLSGEEEVLSFIVTAQSGNTERSESLHDNTLVLMVPLMHEVDTSITGIMSPTSFVYGESVDAANFIQLDDLECHFQPINI
TLQVYNTGPSTLPGSSVSISFPNRLSSGGAEMFHVQEMVIGCNAVSWAPAVVPGSLIDHPSGQKPNYIKRFASGGCDNLIKLWKEEEDGQ
WKEEQKLEAHSDWVRDVAWAPSIGLPTSTIASCSQDGRVFIWTCDDASSNTWSPKLLHKFNDVVWHVSWSITANILAVSGGDNKVTLWKE
1021


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pLDDT score distribution

check button pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
ITGA9_pLDDT.png
all structure
all structure
SEC13_pLDDT.png
all structure
all structure

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
all structure


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Ramachandran Plot of Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.
Fusion AA seq ID in FusionPDB and their Ramachandran plots

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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
ITGA9
SEC13


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to ITGA9-SEC13


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to ITGA9-SEC13


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource