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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:SS18L1-JAM2

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: SS18L1-JAM2
	FusionPDB ID: 86669
	FusionGDB2.0 ID: 86669
		Hgene	Tgene
	Gene symbol	SS18L1	JAM2
	Gene ID	26039	58494
	Gene name	SS18L1 subunit of BAF chromatin remodeling complex	junctional adhesion molecule 2
	Synonyms	CREST\|LP2261	C21orf43\|CD322\|JAM-B\|JAMB\|PRO245\|VE-JAM\|VEJAM
	Cytomap	20q13.33	21q21.3
	Type of gene	protein-coding	protein-coding
	Description	calcium-responsive transactivatorSS18-like protein 1SS18L1, nBAF chromatin remodeling complex subunitSYT homolog 1synovial sarcoma translocation gene on chromosome 18-like 1	junctional adhesion molecule BJAM-2JAM-IT/VE-JAMvascular endothelial junction-associated molecule
	Modification date	20200313	20200313
	UniProtAcc	O75177	P57087
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000331758, ENST00000370848, ENST00000421564, ENST00000491916,	ENST00000477351, ENST00000312957, ENST00000400532, ENST00000425221, ENST00000480456,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	11 X 8 X 7=616	8 X 8 X 4=256
	# samples	12	9
	** MAII score	log2(12/616*10)=-2.35989594508638 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(9/256*10)=-1.50814690367033 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: SS18L1 [Title/Abstract] AND JAM2 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	SS18L1(60740570)-JAM2(27056195), # samples:2
Anticipated loss of major functional domain due to fusion event.	SS18L1-JAM2 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. SS18L1-JAM2 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. SS18L1-JAM2 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. SS18L1-JAM2 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)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Tgene	JAM2	GO:0045123	cellular extravasation	12239159
Tgene	JAM2	GO:0050901	leukocyte tethering or rolling	19740376
Tgene	JAM2	GO:0071593	lymphocyte aggregation	11823489
Tgene	JAM2	GO:2000403	positive regulation of lymphocyte migration	12239159

Fusion gene breakpoints across SS18L1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across JAM2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Fusion Gene Sample Information

Fusion gene information from FusionGDB2.0.

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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	SKCM	TCGA-D3-A2JG-06A	SS18L1	chr20	60740570	+	JAM2	chr21	27056195	+

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Fusion ORF Analysis

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	Seq length (transcript)	BP loci (transcript)	Predicted start (transcript)	Predicted stop (transcript)	Seq length (amino acids)
ENST00000421564	SS18L1	chr20	60740570	+	ENST00000400532	JAM2	chr21	27056195	+	2111	971	55	1842	595
ENST00000421564	SS18L1	chr20	60740570	+	ENST00000480456	JAM2	chr21	27056195	+	4691	971	55	1800	581
ENST00000421564	SS18L1	chr20	60740570	+	ENST00000312957	JAM2	chr21	27056195	+	2052	971	55	1800	581
ENST00000421564	SS18L1	chr20	60740570	+	ENST00000425221	JAM2	chr21	27056195	+	2357	971	55	1692	545
ENST00000331758	SS18L1	chr20	60740570	+	ENST00000400532	JAM2	chr21	27056195	+	2082	942	26	1813	595
ENST00000331758	SS18L1	chr20	60740570	+	ENST00000480456	JAM2	chr21	27056195	+	4662	942	26	1771	581
ENST00000331758	SS18L1	chr20	60740570	+	ENST00000312957	JAM2	chr21	27056195	+	2023	942	26	1771	581
ENST00000331758	SS18L1	chr20	60740570	+	ENST00000425221	JAM2	chr21	27056195	+	2328	942	26	1663	545
ENST00000370848	SS18L1	chr20	60740570	+	ENST00000400532	JAM2	chr21	27056195	+	2065	925	0	1796	598
ENST00000370848	SS18L1	chr20	60740570	+	ENST00000480456	JAM2	chr21	27056195	+	4645	925	0	1754	584
ENST00000370848	SS18L1	chr20	60740570	+	ENST00000312957	JAM2	chr21	27056195	+	2006	925	0	1754	584
ENST00000370848	SS18L1	chr20	60740570	+	ENST00000425221	JAM2	chr21	27056195	+	2311	925	0	1646	548

DeepORF 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.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000421564	ENST00000400532	SS18L1	chr20	60740570	+	JAM2	chr21	27056195	+	0.007939279	0.9920608
ENST00000421564	ENST00000480456	SS18L1	chr20	60740570	+	JAM2	chr21	27056195	+	0.000893502	0.99910647
ENST00000421564	ENST00000312957	SS18L1	chr20	60740570	+	JAM2	chr21	27056195	+	0.004265664	0.9957344
ENST00000421564	ENST00000425221	SS18L1	chr20	60740570	+	JAM2	chr21	27056195	+	0.002732066	0.99726796
ENST00000331758	ENST00000400532	SS18L1	chr20	60740570	+	JAM2	chr21	27056195	+	0.007504143	0.9924959
ENST00000331758	ENST00000480456	SS18L1	chr20	60740570	+	JAM2	chr21	27056195	+	0.000846798	0.99915326
ENST00000331758	ENST00000312957	SS18L1	chr20	60740570	+	JAM2	chr21	27056195	+	0.004046413	0.99595356
ENST00000331758	ENST00000425221	SS18L1	chr20	60740570	+	JAM2	chr21	27056195	+	0.002634582	0.9973654
ENST00000370848	ENST00000400532	SS18L1	chr20	60740570	+	JAM2	chr21	27056195	+	0.010559324	0.98944074
ENST00000370848	ENST00000480456	SS18L1	chr20	60740570	+	JAM2	chr21	27056195	+	0.001098735	0.99890125
ENST00000370848	ENST00000312957	SS18L1	chr20	60740570	+	JAM2	chr21	27056195	+	0.00635664	0.9936434
ENST00000370848	ENST00000425221	SS18L1	chr20	60740570	+	JAM2	chr21	27056195	+	0.00348176	0.99651825

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Fusion Amino Acid Sequences

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

>86669_86669_1_SS18L1-JAM2_SS18L1_chr20_60740570_ENST00000331758_JAM2_chr21_27056195_ENST00000312957_length(amino acids)=581AA_BP=305
MSVAFASARPRGKGEVTQQTIQKMLDENHHLIQCILEYQSKGKTAECTQYQQILHRNLVYLATIADSNQNMQSLLPAPPTQNMNLGPGAL
TQSGSSQGLHSQGSLSDAISTGLPPSSLLQGQIGNGPSHVSMQQTAPNTLPTTSMSISGPGYSHAGPASQGVPMQGQGTIGNYVSRTNIN
MQSNPVSMMQQQAATSHYSSAQGGSQHYQGQSSIAMMGQGSQGSSMMGQRPMAPYRPSQQGSSQQYLGQEEYYGEQYSHSQGAAEPMGQQ
YYPDGHGDYAYQQSSYTEQSYDRSFEESTQHYYEGDHKAYGFSAPKDQQVVTAVEYQEAILACKTPKKTVSSRLEWKKLGRSVSFVYYQQ
TLQGDFKNRAEMIDFNIRIKNVTRSDAGKYRCEVSAPSEQGQNLEEDTVTLEVLVAPAVPSCEVPSSALSGTVVELRCQDKEGNPAPEYT
WFKDGIRLLENPRLGSQSTNSSYTMNTKTGTLQFNTVSKLDTGEYSCEARNSVGYRRCPGKRMQVDDLNISGIIAAVVVVALVISVCGLG

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

>86669_86669_2_SS18L1-JAM2_SS18L1_chr20_60740570_ENST00000331758_JAM2_chr21_27056195_ENST00000400532_length(amino acids)=595AA_BP=305
MSVAFASARPRGKGEVTQQTIQKMLDENHHLIQCILEYQSKGKTAECTQYQQILHRNLVYLATIADSNQNMQSLLPAPPTQNMNLGPGAL
TQSGSSQGLHSQGSLSDAISTGLPPSSLLQGQIGNGPSHVSMQQTAPNTLPTTSMSISGPGYSHAGPASQGVPMQGQGTIGNYVSRTNIN
MQSNPVSMMQQQAATSHYSSAQGGSQHYQGQSSIAMMGQGSQGSSMMGQRPMAPYRPSQQGSSQQYLGQEEYYGEQYSHSQGAAEPMGQQ
YYPDGHGDYAYQQSSYTEQSYDRSFEESTQHYYEGDHKAYGFSAPKDQQVVTAVEYQEAILACKTPKKTVSSRLEWKKLGRSVSFVYYQQ
TLQGDFKNRAEMIDFNIRIKNVTRSDAGKYRCEVSAPSEQGQNLEEDTVTLEVLVAPAVPSCEVPSSALSGTVVELRCQDKEGNPAPEYT
WFKDGIRLLENPRLGSQSTNSSYTMNTKTGTLQFNTVSKLDTGEYSCEARNSVGYRRCPGKRMQVDDLNISGIIAAVVVVALVISVCGLG

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

>86669_86669_3_SS18L1-JAM2_SS18L1_chr20_60740570_ENST00000331758_JAM2_chr21_27056195_ENST00000425221_length(amino acids)=545AA_BP=305
MSVAFASARPRGKGEVTQQTIQKMLDENHHLIQCILEYQSKGKTAECTQYQQILHRNLVYLATIADSNQNMQSLLPAPPTQNMNLGPGAL
TQSGSSQGLHSQGSLSDAISTGLPPSSLLQGQIGNGPSHVSMQQTAPNTLPTTSMSISGPGYSHAGPASQGVPMQGQGTIGNYVSRTNIN
MQSNPVSMMQQQAATSHYSSAQGGSQHYQGQSSIAMMGQGSQGSSMMGQRPMAPYRPSQQGSSQQYLGQEEYYGEQYSHSQGAAEPMGQQ
YYPDGHGDYAYQQSSYTEQSYDRSFEESTQHYYEGDHKAYGFSAPKDQQVVTAVEYQGDFKNRAEMIDFNIRIKNVTRSDAGKYRCEVSA
PSEQGQNLEEDTVTLEVLVAPAVPSCEVPSSALSGTVVELRCQDKEGNPAPEYTWFKDGIRLLENPRLGSQSTNSSYTMNTKTGTLQFNT
VSKLDTGEYSCEARNSVGYRRCPGKRMQVDDLNISGIIAAVVVVALVISVCGLGVCYAQRKGYFSKETSFQKSNSSSKATTMSENDFKHT

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

>86669_86669_4_SS18L1-JAM2_SS18L1_chr20_60740570_ENST00000331758_JAM2_chr21_27056195_ENST00000480456_length(amino acids)=581AA_BP=305
MSVAFASARPRGKGEVTQQTIQKMLDENHHLIQCILEYQSKGKTAECTQYQQILHRNLVYLATIADSNQNMQSLLPAPPTQNMNLGPGAL
TQSGSSQGLHSQGSLSDAISTGLPPSSLLQGQIGNGPSHVSMQQTAPNTLPTTSMSISGPGYSHAGPASQGVPMQGQGTIGNYVSRTNIN
MQSNPVSMMQQQAATSHYSSAQGGSQHYQGQSSIAMMGQGSQGSSMMGQRPMAPYRPSQQGSSQQYLGQEEYYGEQYSHSQGAAEPMGQQ
YYPDGHGDYAYQQSSYTEQSYDRSFEESTQHYYEGDHKAYGFSAPKDQQVVTAVEYQEAILACKTPKKTVSSRLEWKKLGRSVSFVYYQQ
TLQGDFKNRAEMIDFNIRIKNVTRSDAGKYRCEVSAPSEQGQNLEEDTVTLEVLVAPAVPSCEVPSSALSGTVVELRCQDKEGNPAPEYT
WFKDGIRLLENPRLGSQSTNSSYTMNTKTGTLQFNTVSKLDTGEYSCEARNSVGYRRCPGKRMQVDDLNISGIIAAVVVVALVISVCGLG

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

>86669_86669_5_SS18L1-JAM2_SS18L1_chr20_60740570_ENST00000370848_JAM2_chr21_27056195_ENST00000312957_length(amino acids)=584AA_BP=308
MQSLSTEARYVPRVPQHRDQISPRSPQHGGQICPRSPLHRGQICPRSPPARRYQQILHRNLVYLATIADSNQNMQSLLPAPPTQNMNLGP
GALTQSGSSQGLHSQGSLSDAISTGLPPSSLLQGQIGNGPSHVSMQQTAPNTLPTTSMSISGPGYSHAGPASQGVPMQGQGTIGNYVSRT
NINMQSNPVSMMQQQAATSHYSSAQGGSQHYQGQSSIAMMGQGSQGSSMMGQRPMAPYRPSQQGSSQQYLGQEEYYGEQYSHSQGAAEPM
GQQYYPDGHGDYAYQQSSYTEQSYDRSFEESTQHYYEGDHKAYGFSAPKDQQVVTAVEYQEAILACKTPKKTVSSRLEWKKLGRSVSFVY
YQQTLQGDFKNRAEMIDFNIRIKNVTRSDAGKYRCEVSAPSEQGQNLEEDTVTLEVLVAPAVPSCEVPSSALSGTVVELRCQDKEGNPAP
EYTWFKDGIRLLENPRLGSQSTNSSYTMNTKTGTLQFNTVSKLDTGEYSCEARNSVGYRRCPGKRMQVDDLNISGIIAAVVVVALVISVC

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

>86669_86669_6_SS18L1-JAM2_SS18L1_chr20_60740570_ENST00000370848_JAM2_chr21_27056195_ENST00000400532_length(amino acids)=598AA_BP=308
MQSLSTEARYVPRVPQHRDQISPRSPQHGGQICPRSPLHRGQICPRSPPARRYQQILHRNLVYLATIADSNQNMQSLLPAPPTQNMNLGP
GALTQSGSSQGLHSQGSLSDAISTGLPPSSLLQGQIGNGPSHVSMQQTAPNTLPTTSMSISGPGYSHAGPASQGVPMQGQGTIGNYVSRT
NINMQSNPVSMMQQQAATSHYSSAQGGSQHYQGQSSIAMMGQGSQGSSMMGQRPMAPYRPSQQGSSQQYLGQEEYYGEQYSHSQGAAEPM
GQQYYPDGHGDYAYQQSSYTEQSYDRSFEESTQHYYEGDHKAYGFSAPKDQQVVTAVEYQEAILACKTPKKTVSSRLEWKKLGRSVSFVY
YQQTLQGDFKNRAEMIDFNIRIKNVTRSDAGKYRCEVSAPSEQGQNLEEDTVTLEVLVAPAVPSCEVPSSALSGTVVELRCQDKEGNPAP
EYTWFKDGIRLLENPRLGSQSTNSSYTMNTKTGTLQFNTVSKLDTGEYSCEARNSVGYRRCPGKRMQVDDLNISGIIAAVVVVALVISVC

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

>86669_86669_7_SS18L1-JAM2_SS18L1_chr20_60740570_ENST00000370848_JAM2_chr21_27056195_ENST00000425221_length(amino acids)=548AA_BP=308
MQSLSTEARYVPRVPQHRDQISPRSPQHGGQICPRSPLHRGQICPRSPPARRYQQILHRNLVYLATIADSNQNMQSLLPAPPTQNMNLGP
GALTQSGSSQGLHSQGSLSDAISTGLPPSSLLQGQIGNGPSHVSMQQTAPNTLPTTSMSISGPGYSHAGPASQGVPMQGQGTIGNYVSRT
NINMQSNPVSMMQQQAATSHYSSAQGGSQHYQGQSSIAMMGQGSQGSSMMGQRPMAPYRPSQQGSSQQYLGQEEYYGEQYSHSQGAAEPM
GQQYYPDGHGDYAYQQSSYTEQSYDRSFEESTQHYYEGDHKAYGFSAPKDQQVVTAVEYQGDFKNRAEMIDFNIRIKNVTRSDAGKYRCE
VSAPSEQGQNLEEDTVTLEVLVAPAVPSCEVPSSALSGTVVELRCQDKEGNPAPEYTWFKDGIRLLENPRLGSQSTNSSYTMNTKTGTLQ
FNTVSKLDTGEYSCEARNSVGYRRCPGKRMQVDDLNISGIIAAVVVVALVISVCGLGVCYAQRKGYFSKETSFQKSNSSSKATTMSENDF

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

>86669_86669_8_SS18L1-JAM2_SS18L1_chr20_60740570_ENST00000370848_JAM2_chr21_27056195_ENST00000480456_length(amino acids)=584AA_BP=308
MQSLSTEARYVPRVPQHRDQISPRSPQHGGQICPRSPLHRGQICPRSPPARRYQQILHRNLVYLATIADSNQNMQSLLPAPPTQNMNLGP
GALTQSGSSQGLHSQGSLSDAISTGLPPSSLLQGQIGNGPSHVSMQQTAPNTLPTTSMSISGPGYSHAGPASQGVPMQGQGTIGNYVSRT
NINMQSNPVSMMQQQAATSHYSSAQGGSQHYQGQSSIAMMGQGSQGSSMMGQRPMAPYRPSQQGSSQQYLGQEEYYGEQYSHSQGAAEPM
GQQYYPDGHGDYAYQQSSYTEQSYDRSFEESTQHYYEGDHKAYGFSAPKDQQVVTAVEYQEAILACKTPKKTVSSRLEWKKLGRSVSFVY
YQQTLQGDFKNRAEMIDFNIRIKNVTRSDAGKYRCEVSAPSEQGQNLEEDTVTLEVLVAPAVPSCEVPSSALSGTVVELRCQDKEGNPAP
EYTWFKDGIRLLENPRLGSQSTNSSYTMNTKTGTLQFNTVSKLDTGEYSCEARNSVGYRRCPGKRMQVDDLNISGIIAAVVVVALVISVC

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

>86669_86669_9_SS18L1-JAM2_SS18L1_chr20_60740570_ENST00000421564_JAM2_chr21_27056195_ENST00000312957_length(amino acids)=581AA_BP=305
MSVAFASARPRGKGEVTQQTIQKMLDENHHLIQCILEYQSKGKTAECTQYQQILHRNLVYLATIADSNQNMQSLLPAPPTQNMNLGPGAL
TQSGSSQGLHSQGSLSDAISTGLPPSSLLQGQIGNGPSHVSMQQTAPNTLPTTSMSISGPGYSHAGPASQGVPMQGQGTIGNYVSRTNIN
MQSNPVSMMQQQAATSHYSSAQGGSQHYQGQSSIAMMGQGSQGSSMMGQRPMAPYRPSQQGSSQQYLGQEEYYGEQYSHSQGAAEPMGQQ
YYPDGHGDYAYQQSSYTEQSYDRSFEESTQHYYEGDHKAYGFSAPKDQQVVTAVEYQEAILACKTPKKTVSSRLEWKKLGRSVSFVYYQQ
TLQGDFKNRAEMIDFNIRIKNVTRSDAGKYRCEVSAPSEQGQNLEEDTVTLEVLVAPAVPSCEVPSSALSGTVVELRCQDKEGNPAPEYT
WFKDGIRLLENPRLGSQSTNSSYTMNTKTGTLQFNTVSKLDTGEYSCEARNSVGYRRCPGKRMQVDDLNISGIIAAVVVVALVISVCGLG

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

>86669_86669_10_SS18L1-JAM2_SS18L1_chr20_60740570_ENST00000421564_JAM2_chr21_27056195_ENST00000400532_length(amino acids)=595AA_BP=305
MSVAFASARPRGKGEVTQQTIQKMLDENHHLIQCILEYQSKGKTAECTQYQQILHRNLVYLATIADSNQNMQSLLPAPPTQNMNLGPGAL
TQSGSSQGLHSQGSLSDAISTGLPPSSLLQGQIGNGPSHVSMQQTAPNTLPTTSMSISGPGYSHAGPASQGVPMQGQGTIGNYVSRTNIN
MQSNPVSMMQQQAATSHYSSAQGGSQHYQGQSSIAMMGQGSQGSSMMGQRPMAPYRPSQQGSSQQYLGQEEYYGEQYSHSQGAAEPMGQQ
YYPDGHGDYAYQQSSYTEQSYDRSFEESTQHYYEGDHKAYGFSAPKDQQVVTAVEYQEAILACKTPKKTVSSRLEWKKLGRSVSFVYYQQ
TLQGDFKNRAEMIDFNIRIKNVTRSDAGKYRCEVSAPSEQGQNLEEDTVTLEVLVAPAVPSCEVPSSALSGTVVELRCQDKEGNPAPEYT
WFKDGIRLLENPRLGSQSTNSSYTMNTKTGTLQFNTVSKLDTGEYSCEARNSVGYRRCPGKRMQVDDLNISGIIAAVVVVALVISVCGLG

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

>86669_86669_11_SS18L1-JAM2_SS18L1_chr20_60740570_ENST00000421564_JAM2_chr21_27056195_ENST00000425221_length(amino acids)=545AA_BP=305
MSVAFASARPRGKGEVTQQTIQKMLDENHHLIQCILEYQSKGKTAECTQYQQILHRNLVYLATIADSNQNMQSLLPAPPTQNMNLGPGAL
TQSGSSQGLHSQGSLSDAISTGLPPSSLLQGQIGNGPSHVSMQQTAPNTLPTTSMSISGPGYSHAGPASQGVPMQGQGTIGNYVSRTNIN
MQSNPVSMMQQQAATSHYSSAQGGSQHYQGQSSIAMMGQGSQGSSMMGQRPMAPYRPSQQGSSQQYLGQEEYYGEQYSHSQGAAEPMGQQ
YYPDGHGDYAYQQSSYTEQSYDRSFEESTQHYYEGDHKAYGFSAPKDQQVVTAVEYQGDFKNRAEMIDFNIRIKNVTRSDAGKYRCEVSA
PSEQGQNLEEDTVTLEVLVAPAVPSCEVPSSALSGTVVELRCQDKEGNPAPEYTWFKDGIRLLENPRLGSQSTNSSYTMNTKTGTLQFNT
VSKLDTGEYSCEARNSVGYRRCPGKRMQVDDLNISGIIAAVVVVALVISVCGLGVCYAQRKGYFSKETSFQKSNSSSKATTMSENDFKHT

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

>86669_86669_12_SS18L1-JAM2_SS18L1_chr20_60740570_ENST00000421564_JAM2_chr21_27056195_ENST00000480456_length(amino acids)=581AA_BP=305
MSVAFASARPRGKGEVTQQTIQKMLDENHHLIQCILEYQSKGKTAECTQYQQILHRNLVYLATIADSNQNMQSLLPAPPTQNMNLGPGAL
TQSGSSQGLHSQGSLSDAISTGLPPSSLLQGQIGNGPSHVSMQQTAPNTLPTTSMSISGPGYSHAGPASQGVPMQGQGTIGNYVSRTNIN
MQSNPVSMMQQQAATSHYSSAQGGSQHYQGQSSIAMMGQGSQGSSMMGQRPMAPYRPSQQGSSQQYLGQEEYYGEQYSHSQGAAEPMGQQ
YYPDGHGDYAYQQSSYTEQSYDRSFEESTQHYYEGDHKAYGFSAPKDQQVVTAVEYQEAILACKTPKKTVSSRLEWKKLGRSVSFVYYQQ
TLQGDFKNRAEMIDFNIRIKNVTRSDAGKYRCEVSAPSEQGQNLEEDTVTLEVLVAPAVPSCEVPSSALSGTVVELRCQDKEGNPAPEYT
WFKDGIRLLENPRLGSQSTNSSYTMNTKTGTLQFNTVSKLDTGEYSCEARNSVGYRRCPGKRMQVDDLNISGIIAAVVVVALVISVCGLG

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Fusion Protein Functional Features

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr20:60740570/chr21:27056195)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
SS18L1 O75177	JAM2 P57087
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.	FUNCTION: Junctional adhesion protein that mediates heterotypic cell-cell interactions with its cognate receptor JAM3 to regulate different cellular processes (PubMed:11590146, PubMed:11823489, PubMed:24357068). Plays a role in homing and mobilization of hematopoietic stem and progenitor cells within the bone marrow (PubMed:24357068). At the surface of bone marrow stromal cells, it contributes to the retention of the hematopoietic stem and progenitor cells expressing JAM3 (PubMed:11590146, PubMed:24357068). Plays a central role in leukocytes extravasation by facilitating not only transmigration but also tethering and rolling of leukocytes along the endothelium (PubMed:12239159). Tethering and rolling of leukocytes are dependent on the binding by JAM2 of the integrin alpha-4/beta-1 (PubMed:12070135). Plays a role in spermatogenesis where JAM2 and JAM3, which are respectively expressed by Sertoli and germ cells, mediate an interaction between both cell types and play an essential role in the anchorage of germ cells onto Sertoli cells and the assembly of cell polarity complexes during spermatid differentiation (By similarity). Also functions as an inhibitory somatodendritic cue that prevents the myelination of non-axonal parts of neurons (By similarity). During myogenesis, it is involved in myocyte fusion (By similarity). May also play a role in angiogenesis (By similarity). {ECO:0000250\|UniProtKB:A0A0R4IGV4, ECO:0000250\|UniProtKB:Q9JI59, ECO:0000269\|PubMed:11590146, ECO:0000269\|PubMed:11823489, ECO:0000269\|PubMed:12070135, ECO:0000269\|PubMed:12239159, ECO:0000269\|PubMed:24357068}.

Retention 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.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

SS18L1

chr20:60740570

chr21:27056195

ENST00000331758

50_53

305.3333333333333

397.0

Motif

SH2-binding

Hgene

SS18L1

chr20:60740570

chr21:27056195

ENST00000370848

50_53

308.3333333333333

1118.0

Motif

SH2-binding

Hgene

SS18L1

chr20:60740570

chr21:27056195

ENST00000421564

50_53

305.3333333333333

1125.3333333333333

Motif

SH2-binding

Hgene

SS18L1

chr20:60740570

chr21:27056195

ENST00000331758

149_232

305.3333333333333

397.0

Region

Methionine-rich intra-molecular domain

Hgene

SS18L1

chr20:60740570

chr21:27056195

ENST00000370848

149_232

308.3333333333333

1118.0

Region

Methionine-rich intra-molecular domain

Hgene

SS18L1

chr20:60740570

chr21:27056195

ENST00000421564

149_232

305.3333333333333

1125.3333333333333

Region

Methionine-rich intra-molecular domain

Tgene

JAM2

chr20:60740570

chr21:27056195

ENST00000400532

134_238

22.333333333333332

313.0

Domain

Ig-like C2-type

Tgene

JAM2

chr20:60740570

chr21:27056195

ENST00000400532

32_127

22.333333333333332

313.0

Domain

Ig-like V-type

Tgene

JAM2

chr20:60740570

chr21:27056195

ENST00000425221

134_238

22.333333333333332

263.0

Domain

Ig-like C2-type

Tgene

JAM2

chr20:60740570

chr21:27056195

ENST00000425221

32_127

22.333333333333332

263.0

Domain

Ig-like V-type

Tgene

JAM2

chr20:60740570

chr21:27056195

ENST00000480456

134_238

22.333333333333332

299.0

Domain

Ig-like C2-type

Tgene

JAM2

chr20:60740570

chr21:27056195

ENST00000480456

32_127

22.333333333333332

299.0

Domain

Ig-like V-type

Tgene

JAM2

chr20:60740570

chr21:27056195

ENST00000400532

260_298

22.333333333333332

313.0

Topological domain

Cytoplasmic

Tgene

JAM2

chr20:60740570

chr21:27056195

ENST00000400532

29_238

22.333333333333332

313.0

Topological domain

Extracellular

Tgene

JAM2

chr20:60740570

chr21:27056195

ENST00000425221

260_298

22.333333333333332

263.0

Topological domain

Cytoplasmic

Tgene

JAM2

chr20:60740570

chr21:27056195

ENST00000425221

29_238

22.333333333333332

263.0

Topological domain

Extracellular

Tgene

JAM2

chr20:60740570

chr21:27056195

ENST00000480456

260_298

22.333333333333332

299.0

Topological domain

Cytoplasmic

Tgene

JAM2

chr20:60740570

chr21:27056195

ENST00000480456

29_238

22.333333333333332

299.0

Topological domain

Extracellular

Tgene

JAM2

chr20:60740570

chr21:27056195

ENST00000400532

239_259

22.333333333333332

313.0

Transmembrane

Helical

Tgene

JAM2

chr20:60740570

chr21:27056195

ENST00000425221

239_259

22.333333333333332

263.0

Transmembrane

Helical

Tgene

JAM2

chr20:60740570

chr21:27056195

ENST00000480456

239_259

22.333333333333332

299.0

Transmembrane

Helical

- Not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

SS18L1

chr20:60740570

chr21:27056195

ENST00000331758

190_396

305.3333333333333

397.0

Compositional bias

Note=Gln-rich

Hgene

SS18L1

chr20:60740570

chr21:27056195

ENST00000370848

190_396

308.3333333333333

1118.0

Compositional bias

Note=Gln-rich

Hgene

SS18L1

chr20:60740570

chr21:27056195

ENST00000421564

190_396

305.3333333333333

1125.3333333333333

Compositional bias

Note=Gln-rich

Hgene

SS18L1

chr20:60740570

chr21:27056195

ENST00000331758

353_356

305.3333333333333

397.0

Motif

SH2-binding

Hgene

SS18L1

chr20:60740570

chr21:27056195

ENST00000331758

371_379

305.3333333333333

397.0

Motif

SH3-binding

Hgene

SS18L1

chr20:60740570

chr21:27056195

ENST00000331758

391_394

305.3333333333333

397.0

Motif

SH2-binding

Hgene

SS18L1

chr20:60740570

chr21:27056195

ENST00000370848

353_356

308.3333333333333

1118.0

Motif

SH2-binding

Hgene

SS18L1

chr20:60740570

chr21:27056195

ENST00000370848

371_379

308.3333333333333

1118.0

Motif

SH3-binding

Hgene

SS18L1

chr20:60740570

chr21:27056195

ENST00000370848

391_394

308.3333333333333

1118.0

Motif

SH2-binding

Hgene

SS18L1

chr20:60740570

chr21:27056195

ENST00000421564

353_356

305.3333333333333

1125.3333333333333

Motif

SH2-binding

Hgene

SS18L1

chr20:60740570

chr21:27056195

ENST00000421564

371_379

305.3333333333333

1125.3333333333333

Motif

SH3-binding

Hgene

SS18L1

chr20:60740570

chr21:27056195

ENST00000421564

391_394

305.3333333333333

1125.3333333333333

Motif

SH2-binding

Hgene

SS18L1

chr20:60740570

chr21:27056195

ENST00000331758

246_317

305.3333333333333

397.0

Region

MFD domain

Hgene

SS18L1

chr20:60740570

chr21:27056195

ENST00000331758

334_396

305.3333333333333

397.0

Region

Necessary for nuclear localization

Hgene

SS18L1

chr20:60740570

chr21:27056195

ENST00000370848

246_317

308.3333333333333

1118.0

Region

MFD domain

Hgene

SS18L1

chr20:60740570

chr21:27056195

ENST00000370848

334_396

308.3333333333333

1118.0

Region

Necessary for nuclear localization

Hgene

SS18L1

chr20:60740570

chr21:27056195

ENST00000421564

246_317

305.3333333333333

1125.3333333333333

Region

MFD domain

Hgene

SS18L1

chr20:60740570

chr21:27056195

ENST00000421564

334_396

305.3333333333333

1125.3333333333333

Region

Necessary for nuclear localization

Top

Fusion Protein-Protein Interaction

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160)

Gene

PPI interactors

SS18L1

SF3B4, RFX6, CREBBP, EP300, USP30, SMARCA4, ATF3, ELF5, HDAC2, SMAD1, SMAD3, STAT3, TCF7, HDAC4, NR1H3, BRD1, AATF, RLIM, TAF9B, GATAD1, PCGF6, MED30, ANKRD22, WHSC1L1, SKA3, CUL3, DGCR6, CSTF2, LGALS3, CTAGE5, SNRPB, SNRPC, FAM168A, SS18L1, MAPK1IP1L, BMI1, DPF3, DPF2, SMARCE1, SMARCD1, SMARCC1, SMARCC2, HGS, ESR2, TP53BP1, ATN1, GLTSCR1L, ZMIZ2, PAX8, CEP55, C1orf94, NAF1, BAG4, SSBP3, ZMYND19, USP54, TNK1, BRD3, SMARCA2, HNRNPH1, NR3C1, BCL7C, SMARCD3, SS18, SMARCB1, ARID1A, ARID1B, SMARCD2, BCL7A, DPF1, BRD7, ARID2, ACTL6A, PBRM1, PHF10, GLTSCR1, ACTC1, BCL7B, BRD9, STK11IP, T, ERG, ETS1, FEV, FOS, HNF4A, LHX3, MYOD1, PAX6, PAX7, SP7,

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
SS18L1
JAM2

- Retained interactions in fusion protein (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost interactions due to fusion (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

Top

Related Drugs to SS18L1-JAM2

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

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to SS18L1-JAM2

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

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner	Gene	Disease ID	Disease name	# pubmeds	Source
Hgene	SS18L1	C1862939	AMYOTROPHIC LATERAL SCLEROSIS 1	1	GENOMICS_ENGLAND