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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:ST6GAL1-EIF4A2

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: ST6GAL1-EIF4A2
	FusionPDB ID: 86977
	FusionGDB2.0 ID: 86977
		Hgene	Tgene
	Gene symbol	ST6GAL1	EIF4A2
	Gene ID	6480	1974
	Gene name	ST6 beta-galactoside alpha-2,6-sialyltransferase 1	eukaryotic translation initiation factor 4A2
	Synonyms	SIAT1\|ST6GalI\|ST6N	BM-010\|DDX2B\|EIF4A\|EIF4F\|eIF-4A-II\|eIF4A-II
	Cytomap	3q27.3	3q27.3
	Type of gene	protein-coding	protein-coding
	Description	beta-galactoside alpha-2,6-sialyltransferase 1B-cell antigen CD75CMP-N-acetylneuraminate beta-galactosamide alpha-2,6-sialyltransferaseCMP-N-acetylneuraminate-beta-galactosamide-alpha-2,6-sialyltransferase 1ST6 N-acetylgalactosaminide alpha-2,6-sialyl	eukaryotic initiation factor 4A-IIATP-dependent RNA helicase eIF4A-2
	Modification date	20200329	20200322
	UniProtAcc	.	Q14240
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000169298, ENST00000448044, ENST00000457772, ENST00000487031,	ENST00000323963, ENST00000356531, ENST00000440191,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	10 X 7 X 8=560	13 X 14 X 6=1092
	# samples	13	16
	** MAII score	log2(13/560*10)=-2.10691520391651 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(16/1092*10)=-2.77082904603249 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: ST6GAL1 [Title/Abstract] AND EIF4A2 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	ST6GAL1(186769134)-EIF4A2(186505284), # samples:1
Anticipated loss of major functional domain due to fusion event.	ST6GAL1-EIF4A2 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. ST6GAL1-EIF4A2 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
Hgene	ST6GAL1	GO:0006054	N-acetylneuraminate metabolic process	23999306
Hgene	ST6GAL1	GO:0018279	protein N-linked glycosylation via asparagine	23999306
Hgene	ST6GAL1	GO:0097503	sialylation	23999306
Tgene	EIF4A2	GO:1900260	negative regulation of RNA-directed 5'-3' RNA polymerase activity	11922617

Fusion gene breakpoints across ST6GAL1 (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 EIF4A2 (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	OV	TCGA-25-1312-01A	ST6GAL1	chr3	186769134	+	EIF4A2	chr3	186505284	+

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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)
ENST00000169298	ST6GAL1	chr3	186769134	+	ENST00000323963	EIF4A2	chr3	186505284	+	2325	1379	626	1693	355
ENST00000169298	ST6GAL1	chr3	186769134	+	ENST00000440191	EIF4A2	chr3	186505284	+	2322	1379	626	1693	355
ENST00000169298	ST6GAL1	chr3	186769134	+	ENST00000356531	EIF4A2	chr3	186505284	+	2319	1379	626	1693	355
ENST00000457772	ST6GAL1	chr3	186769134	+	ENST00000323963	EIF4A2	chr3	186505284	+	1627	681	597	1	199
ENST00000457772	ST6GAL1	chr3	186769134	+	ENST00000440191	EIF4A2	chr3	186505284	+	1624	681	597	1	199
ENST00000457772	ST6GAL1	chr3	186769134	+	ENST00000356531	EIF4A2	chr3	186505284	+	1621	681	597	1	199
ENST00000448044	ST6GAL1	chr3	186769134	+	ENST00000323963	EIF4A2	chr3	186505284	+	1982	1036	283	1350	355
ENST00000448044	ST6GAL1	chr3	186769134	+	ENST00000440191	EIF4A2	chr3	186505284	+	1979	1036	283	1350	355
ENST00000448044	ST6GAL1	chr3	186769134	+	ENST00000356531	EIF4A2	chr3	186505284	+	1976	1036	283	1350	355

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
ENST00000169298	ENST00000323963	ST6GAL1	chr3	186769134	+	EIF4A2	chr3	186505284	+	0.000994172	0.99900585
ENST00000169298	ENST00000440191	ST6GAL1	chr3	186769134	+	EIF4A2	chr3	186505284	+	0.00099892	0.9990011
ENST00000169298	ENST00000356531	ST6GAL1	chr3	186769134	+	EIF4A2	chr3	186505284	+	0.001020095	0.99897987
ENST00000457772	ENST00000323963	ST6GAL1	chr3	186769134	+	EIF4A2	chr3	186505284	+	0.079855226	0.92014474
ENST00000457772	ENST00000440191	ST6GAL1	chr3	186769134	+	EIF4A2	chr3	186505284	+	0.07480372	0.92519635
ENST00000457772	ENST00000356531	ST6GAL1	chr3	186769134	+	EIF4A2	chr3	186505284	+	0.075481854	0.92451817
ENST00000448044	ENST00000323963	ST6GAL1	chr3	186769134	+	EIF4A2	chr3	186505284	+	0.00047615	0.9995239
ENST00000448044	ENST00000440191	ST6GAL1	chr3	186769134	+	EIF4A2	chr3	186505284	+	0.000481148	0.9995189
ENST00000448044	ENST00000356531	ST6GAL1	chr3	186769134	+	EIF4A2	chr3	186505284	+	0.000500227	0.9994998

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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

>86977_86977_1_ST6GAL1-EIF4A2_ST6GAL1_chr3_186769134_ENST00000169298_EIF4A2_chr3_186505284_ENST00000323963_length(amino acids)=355AA_BP=248
MFSCSEQSDFPEHIFIMIHTNLKKKFSCCVLVFLLFAVICVWKEKKKGSYYDSFKLQTKEFQVLKSLGKLAMGSDSQSVSSSSTQDPHRG
RQTLGSLRGLAKAKPEASFQVWNKDSSSKNLIPRLQKIWKNYLSMNKYKVSYKGPGPGIKFSAEALRCHLRDHVNVSMVEVTDFPFNTSE
WEGYLPKESIRTKAGPWGRCAVVSSAGSLKSSQLGREIDDHDAVLRFNGAPTANFQQDVGTKTTIRLMNSQHGDMDQKERDVIMREFRSG

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

>86977_86977_2_ST6GAL1-EIF4A2_ST6GAL1_chr3_186769134_ENST00000169298_EIF4A2_chr3_186505284_ENST00000356531_length(amino acids)=355AA_BP=248
MFSCSEQSDFPEHIFIMIHTNLKKKFSCCVLVFLLFAVICVWKEKKKGSYYDSFKLQTKEFQVLKSLGKLAMGSDSQSVSSSSTQDPHRG
RQTLGSLRGLAKAKPEASFQVWNKDSSSKNLIPRLQKIWKNYLSMNKYKVSYKGPGPGIKFSAEALRCHLRDHVNVSMVEVTDFPFNTSE
WEGYLPKESIRTKAGPWGRCAVVSSAGSLKSSQLGREIDDHDAVLRFNGAPTANFQQDVGTKTTIRLMNSQHGDMDQKERDVIMREFRSG

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

>86977_86977_3_ST6GAL1-EIF4A2_ST6GAL1_chr3_186769134_ENST00000169298_EIF4A2_chr3_186505284_ENST00000440191_length(amino acids)=355AA_BP=248
MFSCSEQSDFPEHIFIMIHTNLKKKFSCCVLVFLLFAVICVWKEKKKGSYYDSFKLQTKEFQVLKSLGKLAMGSDSQSVSSSSTQDPHRG
RQTLGSLRGLAKAKPEASFQVWNKDSSSKNLIPRLQKIWKNYLSMNKYKVSYKGPGPGIKFSAEALRCHLRDHVNVSMVEVTDFPFNTSE
WEGYLPKESIRTKAGPWGRCAVVSSAGSLKSSQLGREIDDHDAVLRFNGAPTANFQQDVGTKTTIRLMNSQHGDMDQKERDVIMREFRSG

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

>86977_86977_4_ST6GAL1-EIF4A2_ST6GAL1_chr3_186769134_ENST00000448044_EIF4A2_chr3_186505284_ENST00000323963_length(amino acids)=355AA_BP=248
MFSCSEQSDFPEHIFIMIHTNLKKKFSCCVLVFLLFAVICVWKEKKKGSYYDSFKLQTKEFQVLKSLGKLAMGSDSQSVSSSSTQDPHRG
RQTLGSLRGLAKAKPEASFQVWNKDSSSKNLIPRLQKIWKNYLSMNKYKVSYKGPGPGIKFSAEALRCHLRDHVNVSMVEVTDFPFNTSE
WEGYLPKESIRTKAGPWGRCAVVSSAGSLKSSQLGREIDDHDAVLRFNGAPTANFQQDVGTKTTIRLMNSQHGDMDQKERDVIMREFRSG

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

>86977_86977_5_ST6GAL1-EIF4A2_ST6GAL1_chr3_186769134_ENST00000448044_EIF4A2_chr3_186505284_ENST00000356531_length(amino acids)=355AA_BP=248
MFSCSEQSDFPEHIFIMIHTNLKKKFSCCVLVFLLFAVICVWKEKKKGSYYDSFKLQTKEFQVLKSLGKLAMGSDSQSVSSSSTQDPHRG
RQTLGSLRGLAKAKPEASFQVWNKDSSSKNLIPRLQKIWKNYLSMNKYKVSYKGPGPGIKFSAEALRCHLRDHVNVSMVEVTDFPFNTSE
WEGYLPKESIRTKAGPWGRCAVVSSAGSLKSSQLGREIDDHDAVLRFNGAPTANFQQDVGTKTTIRLMNSQHGDMDQKERDVIMREFRSG

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

>86977_86977_6_ST6GAL1-EIF4A2_ST6GAL1_chr3_186769134_ENST00000448044_EIF4A2_chr3_186505284_ENST00000440191_length(amino acids)=355AA_BP=248
MFSCSEQSDFPEHIFIMIHTNLKKKFSCCVLVFLLFAVICVWKEKKKGSYYDSFKLQTKEFQVLKSLGKLAMGSDSQSVSSSSTQDPHRG
RQTLGSLRGLAKAKPEASFQVWNKDSSSKNLIPRLQKIWKNYLSMNKYKVSYKGPGPGIKFSAEALRCHLRDHVNVSMVEVTDFPFNTSE
WEGYLPKESIRTKAGPWGRCAVVSSAGSLKSSQLGREIDDHDAVLRFNGAPTANFQQDVGTKTTIRLMNSQHGDMDQKERDVIMREFRSG

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

>86977_86977_7_ST6GAL1-EIF4A2_ST6GAL1_chr3_186769134_ENST00000457772_EIF4A2_chr3_186505284_ENST00000323963_length(amino acids)=199AA_BP=
MRHDHLLLANPPGAAGPSGPQELALLSMGGKVYWVCRPRPIFLRMIKTHLSTGMDTWHQGLGQAQGGQSISAGLHDIHHFSLDCWLQGSA
QLALPLLAALSAAEAAVAQHARWRPPAPRPRRSVSAPFVNAGQCPRRLPQPGPAQDSPPPGDSRKRARQGQDRPGAGDPTRESRKRGPLG

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

>86977_86977_8_ST6GAL1-EIF4A2_ST6GAL1_chr3_186769134_ENST00000457772_EIF4A2_chr3_186505284_ENST00000356531_length(amino acids)=199AA_BP=
MRHDHLLLANPPGAAGPSGPQELALLSMGGKVYWVCRPRPIFLRMIKTHLSTGMDTWHQGLGQAQGGQSISAGLHDIHHFSLDCWLQGSA
QLALPLLAALSAAEAAVAQHARWRPPAPRPRRSVSAPFVNAGQCPRRLPQPGPAQDSPPPGDSRKRARQGQDRPGAGDPTRESRKRGPLG

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

>86977_86977_9_ST6GAL1-EIF4A2_ST6GAL1_chr3_186769134_ENST00000457772_EIF4A2_chr3_186505284_ENST00000440191_length(amino acids)=199AA_BP=
MRHDHLLLANPPGAAGPSGPQELALLSMGGKVYWVCRPRPIFLRMIKTHLSTGMDTWHQGLGQAQGGQSISAGLHDIHHFSLDCWLQGSA
QLALPLLAALSAAEAAVAQHARWRPPAPRPRRSVSAPFVNAGQCPRRLPQPGPAQDSPPPGDSRKRARQGQDRPGAGDPTRESRKRGPLG

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

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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/chr3:186769134/chr3:186505284)
- 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
.	EIF4A2 Q14240
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: ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.

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

ST6GAL1

chr3:186769134

chr3:186505284

ENST00000169298

1_9

235.0

407.0

Topological domain

Note=Cytoplasmic

Hgene

ST6GAL1

chr3:186769134

chr3:186505284

ENST00000448044

1_9

235.0

407.0

Topological domain

Note=Cytoplasmic

Hgene

ST6GAL1

chr3:186769134

chr3:186505284

ENST00000169298

10_26

235.0

407.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Hgene

ST6GAL1

chr3:186769134

chr3:186505284

ENST00000448044

10_26

235.0

407.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

- 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

ST6GAL1

chr3:186769134

chr3:186505284

ENST00000169298

322_324

235.0

407.0

Region

Substrate binding

Hgene

ST6GAL1

chr3:186769134

chr3:186505284

ENST00000448044

322_324

235.0

407.0

Region

Substrate binding

Hgene

ST6GAL1

chr3:186769134

chr3:186505284

ENST00000169298

27_406

235.0

407.0

Topological domain

Lumenal

Hgene

ST6GAL1

chr3:186769134

chr3:186505284

ENST00000448044

27_406

235.0

407.0

Topological domain

Lumenal

Tgene

EIF4A2

chr3:186769134

chr3:186505284

ENST00000323963

246_407

303.0

408.0

Domain

Helicase C-terminal

Tgene

EIF4A2

chr3:186769134

chr3:186505284

ENST00000323963

64_235

303.0

408.0

Domain

Helicase ATP-binding

Tgene

EIF4A2

chr3:186769134

chr3:186505284

ENST00000440191

246_407

304.0

409.0

Domain

Helicase C-terminal

Tgene

EIF4A2

chr3:186769134

chr3:186505284

ENST00000440191

64_235

304.0

409.0

Domain

Helicase ATP-binding

Tgene

EIF4A2

chr3:186769134

chr3:186505284

ENST00000323963

183_186

303.0

408.0

Motif

Note=DEAD box

Tgene

EIF4A2

chr3:186769134

chr3:186505284

ENST00000323963

33_61

303.0

408.0

Motif

Note=Q motif

Tgene

EIF4A2

chr3:186769134

chr3:186505284

ENST00000440191

183_186

304.0

409.0

Motif

Note=DEAD box

Tgene

EIF4A2

chr3:186769134

chr3:186505284

ENST00000440191

33_61

304.0

409.0

Motif

Note=Q motif

Tgene

EIF4A2

chr3:186769134

chr3:186505284

ENST00000323963

77_84

303.0

408.0

Nucleotide binding

ATP

Tgene

EIF4A2

chr3:186769134

chr3:186505284

ENST00000440191

77_84

304.0

409.0

Nucleotide binding

ATP

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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

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
ST6GAL1
EIF4A2

- 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

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Related Drugs to ST6GAL1-EIF4A2

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

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to ST6GAL1-EIF4A2

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