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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:GTF3C4-LMX1B

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: GTF3C4-LMX1B
	FusionPDB ID: 35285
	FusionGDB2.0 ID: 35285
		Hgene	Tgene
	Gene symbol	GTF3C4	LMX1B
	Gene ID	9329	4010
	Gene name	general transcription factor IIIC subunit 4	LIM homeobox transcription factor 1 beta
	Synonyms	KAT12\|TF3C-delta\|TFIII90\|TFIIIC290\|TFIIIC90\|TFIIICDELTA	LMX1.2\|NPS1
	Cytomap	9q34.13	9q33.3
	Type of gene	protein-coding	protein-coding
	Description	general transcription factor 3C polypeptide 4TFIIIC 90 kDa subunitgeneral transcription factor 3C 4general transcription factor IIIC, polypeptide 4, 90kDatranscription factor IIIC 90 kDa subunittranscription factor IIIC subunit delta	LIM homeobox transcription factor 1-betaLIM/homeobox protein 1.2LMX-1.2
	Modification date	20200313	20200313
	UniProtAcc	Q9UKN8	O60663
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000372146, ENST00000483873,	ENST00000355497, ENST00000373474, ENST00000425646, ENST00000526117, ENST00000561065,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	3 X 3 X 2=18	8 X 7 X 5=280
	# samples	4	10
	** MAII score	log2(4/18*10)=1.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(10/280*10)=-1.48542682717024 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: GTF3C4 [Title/Abstract] AND LMX1B [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	GTF3C4(135559080)-LMX1B(129453115), # samples:2
Anticipated loss of major functional domain due to fusion event.	GTF3C4-LMX1B 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. GTF3C4-LMX1B 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. GTF3C4-LMX1B 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. GTF3C4-LMX1B 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	LMX1B	GO:0006355	regulation of transcription, DNA-templated	10767331

Fusion gene breakpoints across GTF3C4 (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 LMX1B (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	BRCA	TCGA-BH-A0BP-01A	GTF3C4	chr9	135559080	+	LMX1B	chr9	129453115	+
ChimerDB4	BRCA	TCGA-BH-A0BP	GTF3C4	chr9	135559080	+	LMX1B	chr9	129453114	+

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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)
ENST00000372146	GTF3C4	chr9	135559080	+	ENST00000526117	LMX1B	chr9	129453115	+	3741	2879	564	3740	1058
ENST00000372146	GTF3C4	chr9	135559080	+	ENST00000373474	LMX1B	chr9	129453115	+	3860	2879	564	3761	1065
ENST00000372146	GTF3C4	chr9	135559080	+	ENST00000425646	LMX1B	chr9	129453115	+	8322	2879	564	3740	1058
ENST00000372146	GTF3C4	chr9	135559080	+	ENST00000355497	LMX1B	chr9	129453115	+	8355	2879	564	3773	1069
ENST00000372146	GTF3C4	chr9	135559080	+	ENST00000561065	LMX1B	chr9	129453115	+	3872	2879	564	3773	1069
ENST00000372146	GTF3C4	chr9	135559080	+	ENST00000526117	LMX1B	chr9	129453114	+	3741	2879	564	3740	1058
ENST00000372146	GTF3C4	chr9	135559080	+	ENST00000373474	LMX1B	chr9	129453114	+	3860	2879	564	3761	1065
ENST00000372146	GTF3C4	chr9	135559080	+	ENST00000425646	LMX1B	chr9	129453114	+	8322	2879	564	3740	1058
ENST00000372146	GTF3C4	chr9	135559080	+	ENST00000355497	LMX1B	chr9	129453114	+	8355	2879	564	3773	1069
ENST00000372146	GTF3C4	chr9	135559080	+	ENST00000561065	LMX1B	chr9	129453114	+	3872	2879	564	3773	1069

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
ENST00000372146	ENST00000526117	GTF3C4	chr9	135559080	+	LMX1B	chr9	129453115	+	0.003913541	0.9960865
ENST00000372146	ENST00000373474	GTF3C4	chr9	135559080	+	LMX1B	chr9	129453115	+	0.003771861	0.9962282
ENST00000372146	ENST00000425646	GTF3C4	chr9	135559080	+	LMX1B	chr9	129453115	+	0.001400522	0.99859947
ENST00000372146	ENST00000355497	GTF3C4	chr9	135559080	+	LMX1B	chr9	129453115	+	0.001464037	0.998536
ENST00000372146	ENST00000561065	GTF3C4	chr9	135559080	+	LMX1B	chr9	129453115	+	0.004004489	0.9959955
ENST00000372146	ENST00000526117	GTF3C4	chr9	135559080	+	LMX1B	chr9	129453114	+	0.003913541	0.9960865
ENST00000372146	ENST00000373474	GTF3C4	chr9	135559080	+	LMX1B	chr9	129453114	+	0.003771861	0.9962282
ENST00000372146	ENST00000425646	GTF3C4	chr9	135559080	+	LMX1B	chr9	129453114	+	0.001400522	0.99859947
ENST00000372146	ENST00000355497	GTF3C4	chr9	135559080	+	LMX1B	chr9	129453114	+	0.001464037	0.998536
ENST00000372146	ENST00000561065	GTF3C4	chr9	135559080	+	LMX1B	chr9	129453114	+	0.004004489	0.9959955

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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

>35285_35285_1_GTF3C4-LMX1B_GTF3C4_chr9_135559080_ENST00000372146_LMX1B_chr9_129453114_ENST00000355497_length(amino acids)=1069AA_BP=771
MNTADQARVGPADDGPAPSGEEEGEGGGEAGGKEPAADAAPGPSAAFRLMVTRREPAVKLQYAVSGLEPLAWSEDHRVSVSTARSIAVLE
LICDVHNPGQDLVIHRTSVPAPLNSCLLKVGSKTEVAECKEKFAASKDPTVSQTFMLDRVFNPEGKALPPMRGFKYTSWSPMGCDANGRC
LLAALTMDNRLTIQANLNRLQWVQLVDLTEIYGERLYETSYRLSKNEAPEGNLGDFAEFQRRHSMQTPVRMEWSGICTTQQVKHNNECRD
VGSVLLAVLFENGNIAVWQFQLPFVGKESISSCNTIESGITSPSVLFWWEYEHNNRKMSGLIVGSAFGPIKILPVNLKAVKGYFTLRQPV
ILWKEMDQLPVHSIKCVPLYHPYQKCSCSLVVAARGSYVFWCLLLISKAGLNVHNSHVTGLHSLPIVSMTADKQNGTVYTCSSDGKVRQL
IPIFTDVALKFEHQLIKLSDVFGSVRTHGIAVSPCGAYLAIITTEGMINGLHPVNKNYQVQFVTLKTFEEAAAQLLESSVQNLFKQVDLI
DLVRWKILKDKHIPQFLQEALEKKIESSGVTYFWRFKLFLLRILYQSMQKTPSEALWKPTHEDSKILLVDSPGMGNADDEQQEEGTSSKQ
VVKQGLQERSKEGDVEEPTDDSLPTTGDAGGREPMEEKLLEIQGKIEAVEMHLTREHMKRVLGEVYLHTWITENTSIPTRGLCNFLMSDE
EYDDRTARVLIGHISKKMNKQTFPEHCSLCKEILPFTDRKQAVCSNGHIWLRLFAAKCSGCMEKIAPTEFVMRALECVYHLGCFCCCVCE
RQLRKGDEFVLKEGQLLCKGDYEKEKDLLSSVSPDESDSVKSEDEDGDMKPAKGQGSQSKGSGDDGKDPRRPKRPRTILTTQQRRAFKAS
FEVSSKPCRKVRETLAAETGLSVRVVQVWFQNQRAKMKKLARRHQQQQEQQNSQRLGQGEPGPGQGLGQEVLSSRMEGMMASYTPLAPPQ

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

>35285_35285_2_GTF3C4-LMX1B_GTF3C4_chr9_135559080_ENST00000372146_LMX1B_chr9_129453114_ENST00000373474_length(amino acids)=1065AA_BP=771
MNTADQARVGPADDGPAPSGEEEGEGGGEAGGKEPAADAAPGPSAAFRLMVTRREPAVKLQYAVSGLEPLAWSEDHRVSVSTARSIAVLE
LICDVHNPGQDLVIHRTSVPAPLNSCLLKVGSKTEVAECKEKFAASKDPTVSQTFMLDRVFNPEGKALPPMRGFKYTSWSPMGCDANGRC
LLAALTMDNRLTIQANLNRLQWVQLVDLTEIYGERLYETSYRLSKNEAPEGNLGDFAEFQRRHSMQTPVRMEWSGICTTQQVKHNNECRD
VGSVLLAVLFENGNIAVWQFQLPFVGKESISSCNTIESGITSPSVLFWWEYEHNNRKMSGLIVGSAFGPIKILPVNLKAVKGYFTLRQPV
ILWKEMDQLPVHSIKCVPLYHPYQKCSCSLVVAARGSYVFWCLLLISKAGLNVHNSHVTGLHSLPIVSMTADKQNGTVYTCSSDGKVRQL
IPIFTDVALKFEHQLIKLSDVFGSVRTHGIAVSPCGAYLAIITTEGMINGLHPVNKNYQVQFVTLKTFEEAAAQLLESSVQNLFKQVDLI
DLVRWKILKDKHIPQFLQEALEKKIESSGVTYFWRFKLFLLRILYQSMQKTPSEALWKPTHEDSKILLVDSPGMGNADDEQQEEGTSSKQ
VVKQGLQERSKEGDVEEPTDDSLPTTGDAGGREPMEEKLLEIQGKIEAVEMHLTREHMKRVLGEVYLHTWITENTSIPTRGLCNFLMSDE
EYDDRTARVLIGHISKKMNKQTFPEHCSLCKEILPFTDRKQAVCSNGHIWLRLFAAKCSGCMEKIAPTEFVMRALECVYHLGCFCCCVCE
RQLRKGDEFVLKEGQLLCKGDYEKEKDLLSSVSPDESDSVKSEDEDGDMKPAKGQGSQSKGSGDDGKDPRRPKRPRTILTTQQRRAFKAS
FEVSSKPCRKVRETLAAETGLSVRVVQVWFQNQRAKMKKLARRHQQQQEQQNSQRLGQEVLSSRMEGMMASYTPLAPPQQQIVAMEQSPY

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

>35285_35285_3_GTF3C4-LMX1B_GTF3C4_chr9_135559080_ENST00000372146_LMX1B_chr9_129453114_ENST00000425646_length(amino acids)=1058AA_BP=771
MNTADQARVGPADDGPAPSGEEEGEGGGEAGGKEPAADAAPGPSAAFRLMVTRREPAVKLQYAVSGLEPLAWSEDHRVSVSTARSIAVLE
LICDVHNPGQDLVIHRTSVPAPLNSCLLKVGSKTEVAECKEKFAASKDPTVSQTFMLDRVFNPEGKALPPMRGFKYTSWSPMGCDANGRC
LLAALTMDNRLTIQANLNRLQWVQLVDLTEIYGERLYETSYRLSKNEAPEGNLGDFAEFQRRHSMQTPVRMEWSGICTTQQVKHNNECRD
VGSVLLAVLFENGNIAVWQFQLPFVGKESISSCNTIESGITSPSVLFWWEYEHNNRKMSGLIVGSAFGPIKILPVNLKAVKGYFTLRQPV
ILWKEMDQLPVHSIKCVPLYHPYQKCSCSLVVAARGSYVFWCLLLISKAGLNVHNSHVTGLHSLPIVSMTADKQNGTVYTCSSDGKVRQL
IPIFTDVALKFEHQLIKLSDVFGSVRTHGIAVSPCGAYLAIITTEGMINGLHPVNKNYQVQFVTLKTFEEAAAQLLESSVQNLFKQVDLI
DLVRWKILKDKHIPQFLQEALEKKIESSGVTYFWRFKLFLLRILYQSMQKTPSEALWKPTHEDSKILLVDSPGMGNADDEQQEEGTSSKQ
VVKQGLQERSKEGDVEEPTDDSLPTTGDAGGREPMEEKLLEIQGKIEAVEMHLTREHMKRVLGEVYLHTWITENTSIPTRGLCNFLMSDE
EYDDRTARVLIGHISKKMNKQTFPEHCSLCKEILPFTDRKQAVCSNGHIWLRLFAAKCSGCMEKIAPTEFVMRALECVYHLGCFCCCVCE
RQLRKGDEFVLKEGQLLCKGDYEKEKDLLSSVSPDESDSVKSEDEDGDMKPAKGQGSQSKGSGDDGKDPRRPKRPRTILTTQQRRAFKAS
FEVSSKPCRKVRETLAAETGLSVRVVQVWFQNQRAKMKKLARRHQQQQEQQNSQRLGQEVLSSRMEGMMASYTPLAPPQQQIVAMEQSPY

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

>35285_35285_4_GTF3C4-LMX1B_GTF3C4_chr9_135559080_ENST00000372146_LMX1B_chr9_129453114_ENST00000526117_length(amino acids)=1058AA_BP=771
MNTADQARVGPADDGPAPSGEEEGEGGGEAGGKEPAADAAPGPSAAFRLMVTRREPAVKLQYAVSGLEPLAWSEDHRVSVSTARSIAVLE
LICDVHNPGQDLVIHRTSVPAPLNSCLLKVGSKTEVAECKEKFAASKDPTVSQTFMLDRVFNPEGKALPPMRGFKYTSWSPMGCDANGRC
LLAALTMDNRLTIQANLNRLQWVQLVDLTEIYGERLYETSYRLSKNEAPEGNLGDFAEFQRRHSMQTPVRMEWSGICTTQQVKHNNECRD
VGSVLLAVLFENGNIAVWQFQLPFVGKESISSCNTIESGITSPSVLFWWEYEHNNRKMSGLIVGSAFGPIKILPVNLKAVKGYFTLRQPV
ILWKEMDQLPVHSIKCVPLYHPYQKCSCSLVVAARGSYVFWCLLLISKAGLNVHNSHVTGLHSLPIVSMTADKQNGTVYTCSSDGKVRQL
IPIFTDVALKFEHQLIKLSDVFGSVRTHGIAVSPCGAYLAIITTEGMINGLHPVNKNYQVQFVTLKTFEEAAAQLLESSVQNLFKQVDLI
DLVRWKILKDKHIPQFLQEALEKKIESSGVTYFWRFKLFLLRILYQSMQKTPSEALWKPTHEDSKILLVDSPGMGNADDEQQEEGTSSKQ
VVKQGLQERSKEGDVEEPTDDSLPTTGDAGGREPMEEKLLEIQGKIEAVEMHLTREHMKRVLGEVYLHTWITENTSIPTRGLCNFLMSDE
EYDDRTARVLIGHISKKMNKQTFPEHCSLCKEILPFTDRKQAVCSNGHIWLRLFAAKCSGCMEKIAPTEFVMRALECVYHLGCFCCCVCE
RQLRKGDEFVLKEGQLLCKGDYEKEKDLLSSVSPDESDSVKSEDEDGDMKPAKGQGSQSKGSGDDGKDPRRPKRPRTILTTQQRRAFKAS
FEVSSKPCRKVRETLAAETGLSVRVVQVWFQNQRAKMKKLARRHQQQQEQQNSQRLGQEVLSSRMEGMMASYTPLAPPQQQIVAMEQSPY

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

>35285_35285_5_GTF3C4-LMX1B_GTF3C4_chr9_135559080_ENST00000372146_LMX1B_chr9_129453114_ENST00000561065_length(amino acids)=1069AA_BP=771
MNTADQARVGPADDGPAPSGEEEGEGGGEAGGKEPAADAAPGPSAAFRLMVTRREPAVKLQYAVSGLEPLAWSEDHRVSVSTARSIAVLE
LICDVHNPGQDLVIHRTSVPAPLNSCLLKVGSKTEVAECKEKFAASKDPTVSQTFMLDRVFNPEGKALPPMRGFKYTSWSPMGCDANGRC
LLAALTMDNRLTIQANLNRLQWVQLVDLTEIYGERLYETSYRLSKNEAPEGNLGDFAEFQRRHSMQTPVRMEWSGICTTQQVKHNNECRD
VGSVLLAVLFENGNIAVWQFQLPFVGKESISSCNTIESGITSPSVLFWWEYEHNNRKMSGLIVGSAFGPIKILPVNLKAVKGYFTLRQPV
ILWKEMDQLPVHSIKCVPLYHPYQKCSCSLVVAARGSYVFWCLLLISKAGLNVHNSHVTGLHSLPIVSMTADKQNGTVYTCSSDGKVRQL
IPIFTDVALKFEHQLIKLSDVFGSVRTHGIAVSPCGAYLAIITTEGMINGLHPVNKNYQVQFVTLKTFEEAAAQLLESSVQNLFKQVDLI
DLVRWKILKDKHIPQFLQEALEKKIESSGVTYFWRFKLFLLRILYQSMQKTPSEALWKPTHEDSKILLVDSPGMGNADDEQQEEGTSSKQ
VVKQGLQERSKEGDVEEPTDDSLPTTGDAGGREPMEEKLLEIQGKIEAVEMHLTREHMKRVLGEVYLHTWITENTSIPTRGLCNFLMSDE
EYDDRTARVLIGHISKKMNKQTFPEHCSLCKEILPFTDRKQAVCSNGHIWLRLFAAKCSGCMEKIAPTEFVMRALECVYHLGCFCCCVCE
RQLRKGDEFVLKEGQLLCKGDYEKEKDLLSSVSPDESDSVKSEDEDGDMKPAKGQGSQSKGSGDDGKDPRRPKRPRTILTTQQRRAFKAS
FEVSSKPCRKVRETLAAETGLSVRVVQVWFQNQRAKMKKLARRHQQQQEQQNSQRLGQGEPGPGQGLGQEVLSSRMEGMMASYTPLAPPQ

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

>35285_35285_6_GTF3C4-LMX1B_GTF3C4_chr9_135559080_ENST00000372146_LMX1B_chr9_129453115_ENST00000355497_length(amino acids)=1069AA_BP=771
MNTADQARVGPADDGPAPSGEEEGEGGGEAGGKEPAADAAPGPSAAFRLMVTRREPAVKLQYAVSGLEPLAWSEDHRVSVSTARSIAVLE
LICDVHNPGQDLVIHRTSVPAPLNSCLLKVGSKTEVAECKEKFAASKDPTVSQTFMLDRVFNPEGKALPPMRGFKYTSWSPMGCDANGRC
LLAALTMDNRLTIQANLNRLQWVQLVDLTEIYGERLYETSYRLSKNEAPEGNLGDFAEFQRRHSMQTPVRMEWSGICTTQQVKHNNECRD
VGSVLLAVLFENGNIAVWQFQLPFVGKESISSCNTIESGITSPSVLFWWEYEHNNRKMSGLIVGSAFGPIKILPVNLKAVKGYFTLRQPV
ILWKEMDQLPVHSIKCVPLYHPYQKCSCSLVVAARGSYVFWCLLLISKAGLNVHNSHVTGLHSLPIVSMTADKQNGTVYTCSSDGKVRQL
IPIFTDVALKFEHQLIKLSDVFGSVRTHGIAVSPCGAYLAIITTEGMINGLHPVNKNYQVQFVTLKTFEEAAAQLLESSVQNLFKQVDLI
DLVRWKILKDKHIPQFLQEALEKKIESSGVTYFWRFKLFLLRILYQSMQKTPSEALWKPTHEDSKILLVDSPGMGNADDEQQEEGTSSKQ
VVKQGLQERSKEGDVEEPTDDSLPTTGDAGGREPMEEKLLEIQGKIEAVEMHLTREHMKRVLGEVYLHTWITENTSIPTRGLCNFLMSDE
EYDDRTARVLIGHISKKMNKQTFPEHCSLCKEILPFTDRKQAVCSNGHIWLRLFAAKCSGCMEKIAPTEFVMRALECVYHLGCFCCCVCE
RQLRKGDEFVLKEGQLLCKGDYEKEKDLLSSVSPDESDSVKSEDEDGDMKPAKGQGSQSKGSGDDGKDPRRPKRPRTILTTQQRRAFKAS
FEVSSKPCRKVRETLAAETGLSVRVVQVWFQNQRAKMKKLARRHQQQQEQQNSQRLGQGEPGPGQGLGQEVLSSRMEGMMASYTPLAPPQ

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

>35285_35285_7_GTF3C4-LMX1B_GTF3C4_chr9_135559080_ENST00000372146_LMX1B_chr9_129453115_ENST00000373474_length(amino acids)=1065AA_BP=771
MNTADQARVGPADDGPAPSGEEEGEGGGEAGGKEPAADAAPGPSAAFRLMVTRREPAVKLQYAVSGLEPLAWSEDHRVSVSTARSIAVLE
LICDVHNPGQDLVIHRTSVPAPLNSCLLKVGSKTEVAECKEKFAASKDPTVSQTFMLDRVFNPEGKALPPMRGFKYTSWSPMGCDANGRC
LLAALTMDNRLTIQANLNRLQWVQLVDLTEIYGERLYETSYRLSKNEAPEGNLGDFAEFQRRHSMQTPVRMEWSGICTTQQVKHNNECRD
VGSVLLAVLFENGNIAVWQFQLPFVGKESISSCNTIESGITSPSVLFWWEYEHNNRKMSGLIVGSAFGPIKILPVNLKAVKGYFTLRQPV
ILWKEMDQLPVHSIKCVPLYHPYQKCSCSLVVAARGSYVFWCLLLISKAGLNVHNSHVTGLHSLPIVSMTADKQNGTVYTCSSDGKVRQL
IPIFTDVALKFEHQLIKLSDVFGSVRTHGIAVSPCGAYLAIITTEGMINGLHPVNKNYQVQFVTLKTFEEAAAQLLESSVQNLFKQVDLI
DLVRWKILKDKHIPQFLQEALEKKIESSGVTYFWRFKLFLLRILYQSMQKTPSEALWKPTHEDSKILLVDSPGMGNADDEQQEEGTSSKQ
VVKQGLQERSKEGDVEEPTDDSLPTTGDAGGREPMEEKLLEIQGKIEAVEMHLTREHMKRVLGEVYLHTWITENTSIPTRGLCNFLMSDE
EYDDRTARVLIGHISKKMNKQTFPEHCSLCKEILPFTDRKQAVCSNGHIWLRLFAAKCSGCMEKIAPTEFVMRALECVYHLGCFCCCVCE
RQLRKGDEFVLKEGQLLCKGDYEKEKDLLSSVSPDESDSVKSEDEDGDMKPAKGQGSQSKGSGDDGKDPRRPKRPRTILTTQQRRAFKAS
FEVSSKPCRKVRETLAAETGLSVRVVQVWFQNQRAKMKKLARRHQQQQEQQNSQRLGQEVLSSRMEGMMASYTPLAPPQQQIVAMEQSPY

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

>35285_35285_8_GTF3C4-LMX1B_GTF3C4_chr9_135559080_ENST00000372146_LMX1B_chr9_129453115_ENST00000425646_length(amino acids)=1058AA_BP=771
MNTADQARVGPADDGPAPSGEEEGEGGGEAGGKEPAADAAPGPSAAFRLMVTRREPAVKLQYAVSGLEPLAWSEDHRVSVSTARSIAVLE
LICDVHNPGQDLVIHRTSVPAPLNSCLLKVGSKTEVAECKEKFAASKDPTVSQTFMLDRVFNPEGKALPPMRGFKYTSWSPMGCDANGRC
LLAALTMDNRLTIQANLNRLQWVQLVDLTEIYGERLYETSYRLSKNEAPEGNLGDFAEFQRRHSMQTPVRMEWSGICTTQQVKHNNECRD
VGSVLLAVLFENGNIAVWQFQLPFVGKESISSCNTIESGITSPSVLFWWEYEHNNRKMSGLIVGSAFGPIKILPVNLKAVKGYFTLRQPV
ILWKEMDQLPVHSIKCVPLYHPYQKCSCSLVVAARGSYVFWCLLLISKAGLNVHNSHVTGLHSLPIVSMTADKQNGTVYTCSSDGKVRQL
IPIFTDVALKFEHQLIKLSDVFGSVRTHGIAVSPCGAYLAIITTEGMINGLHPVNKNYQVQFVTLKTFEEAAAQLLESSVQNLFKQVDLI
DLVRWKILKDKHIPQFLQEALEKKIESSGVTYFWRFKLFLLRILYQSMQKTPSEALWKPTHEDSKILLVDSPGMGNADDEQQEEGTSSKQ
VVKQGLQERSKEGDVEEPTDDSLPTTGDAGGREPMEEKLLEIQGKIEAVEMHLTREHMKRVLGEVYLHTWITENTSIPTRGLCNFLMSDE
EYDDRTARVLIGHISKKMNKQTFPEHCSLCKEILPFTDRKQAVCSNGHIWLRLFAAKCSGCMEKIAPTEFVMRALECVYHLGCFCCCVCE
RQLRKGDEFVLKEGQLLCKGDYEKEKDLLSSVSPDESDSVKSEDEDGDMKPAKGQGSQSKGSGDDGKDPRRPKRPRTILTTQQRRAFKAS
FEVSSKPCRKVRETLAAETGLSVRVVQVWFQNQRAKMKKLARRHQQQQEQQNSQRLGQEVLSSRMEGMMASYTPLAPPQQQIVAMEQSPY

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

>35285_35285_9_GTF3C4-LMX1B_GTF3C4_chr9_135559080_ENST00000372146_LMX1B_chr9_129453115_ENST00000526117_length(amino acids)=1058AA_BP=771
MNTADQARVGPADDGPAPSGEEEGEGGGEAGGKEPAADAAPGPSAAFRLMVTRREPAVKLQYAVSGLEPLAWSEDHRVSVSTARSIAVLE
LICDVHNPGQDLVIHRTSVPAPLNSCLLKVGSKTEVAECKEKFAASKDPTVSQTFMLDRVFNPEGKALPPMRGFKYTSWSPMGCDANGRC
LLAALTMDNRLTIQANLNRLQWVQLVDLTEIYGERLYETSYRLSKNEAPEGNLGDFAEFQRRHSMQTPVRMEWSGICTTQQVKHNNECRD
VGSVLLAVLFENGNIAVWQFQLPFVGKESISSCNTIESGITSPSVLFWWEYEHNNRKMSGLIVGSAFGPIKILPVNLKAVKGYFTLRQPV
ILWKEMDQLPVHSIKCVPLYHPYQKCSCSLVVAARGSYVFWCLLLISKAGLNVHNSHVTGLHSLPIVSMTADKQNGTVYTCSSDGKVRQL
IPIFTDVALKFEHQLIKLSDVFGSVRTHGIAVSPCGAYLAIITTEGMINGLHPVNKNYQVQFVTLKTFEEAAAQLLESSVQNLFKQVDLI
DLVRWKILKDKHIPQFLQEALEKKIESSGVTYFWRFKLFLLRILYQSMQKTPSEALWKPTHEDSKILLVDSPGMGNADDEQQEEGTSSKQ
VVKQGLQERSKEGDVEEPTDDSLPTTGDAGGREPMEEKLLEIQGKIEAVEMHLTREHMKRVLGEVYLHTWITENTSIPTRGLCNFLMSDE
EYDDRTARVLIGHISKKMNKQTFPEHCSLCKEILPFTDRKQAVCSNGHIWLRLFAAKCSGCMEKIAPTEFVMRALECVYHLGCFCCCVCE
RQLRKGDEFVLKEGQLLCKGDYEKEKDLLSSVSPDESDSVKSEDEDGDMKPAKGQGSQSKGSGDDGKDPRRPKRPRTILTTQQRRAFKAS
FEVSSKPCRKVRETLAAETGLSVRVVQVWFQNQRAKMKKLARRHQQQQEQQNSQRLGQEVLSSRMEGMMASYTPLAPPQQQIVAMEQSPY

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

>35285_35285_10_GTF3C4-LMX1B_GTF3C4_chr9_135559080_ENST00000372146_LMX1B_chr9_129453115_ENST00000561065_length(amino acids)=1069AA_BP=771
MNTADQARVGPADDGPAPSGEEEGEGGGEAGGKEPAADAAPGPSAAFRLMVTRREPAVKLQYAVSGLEPLAWSEDHRVSVSTARSIAVLE
LICDVHNPGQDLVIHRTSVPAPLNSCLLKVGSKTEVAECKEKFAASKDPTVSQTFMLDRVFNPEGKALPPMRGFKYTSWSPMGCDANGRC
LLAALTMDNRLTIQANLNRLQWVQLVDLTEIYGERLYETSYRLSKNEAPEGNLGDFAEFQRRHSMQTPVRMEWSGICTTQQVKHNNECRD
VGSVLLAVLFENGNIAVWQFQLPFVGKESISSCNTIESGITSPSVLFWWEYEHNNRKMSGLIVGSAFGPIKILPVNLKAVKGYFTLRQPV
ILWKEMDQLPVHSIKCVPLYHPYQKCSCSLVVAARGSYVFWCLLLISKAGLNVHNSHVTGLHSLPIVSMTADKQNGTVYTCSSDGKVRQL
IPIFTDVALKFEHQLIKLSDVFGSVRTHGIAVSPCGAYLAIITTEGMINGLHPVNKNYQVQFVTLKTFEEAAAQLLESSVQNLFKQVDLI
DLVRWKILKDKHIPQFLQEALEKKIESSGVTYFWRFKLFLLRILYQSMQKTPSEALWKPTHEDSKILLVDSPGMGNADDEQQEEGTSSKQ
VVKQGLQERSKEGDVEEPTDDSLPTTGDAGGREPMEEKLLEIQGKIEAVEMHLTREHMKRVLGEVYLHTWITENTSIPTRGLCNFLMSDE
EYDDRTARVLIGHISKKMNKQTFPEHCSLCKEILPFTDRKQAVCSNGHIWLRLFAAKCSGCMEKIAPTEFVMRALECVYHLGCFCCCVCE
RQLRKGDEFVLKEGQLLCKGDYEKEKDLLSSVSPDESDSVKSEDEDGDMKPAKGQGSQSKGSGDDGKDPRRPKRPRTILTTQQRRAFKAS
FEVSSKPCRKVRETLAAETGLSVRVVQVWFQNQRAKMKKLARRHQQQQEQQNSQRLGQGEPGPGQGLGQEVLSSRMEGMMASYTPLAPPQ

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

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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/chr9:135559080/chr9:129453115)
- 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
GTF3C4 Q9UKN8	LMX1B O60663
FUNCTION: Essential for RNA polymerase III to make a number of small nuclear and cytoplasmic RNAs, including 5S RNA, tRNA, and adenovirus-associated (VA) RNA of both cellular and viral origin. Has histone acetyltransferase activity (HAT) with unique specificity for free and nucleosomal H3. May cooperate with GTF3C5 in facilitating the recruitment of TFIIIB and RNA polymerase through direct interactions with BRF1, POLR3C and POLR3F. May be localized close to the A box.	FUNCTION: Essential for the specification of dorsal limb fate at both the zeugopodal and autopodal levels.

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

Tgene

LMX1B

chr9:135559080

chr9:129453114

ENST00000355497

282_288

108.66666666666667

407.0

Compositional bias

Note=Poly-Gln

Tgene

LMX1B

chr9:135559080

chr9:129453114

ENST00000373474

282_288

108.66666666666667

403.0

Compositional bias

Note=Poly-Gln

Tgene

LMX1B

chr9:135559080

chr9:129453114

ENST00000425646

282_288

85.66666666666667

373.0

Compositional bias

Note=Poly-Gln

Tgene

LMX1B

chr9:135559080

chr9:129453114

ENST00000526117

282_288

108.66666666666667

396.0

Compositional bias

Note=Poly-Gln

Tgene

LMX1B

chr9:135559080

chr9:129453115

ENST00000355497

282_288

108.66666666666667

407.0

Compositional bias

Note=Poly-Gln

Tgene

LMX1B

chr9:135559080

chr9:129453115

ENST00000373474

282_288

108.66666666666667

403.0

Compositional bias

Note=Poly-Gln

Tgene

LMX1B

chr9:135559080

chr9:129453115

ENST00000425646

282_288

85.66666666666667

373.0

Compositional bias

Note=Poly-Gln

Tgene

LMX1B

chr9:135559080

chr9:129453115

ENST00000526117

282_288

108.66666666666667

396.0

Compositional bias

Note=Poly-Gln

Tgene

LMX1B

chr9:135559080

chr9:129453114

ENST00000355497

219_278

108.66666666666667

407.0

DNA binding

Homeobox

Tgene

LMX1B

chr9:135559080

chr9:129453114

ENST00000373474

219_278

108.66666666666667

403.0

DNA binding

Homeobox

Tgene

LMX1B

chr9:135559080

chr9:129453114

ENST00000425646

219_278

85.66666666666667

373.0

DNA binding

Homeobox

Tgene

LMX1B

chr9:135559080

chr9:129453114

ENST00000526117

219_278

108.66666666666667

396.0

DNA binding

Homeobox

Tgene

LMX1B

chr9:135559080

chr9:129453115

ENST00000355497

219_278

108.66666666666667

407.0

DNA binding

Homeobox

Tgene

LMX1B

chr9:135559080

chr9:129453115

ENST00000373474

219_278

108.66666666666667

403.0

DNA binding

Homeobox

Tgene

LMX1B

chr9:135559080

chr9:129453115

ENST00000425646

219_278

85.66666666666667

373.0

DNA binding

Homeobox

Tgene

LMX1B

chr9:135559080

chr9:129453115

ENST00000526117

219_278

108.66666666666667

396.0

DNA binding

Homeobox

Tgene

LMX1B

chr9:135559080

chr9:129453114

ENST00000355497

115_168

108.66666666666667

407.0

Domain

LIM zinc-binding 2

Tgene

LMX1B

chr9:135559080

chr9:129453114

ENST00000373474

115_168

108.66666666666667

403.0

Domain

LIM zinc-binding 2

Tgene

LMX1B

chr9:135559080

chr9:129453114

ENST00000425646

115_168

85.66666666666667

373.0

Domain

LIM zinc-binding 2

Tgene

LMX1B

chr9:135559080

chr9:129453114

ENST00000526117

115_168

108.66666666666667

396.0

Domain

LIM zinc-binding 2

Tgene

LMX1B

chr9:135559080

chr9:129453115

ENST00000355497

115_168

108.66666666666667

407.0

Domain

LIM zinc-binding 2

Tgene

LMX1B

chr9:135559080

chr9:129453115

ENST00000373474

115_168

108.66666666666667

403.0

Domain

LIM zinc-binding 2

Tgene

LMX1B

chr9:135559080

chr9:129453115

ENST00000425646

115_168

85.66666666666667

373.0

Domain

LIM zinc-binding 2

Tgene

LMX1B

chr9:135559080

chr9:129453115

ENST00000526117

115_168

108.66666666666667

396.0

Domain

LIM zinc-binding 2

- 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

Tgene

LMX1B

chr9:135559080

chr9:129453114

ENST00000355497

56_106

108.66666666666667

407.0

Domain

LIM zinc-binding 1

Tgene

LMX1B

chr9:135559080

chr9:129453114

ENST00000373474

56_106

108.66666666666667

403.0

Domain

LIM zinc-binding 1

Tgene

LMX1B

chr9:135559080

chr9:129453114

ENST00000425646

56_106

85.66666666666667

373.0

Domain

LIM zinc-binding 1

Tgene

LMX1B

chr9:135559080

chr9:129453114

ENST00000526117

56_106

108.66666666666667

396.0

Domain

LIM zinc-binding 1

Tgene

LMX1B

chr9:135559080

chr9:129453115

ENST00000355497

56_106

108.66666666666667

407.0

Domain

LIM zinc-binding 1

Tgene

LMX1B

chr9:135559080

chr9:129453115

ENST00000373474

56_106

108.66666666666667

403.0

Domain

LIM zinc-binding 1

Tgene

LMX1B

chr9:135559080

chr9:129453115

ENST00000425646

56_106

85.66666666666667

373.0

Domain

LIM zinc-binding 1

Tgene

LMX1B

chr9:135559080

chr9:129453115

ENST00000526117

56_106

108.66666666666667

396.0

Domain

LIM zinc-binding 1

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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
GTF3C4
LMX1B

- 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 GTF3C4-LMX1B

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 GTF3C4-LMX1B

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