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level2

	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein Structure
	pLDDT scores
	Ramachandran Plot of Fusion Protein Structure
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:KDM3A-CRIM1

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: KDM3A-CRIM1
	FusionPDB ID: 41759
	FusionGDB2.0 ID: 41759
		Hgene	Tgene
	Gene symbol	KDM3A	CRIM1
	Gene ID	55818	51232
	Gene name	lysine demethylase 3A	cysteine rich transmembrane BMP regulator 1
	Synonyms	JHDM2A\|JHMD2A\|JMJD1\|JMJD1A\|TSGA	CRIM-1\|S52
	Cytomap	2p11.2	2p22.2
	Type of gene	protein-coding	protein-coding
	Description	lysine-specific demethylase 3AjmjC domain-containing histone demethylation protein 2Ajumonji C domain-containing histone demethylase 2Ajumonji domain-containing protein 1Alysine (K)-specific demethylase 3Atestis-specific protein A	cysteine-rich motor neuron 1 proteincysteine rich transmembrane BMP regulator 1 (chordin-like)cysteine-rich repeat-containing protein S52
	Modification date	20200313	20200313
	UniProtAcc	Q9Y4C1	Q9NZV1
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000312912, ENST00000409064, ENST00000409556, ENST00000542128, ENST00000485171,	ENST00000473403, ENST00000280527,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	13 X 12 X 7=1092	8 X 10 X 4=320
	# samples	15	10
	** MAII score	log2(15/1092*10)=-2.86393845042397 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(10/320*10)=-1.67807190511264 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: KDM3A [Title/Abstract] AND CRIM1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	KDM3A(86691339)-CRIM1(36691677), # samples:3
Anticipated loss of major functional domain due to fusion event.	KDM3A-CRIM1 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. KDM3A-CRIM1 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. KDM3A-CRIM1 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. KDM3A-CRIM1 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	KDM3A	GO:0009755	hormone-mediated signaling pathway	16603237
Hgene	KDM3A	GO:0030521	androgen receptor signaling pathway	16603237
Hgene	KDM3A	GO:0033169	histone H3-K9 demethylation	16603237
Hgene	KDM3A	GO:0046293	formaldehyde biosynthetic process	16603237

Fusion gene breakpoints across KDM3A (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 CRIM1 (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	KIRP	TCGA-G7-6792-01A	KDM3A	chr2	86691339	-	CRIM1	chr2	36691677	+
ChimerDB4	KIRP	TCGA-G7-6792-01A	KDM3A	chr2	86691339	+	CRIM1	chr2	36691677	+
ChimerDB4	KIRP	TCGA-G7-6792	KDM3A	chr2	86691339	+	CRIM1	chr2	36691676	+
ChimerDB4	KIRP	TCGA-G7-6792	KDM3A	chr2	86691339	+	CRIM1	chr2	36691677	+

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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)
ENST00000409556	KDM3A	chr2	86691339	+	ENST00000280527	CRIM1	chr2	36691677	+	6048	1372	365	3613	1082
ENST00000312912	KDM3A	chr2	86691339	+	ENST00000280527	CRIM1	chr2	36691677	+	6010	1334	327	3575	1082
ENST00000409064	KDM3A	chr2	86691339	+	ENST00000280527	CRIM1	chr2	36691677	+	5741	1065	58	3306	1082
ENST00000542128	KDM3A	chr2	86691339	+	ENST00000280527	CRIM1	chr2	36691677	+	5527	851	0	3092	1030
ENST00000409556	KDM3A	chr2	86691339	+	ENST00000280527	CRIM1	chr2	36691676	+	6048	1372	365	3613	1082
ENST00000312912	KDM3A	chr2	86691339	+	ENST00000280527	CRIM1	chr2	36691676	+	6010	1334	327	3575	1082
ENST00000409064	KDM3A	chr2	86691339	+	ENST00000280527	CRIM1	chr2	36691676	+	5741	1065	58	3306	1082
ENST00000542128	KDM3A	chr2	86691339	+	ENST00000280527	CRIM1	chr2	36691676	+	5527	851	0	3092	1030

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
ENST00000409556	ENST00000280527	KDM3A	chr2	86691339	+	CRIM1	chr2	36691677	+	0.00013963	0.9998604
ENST00000312912	ENST00000280527	KDM3A	chr2	86691339	+	CRIM1	chr2	36691677	+	0.00012447	0.99987555
ENST00000409064	ENST00000280527	KDM3A	chr2	86691339	+	CRIM1	chr2	36691677	+	9.06E-05	0.9999094
ENST00000542128	ENST00000280527	KDM3A	chr2	86691339	+	CRIM1	chr2	36691677	+	7.96E-05	0.99992037
ENST00000409556	ENST00000280527	KDM3A	chr2	86691339	+	CRIM1	chr2	36691676	+	0.00013963	0.9998604
ENST00000312912	ENST00000280527	KDM3A	chr2	86691339	+	CRIM1	chr2	36691676	+	0.00012447	0.99987555
ENST00000409064	ENST00000280527	KDM3A	chr2	86691339	+	CRIM1	chr2	36691676	+	9.06E-05	0.9999094
ENST00000542128	ENST00000280527	KDM3A	chr2	86691339	+	CRIM1	chr2	36691676	+	7.96E-05	0.99992037

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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

>41759_41759_1_KDM3A-CRIM1_KDM3A_chr2_86691339_ENST00000312912_CRIM1_chr2_36691676_ENST00000280527_length(amino acids)=1082AA_BP=336
MVLTLGESWPVLVGRRFLSLSAADGSDGSHDSWDVERVAEWPWLSGTIRAVSHTDVTKKDLKVCVEFDGESWRKRRWIEVYSLLRRAFLV
EHNLVLAERKSPEISERIVQWPAITYKPLLDKAGLGSITSVRFLGDQQRVFLSKDLLKPIQDVNSLRLSLTDNQIVSKEFQALIVKHLDE
SHLLKGDKNLVGSEVKIYSLDPSTQWFSATVINGNPASKTLQVNCEEIPALKIVDPSLIHVEVVHDNLVTCGNSARIGAVKRKSSENNGT
LVSKQAKSCSEASPSMCPVQSVPTTVFKEILLGCTAATPPSKDPRQQSTPQAANSPPNLGAKIPQGCECLSGLCGFPVCEVGSTPRIVSR
GDGTPGKCCDVFECVNDTKPACVFNNVEYYDGDMFRMDNCRFCRCQGGVAICFTAQCGEINCERYYVPEGECCPVCEDPVYPFNNPAGCY
ANGLILAHGDRWREDDCTFCQCVNGERHCVATVCGQTCTNPVKVPGECCPVCEEPTIITVDPPACGELSNCTLTGKDCINGFKRDHNGCR
TCQCINTEELCSERKQGCTLNCPFGFLTDAQNCEICECRPRPKKCRPIICDKYCPLGLLKNKHGCDICRCKKCPELSCSKICPLGFQQDS
HGCLICKCREASASAGPPILSGTCLTVDGHHHKNEESWHDGCRECYCLNGREMCALITCPVPACGNPTIHPGQCCPSCADDFVVQKPELS
TPSICHAPGGEYFVEGETWNIDSCTQCTCHSGRVLCETEVCPPLLCQNPSRTQDSCCPQCTDQPFRPSLSRNNSVPNYCKNDEGDIFLAA
ESWKPDVCTSCICIDSVISCFSESCPSVSCERPVLRKGQCCPYCIEDTIPKKVVCHFSGKAYADEERWDLDSCTHCYCLQGQTLCSTVSC
PPLPCVEPINVEGSCCPMCPEMYVPEPTNIPIEKTNHRGEVDLEVPLWPTPSENDIVHLPRDMGHLQVDYRDNRLHPSEDSSLDSIASVV
VPIIICLSIIIAFLFINQKKQWIPLLCWYRTPTKPSSLNNQLVSVDCKKGTRVQVDSSQRMLRIAEPDARFSGFYSMQKQNHLQADNFYQ

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

>41759_41759_2_KDM3A-CRIM1_KDM3A_chr2_86691339_ENST00000312912_CRIM1_chr2_36691677_ENST00000280527_length(amino acids)=1082AA_BP=336
MVLTLGESWPVLVGRRFLSLSAADGSDGSHDSWDVERVAEWPWLSGTIRAVSHTDVTKKDLKVCVEFDGESWRKRRWIEVYSLLRRAFLV
EHNLVLAERKSPEISERIVQWPAITYKPLLDKAGLGSITSVRFLGDQQRVFLSKDLLKPIQDVNSLRLSLTDNQIVSKEFQALIVKHLDE
SHLLKGDKNLVGSEVKIYSLDPSTQWFSATVINGNPASKTLQVNCEEIPALKIVDPSLIHVEVVHDNLVTCGNSARIGAVKRKSSENNGT
LVSKQAKSCSEASPSMCPVQSVPTTVFKEILLGCTAATPPSKDPRQQSTPQAANSPPNLGAKIPQGCECLSGLCGFPVCEVGSTPRIVSR
GDGTPGKCCDVFECVNDTKPACVFNNVEYYDGDMFRMDNCRFCRCQGGVAICFTAQCGEINCERYYVPEGECCPVCEDPVYPFNNPAGCY
ANGLILAHGDRWREDDCTFCQCVNGERHCVATVCGQTCTNPVKVPGECCPVCEEPTIITVDPPACGELSNCTLTGKDCINGFKRDHNGCR
TCQCINTEELCSERKQGCTLNCPFGFLTDAQNCEICECRPRPKKCRPIICDKYCPLGLLKNKHGCDICRCKKCPELSCSKICPLGFQQDS
HGCLICKCREASASAGPPILSGTCLTVDGHHHKNEESWHDGCRECYCLNGREMCALITCPVPACGNPTIHPGQCCPSCADDFVVQKPELS
TPSICHAPGGEYFVEGETWNIDSCTQCTCHSGRVLCETEVCPPLLCQNPSRTQDSCCPQCTDQPFRPSLSRNNSVPNYCKNDEGDIFLAA
ESWKPDVCTSCICIDSVISCFSESCPSVSCERPVLRKGQCCPYCIEDTIPKKVVCHFSGKAYADEERWDLDSCTHCYCLQGQTLCSTVSC
PPLPCVEPINVEGSCCPMCPEMYVPEPTNIPIEKTNHRGEVDLEVPLWPTPSENDIVHLPRDMGHLQVDYRDNRLHPSEDSSLDSIASVV
VPIIICLSIIIAFLFINQKKQWIPLLCWYRTPTKPSSLNNQLVSVDCKKGTRVQVDSSQRMLRIAEPDARFSGFYSMQKQNHLQADNFYQ

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

>41759_41759_3_KDM3A-CRIM1_KDM3A_chr2_86691339_ENST00000409064_CRIM1_chr2_36691676_ENST00000280527_length(amino acids)=1082AA_BP=336
MVLTLGESWPVLVGRRFLSLSAADGSDGSHDSWDVERVAEWPWLSGTIRAVSHTDVTKKDLKVCVEFDGESWRKRRWIEVYSLLRRAFLV
EHNLVLAERKSPEISERIVQWPAITYKPLLDKAGLGSITSVRFLGDQQRVFLSKDLLKPIQDVNSLRLSLTDNQIVSKEFQALIVKHLDE
SHLLKGDKNLVGSEVKIYSLDPSTQWFSATVINGNPASKTLQVNCEEIPALKIVDPSLIHVEVVHDNLVTCGNSARIGAVKRKSSENNGT
LVSKQAKSCSEASPSMCPVQSVPTTVFKEILLGCTAATPPSKDPRQQSTPQAANSPPNLGAKIPQGCECLSGLCGFPVCEVGSTPRIVSR
GDGTPGKCCDVFECVNDTKPACVFNNVEYYDGDMFRMDNCRFCRCQGGVAICFTAQCGEINCERYYVPEGECCPVCEDPVYPFNNPAGCY
ANGLILAHGDRWREDDCTFCQCVNGERHCVATVCGQTCTNPVKVPGECCPVCEEPTIITVDPPACGELSNCTLTGKDCINGFKRDHNGCR
TCQCINTEELCSERKQGCTLNCPFGFLTDAQNCEICECRPRPKKCRPIICDKYCPLGLLKNKHGCDICRCKKCPELSCSKICPLGFQQDS
HGCLICKCREASASAGPPILSGTCLTVDGHHHKNEESWHDGCRECYCLNGREMCALITCPVPACGNPTIHPGQCCPSCADDFVVQKPELS
TPSICHAPGGEYFVEGETWNIDSCTQCTCHSGRVLCETEVCPPLLCQNPSRTQDSCCPQCTDQPFRPSLSRNNSVPNYCKNDEGDIFLAA
ESWKPDVCTSCICIDSVISCFSESCPSVSCERPVLRKGQCCPYCIEDTIPKKVVCHFSGKAYADEERWDLDSCTHCYCLQGQTLCSTVSC
PPLPCVEPINVEGSCCPMCPEMYVPEPTNIPIEKTNHRGEVDLEVPLWPTPSENDIVHLPRDMGHLQVDYRDNRLHPSEDSSLDSIASVV
VPIIICLSIIIAFLFINQKKQWIPLLCWYRTPTKPSSLNNQLVSVDCKKGTRVQVDSSQRMLRIAEPDARFSGFYSMQKQNHLQADNFYQ

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

>41759_41759_4_KDM3A-CRIM1_KDM3A_chr2_86691339_ENST00000409064_CRIM1_chr2_36691677_ENST00000280527_length(amino acids)=1082AA_BP=336
MVLTLGESWPVLVGRRFLSLSAADGSDGSHDSWDVERVAEWPWLSGTIRAVSHTDVTKKDLKVCVEFDGESWRKRRWIEVYSLLRRAFLV
EHNLVLAERKSPEISERIVQWPAITYKPLLDKAGLGSITSVRFLGDQQRVFLSKDLLKPIQDVNSLRLSLTDNQIVSKEFQALIVKHLDE
SHLLKGDKNLVGSEVKIYSLDPSTQWFSATVINGNPASKTLQVNCEEIPALKIVDPSLIHVEVVHDNLVTCGNSARIGAVKRKSSENNGT
LVSKQAKSCSEASPSMCPVQSVPTTVFKEILLGCTAATPPSKDPRQQSTPQAANSPPNLGAKIPQGCECLSGLCGFPVCEVGSTPRIVSR
GDGTPGKCCDVFECVNDTKPACVFNNVEYYDGDMFRMDNCRFCRCQGGVAICFTAQCGEINCERYYVPEGECCPVCEDPVYPFNNPAGCY
ANGLILAHGDRWREDDCTFCQCVNGERHCVATVCGQTCTNPVKVPGECCPVCEEPTIITVDPPACGELSNCTLTGKDCINGFKRDHNGCR
TCQCINTEELCSERKQGCTLNCPFGFLTDAQNCEICECRPRPKKCRPIICDKYCPLGLLKNKHGCDICRCKKCPELSCSKICPLGFQQDS
HGCLICKCREASASAGPPILSGTCLTVDGHHHKNEESWHDGCRECYCLNGREMCALITCPVPACGNPTIHPGQCCPSCADDFVVQKPELS
TPSICHAPGGEYFVEGETWNIDSCTQCTCHSGRVLCETEVCPPLLCQNPSRTQDSCCPQCTDQPFRPSLSRNNSVPNYCKNDEGDIFLAA
ESWKPDVCTSCICIDSVISCFSESCPSVSCERPVLRKGQCCPYCIEDTIPKKVVCHFSGKAYADEERWDLDSCTHCYCLQGQTLCSTVSC
PPLPCVEPINVEGSCCPMCPEMYVPEPTNIPIEKTNHRGEVDLEVPLWPTPSENDIVHLPRDMGHLQVDYRDNRLHPSEDSSLDSIASVV
VPIIICLSIIIAFLFINQKKQWIPLLCWYRTPTKPSSLNNQLVSVDCKKGTRVQVDSSQRMLRIAEPDARFSGFYSMQKQNHLQADNFYQ

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

>41759_41759_5_KDM3A-CRIM1_KDM3A_chr2_86691339_ENST00000409556_CRIM1_chr2_36691676_ENST00000280527_length(amino acids)=1082AA_BP=336
MVLTLGESWPVLVGRRFLSLSAADGSDGSHDSWDVERVAEWPWLSGTIRAVSHTDVTKKDLKVCVEFDGESWRKRRWIEVYSLLRRAFLV
EHNLVLAERKSPEISERIVQWPAITYKPLLDKAGLGSITSVRFLGDQQRVFLSKDLLKPIQDVNSLRLSLTDNQIVSKEFQALIVKHLDE
SHLLKGDKNLVGSEVKIYSLDPSTQWFSATVINGNPASKTLQVNCEEIPALKIVDPSLIHVEVVHDNLVTCGNSARIGAVKRKSSENNGT
LVSKQAKSCSEASPSMCPVQSVPTTVFKEILLGCTAATPPSKDPRQQSTPQAANSPPNLGAKIPQGCECLSGLCGFPVCEVGSTPRIVSR
GDGTPGKCCDVFECVNDTKPACVFNNVEYYDGDMFRMDNCRFCRCQGGVAICFTAQCGEINCERYYVPEGECCPVCEDPVYPFNNPAGCY
ANGLILAHGDRWREDDCTFCQCVNGERHCVATVCGQTCTNPVKVPGECCPVCEEPTIITVDPPACGELSNCTLTGKDCINGFKRDHNGCR
TCQCINTEELCSERKQGCTLNCPFGFLTDAQNCEICECRPRPKKCRPIICDKYCPLGLLKNKHGCDICRCKKCPELSCSKICPLGFQQDS
HGCLICKCREASASAGPPILSGTCLTVDGHHHKNEESWHDGCRECYCLNGREMCALITCPVPACGNPTIHPGQCCPSCADDFVVQKPELS
TPSICHAPGGEYFVEGETWNIDSCTQCTCHSGRVLCETEVCPPLLCQNPSRTQDSCCPQCTDQPFRPSLSRNNSVPNYCKNDEGDIFLAA
ESWKPDVCTSCICIDSVISCFSESCPSVSCERPVLRKGQCCPYCIEDTIPKKVVCHFSGKAYADEERWDLDSCTHCYCLQGQTLCSTVSC
PPLPCVEPINVEGSCCPMCPEMYVPEPTNIPIEKTNHRGEVDLEVPLWPTPSENDIVHLPRDMGHLQVDYRDNRLHPSEDSSLDSIASVV
VPIIICLSIIIAFLFINQKKQWIPLLCWYRTPTKPSSLNNQLVSVDCKKGTRVQVDSSQRMLRIAEPDARFSGFYSMQKQNHLQADNFYQ

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

>41759_41759_6_KDM3A-CRIM1_KDM3A_chr2_86691339_ENST00000409556_CRIM1_chr2_36691677_ENST00000280527_length(amino acids)=1082AA_BP=336
MVLTLGESWPVLVGRRFLSLSAADGSDGSHDSWDVERVAEWPWLSGTIRAVSHTDVTKKDLKVCVEFDGESWRKRRWIEVYSLLRRAFLV
EHNLVLAERKSPEISERIVQWPAITYKPLLDKAGLGSITSVRFLGDQQRVFLSKDLLKPIQDVNSLRLSLTDNQIVSKEFQALIVKHLDE
SHLLKGDKNLVGSEVKIYSLDPSTQWFSATVINGNPASKTLQVNCEEIPALKIVDPSLIHVEVVHDNLVTCGNSARIGAVKRKSSENNGT
LVSKQAKSCSEASPSMCPVQSVPTTVFKEILLGCTAATPPSKDPRQQSTPQAANSPPNLGAKIPQGCECLSGLCGFPVCEVGSTPRIVSR
GDGTPGKCCDVFECVNDTKPACVFNNVEYYDGDMFRMDNCRFCRCQGGVAICFTAQCGEINCERYYVPEGECCPVCEDPVYPFNNPAGCY
ANGLILAHGDRWREDDCTFCQCVNGERHCVATVCGQTCTNPVKVPGECCPVCEEPTIITVDPPACGELSNCTLTGKDCINGFKRDHNGCR
TCQCINTEELCSERKQGCTLNCPFGFLTDAQNCEICECRPRPKKCRPIICDKYCPLGLLKNKHGCDICRCKKCPELSCSKICPLGFQQDS
HGCLICKCREASASAGPPILSGTCLTVDGHHHKNEESWHDGCRECYCLNGREMCALITCPVPACGNPTIHPGQCCPSCADDFVVQKPELS
TPSICHAPGGEYFVEGETWNIDSCTQCTCHSGRVLCETEVCPPLLCQNPSRTQDSCCPQCTDQPFRPSLSRNNSVPNYCKNDEGDIFLAA
ESWKPDVCTSCICIDSVISCFSESCPSVSCERPVLRKGQCCPYCIEDTIPKKVVCHFSGKAYADEERWDLDSCTHCYCLQGQTLCSTVSC
PPLPCVEPINVEGSCCPMCPEMYVPEPTNIPIEKTNHRGEVDLEVPLWPTPSENDIVHLPRDMGHLQVDYRDNRLHPSEDSSLDSIASVV
VPIIICLSIIIAFLFINQKKQWIPLLCWYRTPTKPSSLNNQLVSVDCKKGTRVQVDSSQRMLRIAEPDARFSGFYSMQKQNHLQADNFYQ

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

>41759_41759_7_KDM3A-CRIM1_KDM3A_chr2_86691339_ENST00000542128_CRIM1_chr2_36691676_ENST00000280527_length(amino acids)=1030AA_BP=284
MVLTLGESWPVLVGRRFLSLSAADGSDGSHDSWDVERVAEWPWLSGTIRAVSHTDVTKKDLKTYKPLLDKAGLGSITSVRFLGDQQRVFL
SKDLLKPIQDVNSLRLSLTDNQIVSKEFQALIVKHLDESHLLKGDKNLVGSEVKIYSLDPSTQWFSATVINGNPASKTLQVNCEEIPALK
IVDPSLIHVEVVHDNLVTCGNSARIGAVKRKSSENNGTLVSKQAKSCSEASPSMCPVQSVPTTVFKEILLGCTAATPPSKDPRQQSTPQA
ANSPPNLGAKIPQGCECLSGLCGFPVCEVGSTPRIVSRGDGTPGKCCDVFECVNDTKPACVFNNVEYYDGDMFRMDNCRFCRCQGGVAIC
FTAQCGEINCERYYVPEGECCPVCEDPVYPFNNPAGCYANGLILAHGDRWREDDCTFCQCVNGERHCVATVCGQTCTNPVKVPGECCPVC
EEPTIITVDPPACGELSNCTLTGKDCINGFKRDHNGCRTCQCINTEELCSERKQGCTLNCPFGFLTDAQNCEICECRPRPKKCRPIICDK
YCPLGLLKNKHGCDICRCKKCPELSCSKICPLGFQQDSHGCLICKCREASASAGPPILSGTCLTVDGHHHKNEESWHDGCRECYCLNGRE
MCALITCPVPACGNPTIHPGQCCPSCADDFVVQKPELSTPSICHAPGGEYFVEGETWNIDSCTQCTCHSGRVLCETEVCPPLLCQNPSRT
QDSCCPQCTDQPFRPSLSRNNSVPNYCKNDEGDIFLAAESWKPDVCTSCICIDSVISCFSESCPSVSCERPVLRKGQCCPYCIEDTIPKK
VVCHFSGKAYADEERWDLDSCTHCYCLQGQTLCSTVSCPPLPCVEPINVEGSCCPMCPEMYVPEPTNIPIEKTNHRGEVDLEVPLWPTPS
ENDIVHLPRDMGHLQVDYRDNRLHPSEDSSLDSIASVVVPIIICLSIIIAFLFINQKKQWIPLLCWYRTPTKPSSLNNQLVSVDCKKGTR

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

>41759_41759_8_KDM3A-CRIM1_KDM3A_chr2_86691339_ENST00000542128_CRIM1_chr2_36691677_ENST00000280527_length(amino acids)=1030AA_BP=284
MVLTLGESWPVLVGRRFLSLSAADGSDGSHDSWDVERVAEWPWLSGTIRAVSHTDVTKKDLKTYKPLLDKAGLGSITSVRFLGDQQRVFL
SKDLLKPIQDVNSLRLSLTDNQIVSKEFQALIVKHLDESHLLKGDKNLVGSEVKIYSLDPSTQWFSATVINGNPASKTLQVNCEEIPALK
IVDPSLIHVEVVHDNLVTCGNSARIGAVKRKSSENNGTLVSKQAKSCSEASPSMCPVQSVPTTVFKEILLGCTAATPPSKDPRQQSTPQA
ANSPPNLGAKIPQGCECLSGLCGFPVCEVGSTPRIVSRGDGTPGKCCDVFECVNDTKPACVFNNVEYYDGDMFRMDNCRFCRCQGGVAIC
FTAQCGEINCERYYVPEGECCPVCEDPVYPFNNPAGCYANGLILAHGDRWREDDCTFCQCVNGERHCVATVCGQTCTNPVKVPGECCPVC
EEPTIITVDPPACGELSNCTLTGKDCINGFKRDHNGCRTCQCINTEELCSERKQGCTLNCPFGFLTDAQNCEICECRPRPKKCRPIICDK
YCPLGLLKNKHGCDICRCKKCPELSCSKICPLGFQQDSHGCLICKCREASASAGPPILSGTCLTVDGHHHKNEESWHDGCRECYCLNGRE
MCALITCPVPACGNPTIHPGQCCPSCADDFVVQKPELSTPSICHAPGGEYFVEGETWNIDSCTQCTCHSGRVLCETEVCPPLLCQNPSRT
QDSCCPQCTDQPFRPSLSRNNSVPNYCKNDEGDIFLAAESWKPDVCTSCICIDSVISCFSESCPSVSCERPVLRKGQCCPYCIEDTIPKK
VVCHFSGKAYADEERWDLDSCTHCYCLQGQTLCSTVSCPPLPCVEPINVEGSCCPMCPEMYVPEPTNIPIEKTNHRGEVDLEVPLWPTPS
ENDIVHLPRDMGHLQVDYRDNRLHPSEDSSLDSIASVVVPIIICLSIIIAFLFINQKKQWIPLLCWYRTPTKPSSLNNQLVSVDCKKGTR

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

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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/chr2:86691339/chr2:36691677)
- 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
KDM3A Q9Y4C1	CRIM1 Q9NZV1
FUNCTION: Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a central role in histone code. Preferentially demethylates mono- and dimethylated H3 'Lys-9' residue, with a preference for dimethylated residue, while it has weak or no activity on trimethylated H3 'Lys-9'. Demethylation of Lys residue generates formaldehyde and succinate. Involved in hormone-dependent transcriptional activation, by participating in recruitment to androgen-receptor target genes, resulting in H3 'Lys-9' demethylation and transcriptional activation. Involved in spermatogenesis by regulating expression of target genes such as PRM1 and TNP1 which are required for packaging and condensation of sperm chromatin. Involved in obesity resistance through regulation of metabolic genes such as PPARA and UCP1. {ECO:0000269\|PubMed:16603237, ECO:0000269\|PubMed:28262558}.	FUNCTION: May play a role in CNS development by interacting with growth factors implicated in motor neuron differentiation and survival. May play a role in capillary formation and maintenance during angiogenesis. Modulates BMP activity by affecting its processing and delivery to the cell surface. {ECO:0000269\|PubMed:12464430, ECO:0000269\|PubMed:12805376}.

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

CRIM1

chr2:86691339

chr2:36691676

ENST00000280527

334_391

289.6666666666667

1037.0

Domain

VWFC 1

Tgene

CRIM1

chr2:86691339

chr2:36691676

ENST00000280527

401_457

289.6666666666667

1037.0

Domain

VWFC 2

Tgene

CRIM1

chr2:86691339

chr2:36691676

ENST00000280527

469_498

289.6666666666667

1037.0

Domain

Antistasin-like 1

Tgene

CRIM1

chr2:86691339

chr2:36691676

ENST00000280527

505_532

289.6666666666667

1037.0

Domain

Antistasin-like 2

Tgene

CRIM1

chr2:86691339

chr2:36691676

ENST00000280527

539_564

289.6666666666667

1037.0

Domain

Antistasin-like 3

Tgene

CRIM1

chr2:86691339

chr2:36691676

ENST00000280527

567_592

289.6666666666667

1037.0

Domain

Antistasin-like 4

Tgene

CRIM1

chr2:86691339

chr2:36691676

ENST00000280527

606_663

289.6666666666667

1037.0

Domain

VWFC 3

Tgene

CRIM1

chr2:86691339

chr2:36691676

ENST00000280527

677_735

289.6666666666667

1037.0

Domain

VWFC 4

Tgene

CRIM1

chr2:86691339

chr2:36691676

ENST00000280527

751_809

289.6666666666667

1037.0

Domain

VWFC 5

Tgene

CRIM1

chr2:86691339

chr2:36691676

ENST00000280527

817_874

289.6666666666667

1037.0

Domain

VWFC 6

Tgene

CRIM1

chr2:86691339

chr2:36691677

ENST00000280527

334_391

289.6666666666667

1037.0

Domain

VWFC 1

Tgene

CRIM1

chr2:86691339

chr2:36691677

ENST00000280527

401_457

289.6666666666667

1037.0

Domain

VWFC 2

Tgene

CRIM1

chr2:86691339

chr2:36691677

ENST00000280527

469_498

289.6666666666667

1037.0

Domain

Antistasin-like 1

Tgene

CRIM1

chr2:86691339

chr2:36691677

ENST00000280527

505_532

289.6666666666667

1037.0

Domain

Antistasin-like 2

Tgene

CRIM1

chr2:86691339

chr2:36691677

ENST00000280527

539_564

289.6666666666667

1037.0

Domain

Antistasin-like 3

Tgene

CRIM1

chr2:86691339

chr2:36691677

ENST00000280527

567_592

289.6666666666667

1037.0

Domain

Antistasin-like 4

Tgene

CRIM1

chr2:86691339

chr2:36691677

ENST00000280527

606_663

289.6666666666667

1037.0

Domain

VWFC 3

Tgene

CRIM1

chr2:86691339

chr2:36691677

ENST00000280527

677_735

289.6666666666667

1037.0

Domain

VWFC 4

Tgene

CRIM1

chr2:86691339

chr2:36691677

ENST00000280527

751_809

289.6666666666667

1037.0

Domain

VWFC 5

Tgene

CRIM1

chr2:86691339

chr2:36691677

ENST00000280527

817_874

289.6666666666667

1037.0

Domain

VWFC 6

Tgene

CRIM1

chr2:86691339

chr2:36691676

ENST00000280527

314_316

289.6666666666667

1037.0

Motif

Cell attachment site

Tgene

CRIM1

chr2:86691339

chr2:36691677

ENST00000280527

314_316

289.6666666666667

1037.0

Motif

Cell attachment site

Tgene

CRIM1

chr2:86691339

chr2:36691676

ENST00000280527

961_1036

289.6666666666667

1037.0

Topological domain

Cytoplasmic

Tgene

CRIM1

chr2:86691339

chr2:36691677

ENST00000280527

961_1036

289.6666666666667

1037.0

Topological domain

Cytoplasmic

Tgene

CRIM1

chr2:86691339

chr2:36691676

ENST00000280527

940_960

289.6666666666667

1037.0

Transmembrane

Helical

Tgene

CRIM1

chr2:86691339

chr2:36691677

ENST00000280527

940_960

289.6666666666667

1037.0

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

KDM3A

chr2:86691339

chr2:36691676

ENST00000312912

1058_1281

335.6666666666667

1322.0

Domain

JmjC

Hgene

KDM3A

chr2:86691339

chr2:36691676

ENST00000409064

1058_1281

335.6666666666667

1322.0

Domain

JmjC

Hgene

KDM3A

chr2:86691339

chr2:36691676

ENST00000409556

1058_1281

335.6666666666667

1322.0

Domain

JmjC

Hgene

KDM3A

chr2:86691339

chr2:36691677

ENST00000312912

1058_1281

335.6666666666667

1322.0

Domain

JmjC

Hgene

KDM3A

chr2:86691339

chr2:36691677

ENST00000409064

1058_1281

335.6666666666667

1322.0

Domain

JmjC

Hgene

KDM3A

chr2:86691339

chr2:36691677

ENST00000409556

1058_1281

335.6666666666667

1322.0

Domain

JmjC

Hgene

KDM3A

chr2:86691339

chr2:36691676

ENST00000312912

885_889

335.6666666666667

1322.0

Motif

Note=LXXLL motif

Hgene

KDM3A

chr2:86691339

chr2:36691676

ENST00000409064

885_889

335.6666666666667

1322.0

Motif

Note=LXXLL motif

Hgene

KDM3A

chr2:86691339

chr2:36691676

ENST00000409556

885_889

335.6666666666667

1322.0

Motif

Note=LXXLL motif

Hgene

KDM3A

chr2:86691339

chr2:36691677

ENST00000312912

885_889

335.6666666666667

1322.0

Motif

Note=LXXLL motif

Hgene

KDM3A

chr2:86691339

chr2:36691677

ENST00000409064

885_889

335.6666666666667

1322.0

Motif

Note=LXXLL motif

Hgene

KDM3A

chr2:86691339

chr2:36691677

ENST00000409556

885_889

335.6666666666667

1322.0

Motif

Note=LXXLL motif

Hgene

KDM3A

chr2:86691339

chr2:36691676

ENST00000312912

662_687

335.6666666666667

1322.0

Zinc finger

C6-type

Hgene

KDM3A

chr2:86691339

chr2:36691676

ENST00000409064

662_687

335.6666666666667

1322.0

Zinc finger

C6-type

Hgene

KDM3A

chr2:86691339

chr2:36691676

ENST00000409556

662_687

335.6666666666667

1322.0

Zinc finger

C6-type

Hgene

KDM3A

chr2:86691339

chr2:36691677

ENST00000312912

662_687

335.6666666666667

1322.0

Zinc finger

C6-type

Hgene

KDM3A

chr2:86691339

chr2:36691677

ENST00000409064

662_687

335.6666666666667

1322.0

Zinc finger

C6-type

Hgene

KDM3A

chr2:86691339

chr2:36691677

ENST00000409556

662_687

335.6666666666667

1322.0

Zinc finger

C6-type

Tgene

CRIM1

chr2:86691339

chr2:36691676

ENST00000280527

35_112

289.6666666666667

1037.0

Domain

IGFBP N-terminal

Tgene

CRIM1

chr2:86691339

chr2:36691677

ENST00000280527

35_112

289.6666666666667

1037.0

Domain

IGFBP N-terminal

Tgene

CRIM1

chr2:86691339

chr2:36691676

ENST00000280527

35_939

289.6666666666667

1037.0

Topological domain

Extracellular

Tgene

CRIM1

chr2:86691339

chr2:36691677

ENST00000280527

35_939

289.6666666666667

1037.0

Topological domain

Extracellular

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Fusion Protein Structures

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)	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	AA seq	Len(AA seq)
PDB file >>>1852_KDM3A_86691339_CRIM1_36691677_ranked_0.pdb	KDM3A	86691339	86691339	ENST00000280527	CRIM1	chr2	36691677	+	MVLTLGESWPVLVGRRFLSLSAADGSDGSHDSWDVERVAEWPWLSGTIRAVSHTDVTKKDLKVCVEFDGESWRKRRWIEVYSLLRRAFLV EHNLVLAERKSPEISERIVQWPAITYKPLLDKAGLGSITSVRFLGDQQRVFLSKDLLKPIQDVNSLRLSLTDNQIVSKEFQALIVKHLDE SHLLKGDKNLVGSEVKIYSLDPSTQWFSATVINGNPASKTLQVNCEEIPALKIVDPSLIHVEVVHDNLVTCGNSARIGAVKRKSSENNGT LVSKQAKSCSEASPSMCPVQSVPTTVFKEILLGCTAATPPSKDPRQQSTPQAANSPPNLGAKIPQGCECLSGLCGFPVCEVGSTPRIVSR GDGTPGKCCDVFECVNDTKPACVFNNVEYYDGDMFRMDNCRFCRCQGGVAICFTAQCGEINCERYYVPEGECCPVCEDPVYPFNNPAGCY ANGLILAHGDRWREDDCTFCQCVNGERHCVATVCGQTCTNPVKVPGECCPVCEEPTIITVDPPACGELSNCTLTGKDCINGFKRDHNGCR TCQCINTEELCSERKQGCTLNCPFGFLTDAQNCEICECRPRPKKCRPIICDKYCPLGLLKNKHGCDICRCKKCPELSCSKICPLGFQQDS HGCLICKCREASASAGPPILSGTCLTVDGHHHKNEESWHDGCRECYCLNGREMCALITCPVPACGNPTIHPGQCCPSCADDFVVQKPELS TPSICHAPGGEYFVEGETWNIDSCTQCTCHSGRVLCETEVCPPLLCQNPSRTQDSCCPQCTDQPFRPSLSRNNSVPNYCKNDEGDIFLAA ESWKPDVCTSCICIDSVISCFSESCPSVSCERPVLRKGQCCPYCIEDTIPKKVVCHFSGKAYADEERWDLDSCTHCYCLQGQTLCSTVSC PPLPCVEPINVEGSCCPMCPEMYVPEPTNIPIEKTNHRGEVDLEVPLWPTPSENDIVHLPRDMGHLQVDYRDNRLHPSEDSSLDSIASVV VPIIICLSIIIAFLFINQKKQWIPLLCWYRTPTKPSSLNNQLVSVDCKKGTRVQVDSSQRMLRIAEPDARFSGFYSMQKQNHLQADNFYQ	1082

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pLDDT score distribution

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.

KDM3A_pLDDT.png

CRIM1_pLDDT.png

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

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Ramachandran Plot of Fusion Protein Structure

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

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
KDM3A
CRIM1

- 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 KDM3A-CRIM1

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 KDM3A-CRIM1

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