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	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:NFIA-CDK2AP1

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: NFIA-CDK2AP1
	FusionPDB ID: 58863
	FusionGDB2.0 ID: 58863
		Hgene	Tgene
	Gene symbol	NFIA	CDK2AP1
	Gene ID	4774	8099
	Gene name	nuclear factor I A	cyclin dependent kinase 2 associated protein 1
	Synonyms	BRMUTD\|CTF\|NF-I/A\|NF1-A\|NFI-A\|NFI-L	DOC1\|DORC1\|ST19\|doc-1\|p12DOC-1
	Cytomap	1p31.3	12q24.31
	Type of gene	protein-coding	protein-coding
	Description	nuclear factor 1 A-typeCCAAT-box-binding transcription factorTGGCA-binding protein	cyclin-dependent kinase 2-associated protein 1CDK2-associated protein 1Deleted in oral cancer-1deleted in oral cancer 1putative oral cancer suppressor
	Modification date	20200313	20200313
	UniProtAcc	Q12857	O14519
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000357977, ENST00000371184, ENST00000371185, ENST00000371187, ENST00000371189, ENST00000371191, ENST00000403491, ENST00000407417, ENST00000479364, ENST00000485903,	ENST00000535979, ENST00000538446, ENST00000542174, ENST00000544658, ENST00000261692,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	21 X 22 X 8=3696	9 X 5 X 5=225
	# samples	25	9
	** MAII score	log2(25/3696*10)=-3.88596475675397 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(9/225*10)=-1.32192809488736 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: NFIA [Title/Abstract] AND CDK2AP1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	NFIA(61872399)-CDK2AP1(123751829), # samples:4
Anticipated loss of major functional domain due to fusion event.	NFIA-CDK2AP1 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. NFIA-CDK2AP1 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. NFIA-CDK2AP1 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. NFIA-CDK2AP1 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. NFIA-CDK2AP1 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF. NFIA-CDK2AP1 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF. NFIA-CDK2AP1 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor due to the frame-shifted 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	NFIA	GO:0045944	positive regulation of transcription by RNA polymerase II	17010934
Tgene	CDK2AP1	GO:0001934	positive regulation of protein phosphorylation	9506968

Fusion gene breakpoints across NFIA (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 CDK2AP1 (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	THYM	TCGA-XU-A92Z-01A	NFIA	chr1	61872398	+	CDK2AP1	chr12	123751828	-
ChimerDB4	THYM	TCGA-XU-A92Z-01A	NFIA	chr1	61872399	-	CDK2AP1	chr12	123751829	-
ChimerDB4	THYM	TCGA-XU-A92Z-01A	NFIA	chr1	61872399	+	CDK2AP1	chr12	123751829	-
ChimerDB4	THYM	TCGA-XU-A92Z	NFIA	chr1	61872399	+	CDK2AP1	chr12	123751829	-

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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)
ENST00000371191	NFIA	chr1	61872399	+	ENST00000261692	CDK2AP1	chr12	123751829	-	2649	1601	112	1893	593
ENST00000407417	NFIA	chr1	61872399	+	ENST00000261692	CDK2AP1	chr12	123751829	-	2796	1748	310	2040	576
ENST00000371189	NFIA	chr1	61872399	+	ENST00000261692	CDK2AP1	chr12	123751829	-	2685	1637	82	1929	615
ENST00000403491	NFIA	chr1	61872399	+	ENST00000261692	CDK2AP1	chr12	123751829	-	2952	1904	343	2196	617
ENST00000371187	NFIA	chr1	61872399	+	ENST00000261692	CDK2AP1	chr12	123751829	-	2639	1591	30	1883	617
ENST00000485903	NFIA	chr1	61872399	+	ENST00000261692	CDK2AP1	chr12	123751829	-	2408	1360	69	1652	527
ENST00000371185	NFIA	chr1	61872399	+	ENST00000261692	CDK2AP1	chr12	123751829	-	2446	1398	44	1690	548
ENST00000371184	NFIA	chr1	61872399	+	ENST00000261692	CDK2AP1	chr12	123751829	-	2119	1071	38	1363	441
ENST00000357977	NFIA	chr1	61872399	+	ENST00000261692	CDK2AP1	chr12	123751829	-	1421	373	6	665	219
ENST00000371191	NFIA	chr1	61872398	+	ENST00000261692	CDK2AP1	chr12	123751828	-	2649	1601	112	1893	593
ENST00000407417	NFIA	chr1	61872398	+	ENST00000261692	CDK2AP1	chr12	123751828	-	2796	1748	310	2040	576
ENST00000371189	NFIA	chr1	61872398	+	ENST00000261692	CDK2AP1	chr12	123751828	-	2685	1637	82	1929	615
ENST00000403491	NFIA	chr1	61872398	+	ENST00000261692	CDK2AP1	chr12	123751828	-	2952	1904	343	2196	617
ENST00000371187	NFIA	chr1	61872398	+	ENST00000261692	CDK2AP1	chr12	123751828	-	2639	1591	30	1883	617
ENST00000485903	NFIA	chr1	61872398	+	ENST00000261692	CDK2AP1	chr12	123751828	-	2408	1360	69	1652	527
ENST00000371185	NFIA	chr1	61872398	+	ENST00000261692	CDK2AP1	chr12	123751828	-	2446	1398	44	1690	548
ENST00000371184	NFIA	chr1	61872398	+	ENST00000261692	CDK2AP1	chr12	123751828	-	2119	1071	38	1363	441
ENST00000357977	NFIA	chr1	61872398	+	ENST00000261692	CDK2AP1	chr12	123751828	-	1421	373	6	665	219

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
ENST00000371191	ENST00000261692	NFIA	chr1	61872399	+	CDK2AP1	chr12	123751829	-	0.002106729	0.9978933
ENST00000407417	ENST00000261692	NFIA	chr1	61872399	+	CDK2AP1	chr12	123751829	-	0.00135413	0.99864584
ENST00000371189	ENST00000261692	NFIA	chr1	61872399	+	CDK2AP1	chr12	123751829	-	0.004603586	0.99539644
ENST00000403491	ENST00000261692	NFIA	chr1	61872399	+	CDK2AP1	chr12	123751829	-	0.003004923	0.9969951
ENST00000371187	ENST00000261692	NFIA	chr1	61872399	+	CDK2AP1	chr12	123751829	-	0.002279004	0.997721
ENST00000485903	ENST00000261692	NFIA	chr1	61872399	+	CDK2AP1	chr12	123751829	-	0.001064536	0.9989355
ENST00000371185	ENST00000261692	NFIA	chr1	61872399	+	CDK2AP1	chr12	123751829	-	0.004916437	0.9950836
ENST00000371184	ENST00000261692	NFIA	chr1	61872399	+	CDK2AP1	chr12	123751829	-	0.002255004	0.99774504
ENST00000357977	ENST00000261692	NFIA	chr1	61872399	+	CDK2AP1	chr12	123751829	-	0.013302585	0.9866974
ENST00000371191	ENST00000261692	NFIA	chr1	61872398	+	CDK2AP1	chr12	123751828	-	0.002106729	0.9978933
ENST00000407417	ENST00000261692	NFIA	chr1	61872398	+	CDK2AP1	chr12	123751828	-	0.00135413	0.99864584
ENST00000371189	ENST00000261692	NFIA	chr1	61872398	+	CDK2AP1	chr12	123751828	-	0.004603586	0.99539644
ENST00000403491	ENST00000261692	NFIA	chr1	61872398	+	CDK2AP1	chr12	123751828	-	0.003004923	0.9969951
ENST00000371187	ENST00000261692	NFIA	chr1	61872398	+	CDK2AP1	chr12	123751828	-	0.002279004	0.997721
ENST00000485903	ENST00000261692	NFIA	chr1	61872398	+	CDK2AP1	chr12	123751828	-	0.001064536	0.9989355
ENST00000371185	ENST00000261692	NFIA	chr1	61872398	+	CDK2AP1	chr12	123751828	-	0.004916437	0.9950836
ENST00000371184	ENST00000261692	NFIA	chr1	61872398	+	CDK2AP1	chr12	123751828	-	0.002255004	0.99774504
ENST00000357977	ENST00000261692	NFIA	chr1	61872398	+	CDK2AP1	chr12	123751828	-	0.013302585	0.9866974

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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

>58863_58863_1_NFIA-CDK2AP1_NFIA_chr1_61872398_ENST00000357977_CDK2AP1_chr12_123751828_ENST00000261692_length(amino acids)=219AA_BP=123
MMFSFPAASPHATPSTLHFPTSPIIQQPGPYFSHPAIRYHPQETLKEFVQLVCPDAGQQAGQVGFLNPNGSSQGKVHNPFLPTPMLPPPP
PPPMARPVPLPVPDTKPPTTSTEGGAASPTSPTGSVHSPSTSMATSSQYRQLLSDYGPPSLGYTQGTGNSQVPQSKYAELLAIIEELGKE

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

>58863_58863_2_NFIA-CDK2AP1_NFIA_chr1_61872398_ENST00000371184_CDK2AP1_chr12_123751828_ENST00000261692_length(amino acids)=441AA_BP=345
MYSPLCLTQDEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKKHEKRMSKEEERAVKDELLSEKPEVKQKWASRLLAKLRKDIRPEYRED
FVLTVTGKKPPCCVLSNPDQKGKMRRIDCLRQADKVWRLDLVMVILFKGIPLESTDGERLVKSPQCSNPGLCVQPHHIGVSVKELDLYLA
YFVHAAGMPSPTTLKKSEKSGFSSPSPSQTSSLGTAFTQHHRPVITGPRASPHATPSTLHFPTSPIIQQPGPYFSHPAIRYHPQETLKEF
VQLVCPDAGQQAGQVGFLNPNGSSQGKVHNPFLPTPMLPPPPPPPMARPVPLPVPDTKPPTTSTEGGAASPTSPTGSVHSPSTSMATSSQ

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

>58863_58863_3_NFIA-CDK2AP1_NFIA_chr1_61872398_ENST00000371185_CDK2AP1_chr12_123751828_ENST00000261692_length(amino acids)=548AA_BP=452
MYSPLCLTQDEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKKHEKRMSKEEERAVKDELLSEKPEVKQKWASRLLAKLRKDIRPEYRED
FVLTVTGKKPPCCVLSNPDQKGKMRRIDCLRQADKVWRLDLVMVILFKGIPLESTDGERLVKSPQCSNPGLCVQPHHIGVSVKELDLYLA
YFVHAAGHLGFQDSFVTSGVFSVTELVRVSQTPIAAGTGPNFSLSDLESSSYYSMSPGAMRRSLPSTSSTSSTKRLKSVEDEMDSPGEEP
FYTGQGRSPGSGSQSSGWHEVEPGMPSPTTLKKSEKSGFSSPSPSQTSSLGTAFTQHHRPVITGPRASPHATPSTLHFPTSPIIQQPGPY
FSHPAIRYHPQETLKEFVQLVCPDAGQQAGQVGFLNPNGSSQGKVHNPFLPTPMLPPPPPPPMARPVPLPVPDTKPPTTSTEGGAASPTS
PTGSVHSPSTSMATSSQYRQLLSDYGPPSLGYTQGTGNSQVPQSKYAELLAIIEELGKEIRPTYAGSKSAMERLKRGIIHARGLVRECLA

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

>58863_58863_4_NFIA-CDK2AP1_NFIA_chr1_61872398_ENST00000371187_CDK2AP1_chr12_123751828_ENST00000261692_length(amino acids)=617AA_BP=521
MIFFSPPFSLSLSLSLPLSLFLLSHPHSRTPPNRTPRRTRIPQRPAVMYSPLCLTQDEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKK
HEKRMSKEEERAVKDELLSEKPEVKQKWASRLLAKLRKDIRPEYREDFVLTVTGKKPPCCVLSNPDQKGKMRRIDCLRQADKVWRLDLVM
VILFKGIPLESTDGERLVKSPQCSNPGLCVQPHHIGVSVKELDLYLAYFVHAADSSQSESPSQPSDADIKDQPENGHLGFQDSFVTSGVF
SVTELVRVSQTPIAAGTGPNFSLSDLESSSYYSMSPGAMRRSLPSTSSTSSTKRLKSVEDEMDSPGEEPFYTGQGRSPGSGSQSSGWHEV
EPGMPSPTTLKKSEKSGFSSPSPSQTSSLGTAFTQHHRPVITGPRASPHATPSTLHFPTSPIIQQPGPYFSHPAIRYHPQETLKEFVQLV
CPDAGQQAGQVGFLNPNGSSQGKVHNPFLPTPMLPPPPPPPMARPVPLPVPDTKPPTTSTEGGAASPTSPTGSVHSPSTSMATSSQYRQL

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

>58863_58863_5_NFIA-CDK2AP1_NFIA_chr1_61872398_ENST00000371189_CDK2AP1_chr12_123751828_ENST00000261692_length(amino acids)=615AA_BP=519
MQMCRPASSSVLYVPTRWPGGCGATWQSCPSPPPRRTRIPQRPAVMYSPLCLTQDEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKKHE
KRMSKEEERAVKDELLSEKPEVKQKWASRLLAKLRKDIRPEYREDFVLTVTGKKPPCCVLSNPDQKGKMRRIDCLRQADKVWRLDLVMVI
LFKGIPLESTDGERLVKSPQCSNPGLCVQPHHIGVSVKELDLYLAYFVHAADSSQSESPSQPSDADIKDQPENGHLGFQDSFVTSGVFSV
TELVRVSQTPIAAGTGPNFSLSDLESSSYYSMSPGAMRRSLPSTSSTSSTKRLKSVEDEMDSPGEEPFYTGQGRSPGSGSQSSGWHEVEP
GMPSPTTLKKSEKSGFSSPSPSQTSSLGTAFTQHHRPVITGPRASPHATPSTLHFPTSPIIQQPGPYFSHPAIRYHPQETLKEFVQLVCP
DAGQQAGQVGFLNPNGSSQGKVHNPFLPTPMLPPPPPPPMARPVPLPVPDTKPPTTSTEGGAASPTSPTGSVHSPSTSMATSSQYRQLLS

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

>58863_58863_6_NFIA-CDK2AP1_NFIA_chr1_61872398_ENST00000371191_CDK2AP1_chr12_123751828_ENST00000261692_length(amino acids)=593AA_BP=497
MKLADSVMAGKASDGSIKWQLCYDISARTWWMDEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKKHEKRMSKEEERAVKDELLSEKPEV
KQKWASRLLAKLRKDIRPEYREDFVLTVTGKKPPCCVLSNPDQKGKMRRIDCLRQADKVWRLDLVMVILFKGIPLESTDGERLVKSPQCS
NPGLCVQPHHIGVSVKELDLYLAYFVHAADSSQSESPSQPSDADIKDQPENGHLGFQDSFVTSGVFSVTELVRVSQTPIAAGTGPNFSLS
DLESSSYYSMSPGAMRRSLPSTSSTSSTKRLKSVEDEMDSPGEEPFYTGQGRSPGSGSQSSGWHEVEPGMPSPTTLKKSEKSGFSSPSPS
QTSSLGTAFTQHHRPVITGPRASPHATPSTLHFPTSPIIQQPGPYFSHPAIRYHPQETLKEFVQLVCPDAGQQAGQVGFLNPNGSSQGKV
HNPFLPTPMLPPPPPPPMARPVPLPVPDTKPPTTSTEGGAASPTSPTGSVHSPSTSMATSSQYRQLLSDYGPPSLGYTQGTGNSQVPQSK

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

>58863_58863_7_NFIA-CDK2AP1_NFIA_chr1_61872398_ENST00000403491_CDK2AP1_chr12_123751828_ENST00000261692_length(amino acids)=617AA_BP=521
MIFFSPPFSLSLSLSLPLSLFLLSHPHSRTPPNRTPRRTRIPQRPAVMYSPLCLTQDEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKK
HEKRMSKEEERAVKDELLSEKPEVKQKWASRLLAKLRKDIRPEYREDFVLTVTGKKPPCCVLSNPDQKGKMRRIDCLRQADKVWRLDLVM
VILFKGIPLESTDGERLVKSPQCSNPGLCVQPHHIGVSVKELDLYLAYFVHAADSSQSESPSQPSDADIKDQPENGHLGFQDSFVTSGVF
SVTELVRVSQTPIAAGTGPNFSLSDLESSSYYSMSPGAMRRSLPSTSSTSSTKRLKSVEDEMDSPGEEPFYTGQGRSPGSGSQSSGWHEV
EPGMPSPTTLKKSEKSGFSSPSPSQTSSLGTAFTQHHRPVITGPRASPHATPSTLHFPTSPIIQQPGPYFSHPAIRYHPQETLKEFVQLV
CPDAGQQAGQVGFLNPNGSSQGKVHNPFLPTPMLPPPPPPPMARPVPLPVPDTKPPTTSTEGGAASPTSPTGSVHSPSTSMATSSQYRQL

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

>58863_58863_8_NFIA-CDK2AP1_NFIA_chr1_61872398_ENST00000407417_CDK2AP1_chr12_123751828_ENST00000261692_length(amino acids)=576AA_BP=480
MSILKFLTYSFYIAMDEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKKHEKRMSKEEERAVKDELLSEKPEVKQKWASRLLAKLRKDIR
PEYREDFVLTVTGKKPPCCVLSNPDQKGKMRRIDCLRQADKVWRLDLVMVILFKGIPLESTDGERLVKSPQCSNPGLCVQPHHIGVSVKE
LDLYLAYFVHAADSSQSESPSQPSDADIKDQPENGHLGFQDSFVTSGVFSVTELVRVSQTPIAAGTGPNFSLSDLESSSYYSMSPGAMRR
SLPSTSSTSSTKRLKSVEDEMDSPGEEPFYTGQGRSPGSGSQSSGWHEVEPGMPSPTTLKKSEKSGFSSPSPSQTSSLGTAFTQHHRPVI
TGPRASPHATPSTLHFPTSPIIQQPGPYFSHPAIRYHPQETLKEFVQLVCPDAGQQAGQVGFLNPNGSSQGKVHNPFLPTPMLPPPPPPP
MARPVPLPVPDTKPPTTSTEGGAASPTSPTGSVHSPSTSMATSSQYRQLLSDYGPPSLGYTQGTGNSQVPQSKYAELLAIIEELGKEIRP

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

>58863_58863_9_NFIA-CDK2AP1_NFIA_chr1_61872398_ENST00000485903_CDK2AP1_chr12_123751828_ENST00000261692_length(amino acids)=527AA_BP=431
MYSPLCLTQDEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKKHEKRMSKEEERAVKDELLSEKPEVKQKWASRLLAKLRKDIRPEYRED
FVLTVTGKKPPCCVLSNPDQKGKMRRIDCLRQADKVWRLDLVMVILFKGIPLESTDGERLVKSPQCSNPGLCVQPHHIGVSVKELDLYLA
YFVHAADSSQSESPSQPSDADIKDQPENGHLGFQDSFVTSGVFSVTELVRVSQTPIAAGTGPNFSLSDLESSSYYSMSPGAMRRSLPSTS
STSSTKRLKSVEDEMDSPGEEPFYTGQGRSPGSGSQSSGWHEVEPASPHATPSTLHFPTSPIIQQPGPYFSHPAIRYHPQETLKEFVQLV
CPDAGQQAGQVGFLNPNGSSQGKVHNPFLPTPMLPPPPPPPMARPVPLPVPDTKPPTTSTEGGAASPTSPTGSVHSPSTSMATSSQYRQL

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

>58863_58863_10_NFIA-CDK2AP1_NFIA_chr1_61872399_ENST00000357977_CDK2AP1_chr12_123751829_ENST00000261692_length(amino acids)=219AA_BP=123
MMFSFPAASPHATPSTLHFPTSPIIQQPGPYFSHPAIRYHPQETLKEFVQLVCPDAGQQAGQVGFLNPNGSSQGKVHNPFLPTPMLPPPP
PPPMARPVPLPVPDTKPPTTSTEGGAASPTSPTGSVHSPSTSMATSSQYRQLLSDYGPPSLGYTQGTGNSQVPQSKYAELLAIIEELGKE

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

>58863_58863_11_NFIA-CDK2AP1_NFIA_chr1_61872399_ENST00000371184_CDK2AP1_chr12_123751829_ENST00000261692_length(amino acids)=441AA_BP=345
MYSPLCLTQDEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKKHEKRMSKEEERAVKDELLSEKPEVKQKWASRLLAKLRKDIRPEYRED
FVLTVTGKKPPCCVLSNPDQKGKMRRIDCLRQADKVWRLDLVMVILFKGIPLESTDGERLVKSPQCSNPGLCVQPHHIGVSVKELDLYLA
YFVHAAGMPSPTTLKKSEKSGFSSPSPSQTSSLGTAFTQHHRPVITGPRASPHATPSTLHFPTSPIIQQPGPYFSHPAIRYHPQETLKEF
VQLVCPDAGQQAGQVGFLNPNGSSQGKVHNPFLPTPMLPPPPPPPMARPVPLPVPDTKPPTTSTEGGAASPTSPTGSVHSPSTSMATSSQ

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

>58863_58863_12_NFIA-CDK2AP1_NFIA_chr1_61872399_ENST00000371185_CDK2AP1_chr12_123751829_ENST00000261692_length(amino acids)=548AA_BP=452
MYSPLCLTQDEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKKHEKRMSKEEERAVKDELLSEKPEVKQKWASRLLAKLRKDIRPEYRED
FVLTVTGKKPPCCVLSNPDQKGKMRRIDCLRQADKVWRLDLVMVILFKGIPLESTDGERLVKSPQCSNPGLCVQPHHIGVSVKELDLYLA
YFVHAAGHLGFQDSFVTSGVFSVTELVRVSQTPIAAGTGPNFSLSDLESSSYYSMSPGAMRRSLPSTSSTSSTKRLKSVEDEMDSPGEEP
FYTGQGRSPGSGSQSSGWHEVEPGMPSPTTLKKSEKSGFSSPSPSQTSSLGTAFTQHHRPVITGPRASPHATPSTLHFPTSPIIQQPGPY
FSHPAIRYHPQETLKEFVQLVCPDAGQQAGQVGFLNPNGSSQGKVHNPFLPTPMLPPPPPPPMARPVPLPVPDTKPPTTSTEGGAASPTS
PTGSVHSPSTSMATSSQYRQLLSDYGPPSLGYTQGTGNSQVPQSKYAELLAIIEELGKEIRPTYAGSKSAMERLKRGIIHARGLVRECLA

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

>58863_58863_13_NFIA-CDK2AP1_NFIA_chr1_61872399_ENST00000371187_CDK2AP1_chr12_123751829_ENST00000261692_length(amino acids)=617AA_BP=521
MIFFSPPFSLSLSLSLPLSLFLLSHPHSRTPPNRTPRRTRIPQRPAVMYSPLCLTQDEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKK
HEKRMSKEEERAVKDELLSEKPEVKQKWASRLLAKLRKDIRPEYREDFVLTVTGKKPPCCVLSNPDQKGKMRRIDCLRQADKVWRLDLVM
VILFKGIPLESTDGERLVKSPQCSNPGLCVQPHHIGVSVKELDLYLAYFVHAADSSQSESPSQPSDADIKDQPENGHLGFQDSFVTSGVF
SVTELVRVSQTPIAAGTGPNFSLSDLESSSYYSMSPGAMRRSLPSTSSTSSTKRLKSVEDEMDSPGEEPFYTGQGRSPGSGSQSSGWHEV
EPGMPSPTTLKKSEKSGFSSPSPSQTSSLGTAFTQHHRPVITGPRASPHATPSTLHFPTSPIIQQPGPYFSHPAIRYHPQETLKEFVQLV
CPDAGQQAGQVGFLNPNGSSQGKVHNPFLPTPMLPPPPPPPMARPVPLPVPDTKPPTTSTEGGAASPTSPTGSVHSPSTSMATSSQYRQL

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

>58863_58863_14_NFIA-CDK2AP1_NFIA_chr1_61872399_ENST00000371189_CDK2AP1_chr12_123751829_ENST00000261692_length(amino acids)=615AA_BP=519
MQMCRPASSSVLYVPTRWPGGCGATWQSCPSPPPRRTRIPQRPAVMYSPLCLTQDEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKKHE
KRMSKEEERAVKDELLSEKPEVKQKWASRLLAKLRKDIRPEYREDFVLTVTGKKPPCCVLSNPDQKGKMRRIDCLRQADKVWRLDLVMVI
LFKGIPLESTDGERLVKSPQCSNPGLCVQPHHIGVSVKELDLYLAYFVHAADSSQSESPSQPSDADIKDQPENGHLGFQDSFVTSGVFSV
TELVRVSQTPIAAGTGPNFSLSDLESSSYYSMSPGAMRRSLPSTSSTSSTKRLKSVEDEMDSPGEEPFYTGQGRSPGSGSQSSGWHEVEP
GMPSPTTLKKSEKSGFSSPSPSQTSSLGTAFTQHHRPVITGPRASPHATPSTLHFPTSPIIQQPGPYFSHPAIRYHPQETLKEFVQLVCP
DAGQQAGQVGFLNPNGSSQGKVHNPFLPTPMLPPPPPPPMARPVPLPVPDTKPPTTSTEGGAASPTSPTGSVHSPSTSMATSSQYRQLLS

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

>58863_58863_15_NFIA-CDK2AP1_NFIA_chr1_61872399_ENST00000371191_CDK2AP1_chr12_123751829_ENST00000261692_length(amino acids)=593AA_BP=497
MKLADSVMAGKASDGSIKWQLCYDISARTWWMDEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKKHEKRMSKEEERAVKDELLSEKPEV
KQKWASRLLAKLRKDIRPEYREDFVLTVTGKKPPCCVLSNPDQKGKMRRIDCLRQADKVWRLDLVMVILFKGIPLESTDGERLVKSPQCS
NPGLCVQPHHIGVSVKELDLYLAYFVHAADSSQSESPSQPSDADIKDQPENGHLGFQDSFVTSGVFSVTELVRVSQTPIAAGTGPNFSLS
DLESSSYYSMSPGAMRRSLPSTSSTSSTKRLKSVEDEMDSPGEEPFYTGQGRSPGSGSQSSGWHEVEPGMPSPTTLKKSEKSGFSSPSPS
QTSSLGTAFTQHHRPVITGPRASPHATPSTLHFPTSPIIQQPGPYFSHPAIRYHPQETLKEFVQLVCPDAGQQAGQVGFLNPNGSSQGKV
HNPFLPTPMLPPPPPPPMARPVPLPVPDTKPPTTSTEGGAASPTSPTGSVHSPSTSMATSSQYRQLLSDYGPPSLGYTQGTGNSQVPQSK

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

>58863_58863_16_NFIA-CDK2AP1_NFIA_chr1_61872399_ENST00000403491_CDK2AP1_chr12_123751829_ENST00000261692_length(amino acids)=617AA_BP=521
MIFFSPPFSLSLSLSLPLSLFLLSHPHSRTPPNRTPRRTRIPQRPAVMYSPLCLTQDEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKK
HEKRMSKEEERAVKDELLSEKPEVKQKWASRLLAKLRKDIRPEYREDFVLTVTGKKPPCCVLSNPDQKGKMRRIDCLRQADKVWRLDLVM
VILFKGIPLESTDGERLVKSPQCSNPGLCVQPHHIGVSVKELDLYLAYFVHAADSSQSESPSQPSDADIKDQPENGHLGFQDSFVTSGVF
SVTELVRVSQTPIAAGTGPNFSLSDLESSSYYSMSPGAMRRSLPSTSSTSSTKRLKSVEDEMDSPGEEPFYTGQGRSPGSGSQSSGWHEV
EPGMPSPTTLKKSEKSGFSSPSPSQTSSLGTAFTQHHRPVITGPRASPHATPSTLHFPTSPIIQQPGPYFSHPAIRYHPQETLKEFVQLV
CPDAGQQAGQVGFLNPNGSSQGKVHNPFLPTPMLPPPPPPPMARPVPLPVPDTKPPTTSTEGGAASPTSPTGSVHSPSTSMATSSQYRQL

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

>58863_58863_17_NFIA-CDK2AP1_NFIA_chr1_61872399_ENST00000407417_CDK2AP1_chr12_123751829_ENST00000261692_length(amino acids)=576AA_BP=480
MSILKFLTYSFYIAMDEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKKHEKRMSKEEERAVKDELLSEKPEVKQKWASRLLAKLRKDIR
PEYREDFVLTVTGKKPPCCVLSNPDQKGKMRRIDCLRQADKVWRLDLVMVILFKGIPLESTDGERLVKSPQCSNPGLCVQPHHIGVSVKE
LDLYLAYFVHAADSSQSESPSQPSDADIKDQPENGHLGFQDSFVTSGVFSVTELVRVSQTPIAAGTGPNFSLSDLESSSYYSMSPGAMRR
SLPSTSSTSSTKRLKSVEDEMDSPGEEPFYTGQGRSPGSGSQSSGWHEVEPGMPSPTTLKKSEKSGFSSPSPSQTSSLGTAFTQHHRPVI
TGPRASPHATPSTLHFPTSPIIQQPGPYFSHPAIRYHPQETLKEFVQLVCPDAGQQAGQVGFLNPNGSSQGKVHNPFLPTPMLPPPPPPP
MARPVPLPVPDTKPPTTSTEGGAASPTSPTGSVHSPSTSMATSSQYRQLLSDYGPPSLGYTQGTGNSQVPQSKYAELLAIIEELGKEIRP

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

>58863_58863_18_NFIA-CDK2AP1_NFIA_chr1_61872399_ENST00000485903_CDK2AP1_chr12_123751829_ENST00000261692_length(amino acids)=527AA_BP=431
MYSPLCLTQDEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKKHEKRMSKEEERAVKDELLSEKPEVKQKWASRLLAKLRKDIRPEYRED
FVLTVTGKKPPCCVLSNPDQKGKMRRIDCLRQADKVWRLDLVMVILFKGIPLESTDGERLVKSPQCSNPGLCVQPHHIGVSVKELDLYLA
YFVHAADSSQSESPSQPSDADIKDQPENGHLGFQDSFVTSGVFSVTELVRVSQTPIAAGTGPNFSLSDLESSSYYSMSPGAMRRSLPSTS
STSSTKRLKSVEDEMDSPGEEPFYTGQGRSPGSGSQSSGWHEVEPASPHATPSTLHFPTSPIIQQPGPYFSHPAIRYHPQETLKEFVQLV
CPDAGQQAGQVGFLNPNGSSQGKVHNPFLPTPMLPPPPPPPMARPVPLPVPDTKPPTTSTEGGAASPTSPTGSVHSPSTSMATSSQYRQL

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

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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/chr1:61872399/chr12:123751829)
- 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
NFIA Q12857	CDK2AP1 O14519
FUNCTION: Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication.	FUNCTION: specific inhibitor of the cell-cycle kinase CDK2. {ECO:0000250}.

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

NFIA

chr1:61872398

chr12:123751828

ENST00000371187

1_194

473.3333333333333

499.0

DNA binding

CTF/NF-I

Hgene

NFIA

chr1:61872398

chr12:123751828

ENST00000371189

1_194

518.3333333333334

555.0

DNA binding

CTF/NF-I

Hgene

NFIA

chr1:61872398

chr12:123751828

ENST00000403491

1_194

473.3333333333333

510.0

DNA binding

CTF/NF-I

Hgene

NFIA

chr1:61872398

chr12:123751828

ENST00000407417

1_194

465.3333333333333

502.0

DNA binding

CTF/NF-I

Hgene

NFIA

chr1:61872399

chr12:123751829

ENST00000371187

1_194

473.3333333333333

499.0

DNA binding

CTF/NF-I

Hgene

NFIA

chr1:61872399

chr12:123751829

ENST00000371189

1_194

518.3333333333334

555.0

DNA binding

CTF/NF-I

Hgene

NFIA

chr1:61872399

chr12:123751829

ENST00000403491

1_194

473.3333333333333

510.0

DNA binding

CTF/NF-I

Hgene

NFIA

chr1:61872399

chr12:123751829

ENST00000407417

1_194

465.3333333333333

502.0

DNA binding

CTF/NF-I

Hgene

NFIA

chr1:61872398

chr12:123751828

ENST00000371187

394_402

473.3333333333333

499.0

Motif

9aaTAD

Hgene

NFIA

chr1:61872398

chr12:123751828

ENST00000371189

394_402

518.3333333333334

555.0

Motif

9aaTAD

Hgene

NFIA

chr1:61872398

chr12:123751828

ENST00000403491

394_402

473.3333333333333

510.0

Motif

9aaTAD

Hgene

NFIA

chr1:61872398

chr12:123751828

ENST00000407417

394_402

465.3333333333333

502.0

Motif

9aaTAD

Hgene

NFIA

chr1:61872399

chr12:123751829

ENST00000371187

394_402

473.3333333333333

499.0

Motif

9aaTAD

Hgene

NFIA

chr1:61872399

chr12:123751829

ENST00000371189

394_402

518.3333333333334

555.0

Motif

9aaTAD

Hgene

NFIA

chr1:61872399

chr12:123751829

ENST00000403491

394_402

473.3333333333333

510.0

Motif

9aaTAD

Hgene

NFIA

chr1:61872399

chr12:123751829

ENST00000407417

394_402

465.3333333333333

502.0

Motif

9aaTAD

Tgene

CDK2AP1

chr1:61872398

chr12:123751828

ENST00000535979

1_60

88.0

Region

Note=Intrinsically disordered

Tgene

CDK2AP1

chr1:61872398

chr12:123751828

ENST00000538446

1_60

88.0

Region

Note=Intrinsically disordered

Tgene

CDK2AP1

chr1:61872398

chr12:123751828

ENST00000542174

1_60

88.0

Region

Note=Intrinsically disordered

Tgene

CDK2AP1

chr1:61872398

chr12:123751828

ENST00000544658

1_60

88.0

Region

Note=Intrinsically disordered

Tgene

CDK2AP1

chr1:61872399

chr12:123751829

ENST00000535979

1_60

88.0

Region

Note=Intrinsically disordered

Tgene

CDK2AP1

chr1:61872399

chr12:123751829

ENST00000538446

1_60

88.0

Region

Note=Intrinsically disordered

Tgene

CDK2AP1

chr1:61872399

chr12:123751829

ENST00000542174

1_60

88.0

Region

Note=Intrinsically disordered

Tgene

CDK2AP1

chr1:61872399

chr12:123751829

ENST00000544658

1_60

88.0

Region

Note=Intrinsically disordered

- 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

CDK2AP1

chr1:61872398

chr12:123751828

ENST00000261692

1_60

18.333333333333332

116.0

Region

Note=Intrinsically disordered

Tgene

CDK2AP1

chr1:61872399

chr12:123751829

ENST00000261692

1_60

18.333333333333332

116.0

Region

Note=Intrinsically disordered

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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 >>>1300_NFIA_61872399_CDK2AP1_123751829_1300_NFIA_61872399_CDK2AP1_123751829_ranked_0.pdb	NFIA	61872398	61872399	ENST00000261692	CDK2AP1	chr12	123751829	-	MIFFSPPFSLSLSLSLPLSLFLLSHPHSRTPPNRTPRRTRIPQRPAVMYSPLCLTQDEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKK HEKRMSKEEERAVKDELLSEKPEVKQKWASRLLAKLRKDIRPEYREDFVLTVTGKKPPCCVLSNPDQKGKMRRIDCLRQADKVWRLDLVM VILFKGIPLESTDGERLVKSPQCSNPGLCVQPHHIGVSVKELDLYLAYFVHAADSSQSESPSQPSDADIKDQPENGHLGFQDSFVTSGVF SVTELVRVSQTPIAAGTGPNFSLSDLESSSYYSMSPGAMRRSLPSTSSTSSTKRLKSVEDEMDSPGEEPFYTGQGRSPGSGSQSSGWHEV EPGMPSPTTLKKSEKSGFSSPSPSQTSSLGTAFTQHHRPVITGPRASPHATPSTLHFPTSPIIQQPGPYFSHPAIRYHPQETLKEFVQLV CPDAGQQAGQVGFLNPNGSSQGKVHNPFLPTPMLPPPPPPPMARPVPLPVPDTKPPTTSTEGGAASPTSPTGSVHSPSTSMATSSQYRQL	617

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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.

NFIA_pLDDT.png

CDK2AP1_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
NFIA
CDK2AP1

- 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 NFIA-CDK2AP1

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 NFIA-CDK2AP1

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