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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:TK1-AFMID (FusionGDB2 ID:90438)

Fusion Gene Summary for TK1-AFMID

check button Fusion gene summary
Fusion gene informationFusion gene name: TK1-AFMID
Fusion gene ID: 90438
HgeneTgene
Gene symbol

TK1

AFMID

Gene ID

7083

125061

Gene namethymidine kinase 1arylformamidase
SynonymsTK2FKF|KF|KFA
Cytomap

17q25.3

17q25.3

Type of geneprotein-codingprotein-coding
Descriptionthymidine kinase, cytosoliccytosolic thymidine kinaseepididymis secretory sperm binding proteinthymidine kinase 1 soluble isoformkynurenine formamidaseKFaseN-formylkynurenine formamidaseprobable arylformamidase
Modification date2020031320200313
UniProtAcc.

Q63HM1

Ensembl transtripts involved in fusion geneENST00000301634, ENST00000405273, 
ENST00000588734, ENST00000590862, 
ENST00000590430, 		ENST00000409257, 
ENST00000589256, ENST00000588800, 
ENST00000591952, ENST00000327898, 
ENST00000586731, ENST00000589664, 
Fusion gene scores* DoF score5 X 5 X 4=1006 X 6 X 5=180
# samples 68
** MAII scorelog2(6/100*10)=-0.736965594166206
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/180*10)=-1.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TK1 [Title/Abstract] AND AFMID [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTK1(76171131)-AFMID(76187051), # samples:1
Anticipated loss of major functional domain due to fusion event.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID

check buttonFusion gene breakpoints across TK1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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

check button 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4UCECTCGA-EY-A2ON-01ATK1chr17

76171131

-AFMIDchr17

76187051

+


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Fusion Gene ORF analysis for TK1-AFMID

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
In-frameENST00000301634ENST00000409257TK1chr17

76171131

-AFMIDchr17

76187051

+
In-frameENST00000301634ENST00000589256TK1chr17

76171131

-AFMIDchr17

76187051

+
In-frameENST00000301634ENST00000588800TK1chr17

76171131

-AFMIDchr17

76187051

+
In-frameENST00000301634ENST00000591952TK1chr17

76171131

-AFMIDchr17

76187051

+
In-frameENST00000301634ENST00000327898TK1chr17

76171131

-AFMIDchr17

76187051

+
In-frameENST00000301634ENST00000586731TK1chr17

76171131

-AFMIDchr17

76187051

+
5CDS-intronENST00000301634ENST00000589664TK1chr17

76171131

-AFMIDchr17

76187051

+
In-frameENST00000405273ENST00000409257TK1chr17

76171131

-AFMIDchr17

76187051

+
In-frameENST00000405273ENST00000589256TK1chr17

76171131

-AFMIDchr17

76187051

+
In-frameENST00000405273ENST00000588800TK1chr17

76171131

-AFMIDchr17

76187051

+
In-frameENST00000405273ENST00000591952TK1chr17

76171131

-AFMIDchr17

76187051

+
In-frameENST00000405273ENST00000327898TK1chr17

76171131

-AFMIDchr17

76187051

+
In-frameENST00000405273ENST00000586731TK1chr17

76171131

-AFMIDchr17

76187051

+
5CDS-intronENST00000405273ENST00000589664TK1chr17

76171131

-AFMIDchr17

76187051

+
intron-3CDSENST00000588734ENST00000409257TK1chr17

76171131

-AFMIDchr17

76187051

+
intron-3CDSENST00000588734ENST00000589256TK1chr17

76171131

-AFMIDchr17

76187051

+
intron-3CDSENST00000588734ENST00000588800TK1chr17

76171131

-AFMIDchr17

76187051

+
intron-3CDSENST00000588734ENST00000591952TK1chr17

76171131

-AFMIDchr17

76187051

+
intron-3CDSENST00000588734ENST00000327898TK1chr17

76171131

-AFMIDchr17

76187051

+
intron-3CDSENST00000588734ENST00000586731TK1chr17

76171131

-AFMIDchr17

76187051

+
intron-intronENST00000588734ENST00000589664TK1chr17

76171131

-AFMIDchr17

76187051

+
In-frameENST00000590862ENST00000409257TK1chr17

76171131

-AFMIDchr17

76187051

+
In-frameENST00000590862ENST00000589256TK1chr17

76171131

-AFMIDchr17

76187051

+
In-frameENST00000590862ENST00000588800TK1chr17

76171131

-AFMIDchr17

76187051

+
In-frameENST00000590862ENST00000591952TK1chr17

76171131

-AFMIDchr17

76187051

+
In-frameENST00000590862ENST00000327898TK1chr17

76171131

-AFMIDchr17

76187051

+
In-frameENST00000590862ENST00000586731TK1chr17

76171131

-AFMIDchr17

76187051

+
5CDS-intronENST00000590862ENST00000589664TK1chr17

76171131

-AFMIDchr17

76187051

+
intron-3CDSENST00000590430ENST00000409257TK1chr17

76171131

-AFMIDchr17

76187051

+
intron-3CDSENST00000590430ENST00000589256TK1chr17

76171131

-AFMIDchr17

76187051

+
intron-3CDSENST00000590430ENST00000588800TK1chr17

76171131

-AFMIDchr17

76187051

+
intron-3CDSENST00000590430ENST00000591952TK1chr17

76171131

-AFMIDchr17

76187051

+
intron-3CDSENST00000590430ENST00000327898TK1chr17

76171131

-AFMIDchr17

76187051

+
intron-3CDSENST00000590430ENST00000586731TK1chr17

76171131

-AFMIDchr17

76187051

+
intron-intronENST00000590430ENST00000589664TK1chr17

76171131

-AFMIDchr17

76187051

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF 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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for TK1-AFMID


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)
TK1chr1776171130-AFMIDchr1776187050+1.01E-050.99998987
TK1chr1776171130-AFMIDchr1776187050+1.01E-050.99998987

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for TK1-AFMID


check button Go to

FGviewer for the breakpoints of chr17:76171131-chr17:76187051

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.AFMID

Q63HM1

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: Catalyzes the hydrolysis of N-formyl-L-kynurenine to L-kynurenine, the second step in the kynurenine pathway of tryptophan degradation. Kynurenine may be further oxidized to nicotinic acid, NAD(H) and NADP(H). Required for elimination of toxic metabolites. {ECO:0000255|HAMAP-Rule:MF_03014}.

check buttonRetention 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.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneTK1chr17:76171131chr17:76187051ENST00000301634-6726_33171.0235.0Nucleotide bindingATP
HgeneTK1chr17:76171131chr17:76187051ENST00000301634-6758_60171.0235.0Nucleotide bindingATP
HgeneTK1chr17:76171131chr17:76187051ENST00000301634-6797_100171.0235.0Nucleotide bindingATP
HgeneTK1chr17:76171131chr17:76187051ENST00000405273-6826_33171.0350.0Nucleotide bindingATP
HgeneTK1chr17:76171131chr17:76187051ENST00000405273-6858_60171.0350.0Nucleotide bindingATP
HgeneTK1chr17:76171131chr17:76187051ENST00000405273-6897_100171.0350.0Nucleotide bindingATP
TgeneAFMIDchr17:76171131chr17:76187051ENST0000032789801195_9921.0309.0MotifNote=HGGXW
TgeneAFMIDchr17:76171131chr17:76187051ENST0000040925701195_9921.0304.0MotifNote=HGGXW

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneTK1chr17:76171131chr17:76187051ENST00000301634-67172_176171.0235.0RegionSubstrate binding
HgeneTK1chr17:76171131chr17:76187051ENST00000405273-68172_176171.0350.0RegionSubstrate binding


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Fusion Gene Sequence for TK1-AFMID


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for TK1-AFMID


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for TK1-AFMID


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for TK1-AFMID


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneTK1C0009402Colorectal Carcinoma1CTD_human
HgeneTK1C0009404Colorectal Neoplasms1CTD_human
HgeneTK1C0019207Hepatoma, Morris1CTD_human
HgeneTK1C0019208Hepatoma, Novikoff1CTD_human
HgeneTK1C0023904Liver Neoplasms, Experimental1CTD_human
HgeneTK1C0086404Experimental Hepatoma1CTD_human
HgeneTK1C0152013Adenocarcinoma of lung (disorder)1CTD_human
HgeneTK1C2239176Liver carcinoma1CTD_human