Home

Download

Statistics

Examples

Help

Contact

	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:CCDC6-IFIT1 (FusionGDB2 ID:13887)

Fusion Gene Summary for CCDC6-IFIT1

Fusion gene summary

Fusion gene information	Fusion gene name: CCDC6-IFIT1
	Fusion gene ID: 13887
		Hgene	Tgene
	Gene symbol	CCDC6	IFIT1
	Gene ID	8030	3434
	Gene name	coiled-coil domain containing 6	interferon induced protein with tetratricopeptide repeats 1
	Synonyms	D10S170\|H4\|PTC\|TPC\|TST1	C56\|G10P1\|IFI-56\|IFI-56K\|IFI56\|IFIT-1\|IFNAI1\|ISG56\|P56\|RNM561
	Cytomap	10q21.2	10q23.31
	Type of gene	protein-coding	protein-coding
	Description	coiled-coil domain-containing protein 6papillary thyroid carcinoma-encoded protein	interferon-induced protein with tetratricopeptide repeats 1interferon, alpha-inducible protein (MW 56kD)interferon-induced 56 kDa proteininterferon-inducible mRNA 561
	Modification date	20200327	20200313
	UniProtAcc	Q16204	Q5T764
	Ensembl transtripts involved in fusion gene	ENST00000263102,	ENST00000546318, ENST00000371804,
Fusion gene scores	* DoF score	15 X 22 X 10=3300	4 X 2 X 3=24
	# samples	38	4
	** MAII score	log2(38/3300*10)=-3.11839470080223 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(4/24*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Context	PubMed: CCDC6 [Title/Abstract] AND IFIT1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	CCDC6(61612311)-IFIT1(91162038), # 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)

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	IFIT1	GO:0009615	response to virus	19416887
Tgene	IFIT1	GO:0019060	intracellular transport of viral protein in host cell	19008854
Tgene	IFIT1	GO:0032091	negative regulation of protein binding	19416887
Tgene	IFIT1	GO:0045070	positive regulation of viral genome replication	19416887
Tgene	IFIT1	GO:0051097	negative regulation of helicase activity	19008854
Tgene	IFIT1	GO:0071357	cellular response to type I interferon	19008854
Tgene	IFIT1	GO:0071360	cellular response to exogenous dsRNA	19008854

Fusion gene breakpoints across CCDC6 (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 IFIT1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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	STAD	TCGA-BR-A4IY-01A	CCDC6	chr10	61612311	-	IFIT1	chr10	91162038	+

Top

Fusion Gene ORF analysis for CCDC6-IFIT1

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.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
5CDS-5UTR	ENST00000263102	ENST00000546318	CCDC6	chr10	61612311	-	IFIT1	chr10	91162038	+
In-frame	ENST00000263102	ENST00000371804	CCDC6	chr10	61612311	-	IFIT1	chr10	91162038	+

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

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)

ENST00000263102

CCDC6

chr10

61612311

ENST00000371804

IFIT1

chr10

91162038

2393

685

719

2116

465

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
ENST00000263102	ENST00000371804	CCDC6	chr10	61612311	-	IFIT1	chr10	91162038	+	0.001762526	0.9982375

Top

Fusion Genomic Features for CCDC6-IFIT1

FusionAI 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.

Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	1-p	p (fusion gene breakpoint)
CCDC6	chr10	61612310	-	IFIT1	chr10	91162037	+	1.54E-08	1
CCDC6	chr10	61612310	-	IFIT1	chr10	91162037	+	1.54E-08	1

Distribution 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.

Distribution 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.

Top

Fusion Protein Features for CCDC6-IFIT1

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr10:61612311/chr10:91162038)
- 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
CCDC6 Q16204	IFIT1 Q5T764

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.

- In-frame and 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

CCDC6

chr10:61612311

chr10:91162038

ENST00000263102

17_20

151

475.0

Compositional bias

Note=Poly-Ser

Hgene

CCDC6

chr10:61612311

chr10:91162038

ENST00000263102

32_44

151

475.0

Compositional bias

Note=Poly-Gly

Hgene

CCDC6

chr10:61612311

chr10:91162038

ENST00000263102

106_134

151

475.0

Repeat

Note=1

Tgene

IFIT1

chr10:61612311

chr10:91162038

ENST00000371804

139_174

479.0

Repeat

Note=TPR 3

Tgene

IFIT1

chr10:61612311

chr10:91162038

ENST00000371804

183_216

479.0

Repeat

Note=TPR 4

Tgene

IFIT1

chr10:61612311

chr10:91162038

ENST00000371804

218_249

479.0

Repeat

Note=TPR 5

Tgene

IFIT1

chr10:61612311

chr10:91162038

ENST00000371804

251_284

479.0

Repeat

Note=TPR 6

Tgene

IFIT1

chr10:61612311

chr10:91162038

ENST00000371804

305_339

479.0

Repeat

Note=TPR 7

Tgene

IFIT1

chr10:61612311

chr10:91162038

ENST00000371804

340_373

479.0

Repeat

Note=TPR 8

Tgene

IFIT1

chr10:61612311

chr10:91162038

ENST00000371804

378_412

479.0

Repeat

Note=TPR 9

Tgene

IFIT1

chr10:61612311

chr10:91162038

ENST00000371804

437_470

479.0

Repeat

Note=TPR 10

Tgene

IFIT1

chr10:61612311

chr10:91162038

ENST00000371804

52_85

479.0

Repeat

Note=TPR 1

Tgene

IFIT1

chr10:61612311

chr10:91162038

ENST00000371804

95_128

479.0

Repeat

Note=TPR 2

- In-frame and 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

CCDC6

chr10:61612311

chr10:91162038

ENST00000263102

253_332

151

475.0

Coiled coil

Ontology_term=ECO:0000255

Hgene

CCDC6

chr10:61612311

chr10:91162038

ENST00000263102

53_237

151

475.0

Coiled coil

Ontology_term=ECO:0000255

Hgene

CCDC6

chr10:61612311

chr10:91162038

ENST00000263102

440_448

151

475.0

Compositional bias

Note=Poly-Pro

Hgene

CCDC6

chr10:61612311

chr10:91162038

ENST00000263102

442_451

151

475.0

Motif

SH3-binding

Hgene

CCDC6

chr10:61612311

chr10:91162038

ENST00000263102

106_235

151

475.0

Region

Note=5 X 29 AA tandem repeats

Hgene

CCDC6

chr10:61612311

chr10:91162038

ENST00000263102

135_163

151

475.0

Repeat

Note=2

Hgene

CCDC6

chr10:61612311

chr10:91162038

ENST00000263102

164_192

151

475.0

Repeat

Note=3

Hgene

CCDC6

chr10:61612311

chr10:91162038

ENST00000263102

193_206

151

475.0

Repeat

Note=4%3B approximate

Hgene

CCDC6

chr10:61612311

chr10:91162038

ENST00000263102

207_235

151

475.0

Repeat

Note=5

Top

Fusion Gene Sequence for CCDC6-IFIT1

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.

>13887_13887_1_CCDC6-IFIT1_CCDC6_chr10_61612311_ENST00000263102_IFIT1_chr10_91162038_ENST00000371804_length(transcript)=2393nt_BP=685nt
AGTGCAATACTGCCCAAGCCCGGGCGGGGTCTCTGTTCTCTGGCAGAGGAGGTCCCTTGGCAGCGGGAAGCGCCCTCTCTTTCTCTCGCC
GCCGCTCCGAGTCTGCGCCCTGGTGCCAGGCGCTCAGCTCGGCGCTCCCCTGTGCTCGCCCGGCGCCCACTCATTCGCAGCCCGGCCTTC
GTCGCCGCCGCCTCCCTGCTGCTCCTCCTCCTTTCCCCAGCCCGCCGCGGCCATGGCGGACAGCGCCAGCGAGAGCGACACGGACGGGGC
GGGGGGCAACAGCAGCAGCTCGGCCGCCATGCAGTCGTCCTGCTCGTCGACCTCGGGCGGCGGCGGTGGCGGCGGGGGAGGCGGCGGCGG
TGGGAAGTCGGGGGGCATTGTCATCTCGCCGTTCCGCCTGGAGGAGCTCACCAACCGCCTGGCCTCGCTGCAGCAAGAGAACAAGGTGCT
GAAGATAGAGCTGGAGACCTACAAACTGAAGTGCAAGGCACTGCAGGAGGAGAACCGCGACCTGCGCAAAGCCAGCGTGACCATCCAAGC
CAGGGCTGAGCAGGAAGAAGAATTCATTAGTAACACTTTATTCAAGAAAATTCAGGCTTTGCAGAAGGAGAAAGAAACCCTTGCTGTAAA
TTATGAGAAAGAAGAAGAATTCCTCACTAATGAGCTCTCCAGAAAATTGATGCAGTACAAATGGTGATGATCATCAGGTCAAGGATAGTC
TGGAGCAATTGAGATGTCACTTTACATGGGAGTTATCCATTGATGACGATGAAATGCCTGATTTAGAAAACAGAGTCTTGGATCAGATTG
AATTCCTAGACACCAAATACAGTGTGGGAATACACAACCTACTAGCCTATGTGAAACACCTGAAAGGCCAGAATGAGGAAGCCCTGAAGA
GCTTAAAAGAAGCTGAAAACTTAATGCAGGAAGAACATGACAACCAAGCAAATGTGAGGAGTCTGGTGACCTGGGGCAACTTTGCCTGGA
TGTATTACCACATGGGCAGACTGGCAGAAGCCCAGACTTACCTGGACAAGGTGGAGAACATTTGCAAGAAGCTTTCAAATCCCTTCCGCT
ATAGAATGGAGTGTCCAGAAATAGACTGTGAGGAAGGATGGGCCTTGCTGAAGTGTGGAGGAAAAAATTATGAACGGGCCAAGGCCTGCT
TTGAAAAGGTGCTTGAAGTGGACCCTGAAAACCCTGAATCCAGCGCTGGGTATGCGATCTCTGCCTATCGCCTGGATGGCTTTAAATTAG
CCACAAAAAATCACAAGCCATTTTCTTTGCTTCCCCTAAGGCAGGCTGTCCGCTTAAATCCAGACAATGGATATATTAAGGTTCTCCTTG
CCCTGAAGCTTCAGGATGAAGGACAGGAAGCTGAAGGAGAAAAGTACATTGAAGAAGCTCTAGCCAACATGTCCTCACAGACCTATGTCT
TTCGATATGCAGCCAAGTTTTACCGAAGAAAAGGCTCTGTGGATAAAGCTCTTGAGTTATTAAAAAAGGCCTTGCAGGAAACACCCACTT
CTGTCTTACTGCATCACCAGATAGGGCTTTGCTACAAGGCACAAATGATCCAAATCAAGGAGGCTACAAAAGGGCAGCCTAGAGGGCAGA
ACAGAGAAAAGCTAGACAAAATGATAAGATCAGCCATATTTCATTTTGAATCTGCAGTGGAAAAAAAGCCCACATTTGAGGTGGCTCATC
TAGACCTGGCAAGAATGTATATAGAAGCAGGCAATCACAGAAAAGCTGAAGAGAATTTTCAAAAATTGTTATGCATGAAACCAGTGGTAG
AAGAAACAATGCAAGACATACATTTCCACTATGGTCGGTTTCAGGAATTTCAAAAGAAATCTGACGTCAATGCAATTATCCATTATTTAA
AAGCTATAAAAATAGAACAGGCATCATTAACAAGGGATAAAAGTATCAATTCTTTGAAGAAATTGGTTTTAAGGAAACTTCGGAGAAAGG
CATTAGATCTGGAAAGCTTGAGCCTCCTTGGGTTCGTCTACAAATTGGAAGGAAATATGAATGAAGCCCTGGAGTACTATGAGCGGGCCC
TGAGACTGGCTGCTGACTTTGAGAACTCTGTGAGACAAGGTCCTTAGGCACCCAGATATCAGCCACTTTCACATTTCATTTCATTTTATG
CTAACATTTACTAATCATCTTTTCTGCTTACTGTTTTCAGAAACATTATAATTCACTGTAATGATGTAATTCTTGAATAATAAATCTGAC
AAAATATTAGTTGTGTTCAACAATTAGTGAAACAGAATGTGTGTATGCATGTAAGAAAGAGAAATCATTTGTATGAGTGCTATGTAGTAG

>13887_13887_1_CCDC6-IFIT1_CCDC6_chr10_61612311_ENST00000263102_IFIT1_chr10_91162038_ENST00000371804_length(amino acids)=465AA_BP=2
MEQLRCHFTWELSIDDDEMPDLENRVLDQIEFLDTKYSVGIHNLLAYVKHLKGQNEEALKSLKEAENLMQEEHDNQANVRSLVTWGNFAW
MYYHMGRLAEAQTYLDKVENICKKLSNPFRYRMECPEIDCEEGWALLKCGGKNYERAKACFEKVLEVDPENPESSAGYAISAYRLDGFKL
ATKNHKPFSLLPLRQAVRLNPDNGYIKVLLALKLQDEGQEAEGEKYIEEALANMSSQTYVFRYAAKFYRRKGSVDKALELLKKALQETPT
SVLLHHQIGLCYKAQMIQIKEATKGQPRGQNREKLDKMIRSAIFHFESAVEKKPTFEVAHLDLARMYIEAGNHRKAEENFQKLLCMKPVV
EETMQDIHFHYGRFQEFQKKSDVNAIIHYLKAIKIEQASLTRDKSINSLKKLVLRKLRRKALDLESLSLLGFVYKLEGNMNEALEYYERA

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

Top

Fusion Gene PPI Analysis for CCDC6-IFIT1

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 (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner	Gene	Hbp	Tbp	ENST	Strand	BPexon	TotalExon	Protein feature loci	*BPloci	TotalLen	Still interaction with
Tgene	IFIT1	chr10:61612311	chr10:91162038	ENST00000371804		0	2	256_262	1.6666666666666667	479.0	the 5'-triphosphate group of PPP-RNA

- Lost PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

Top

Related Drugs for CCDC6-IFIT1

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

Top

Related Diseases for CCDC6-IFIT1

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source