UTHEALTH HOME ABOUT SBMI A-Z WEBMAIL INSIDE THE UNIVERSITY

Home

Download

Statistics

Examples

Help

Contact

level1

	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:CIRBP-PKNOX1

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: CIRBP-PKNOX1
	FusionPDB ID: 16835
	FusionGDB2.0 ID: 16835
		Hgene	Tgene
	Gene symbol	CIRBP	PKNOX1
	Gene ID	1153	5316
	Gene name	cold inducible RNA binding protein	PBX/knotted 1 homeobox 1
	Synonyms	CIRP	PREP1\|pkonx1c
	Cytomap	19p13.3	21q22.3
	Type of gene	protein-coding	protein-coding
	Description	cold-inducible RNA-binding proteinA18 hnRNPglycine-rich RNA binding proteintesticular tissue protein Li 39	homeobox protein PKNOX1PBX/knotted homeobox 1Pbx regulating protein-1homeobox protein PREP-1human homeobox-containing protein
	Modification date	20200327	20200313
	UniProtAcc	Q14011	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000320936, ENST00000444172, ENST00000585630, ENST00000586472, ENST00000586773, ENST00000587323, ENST00000587896, ENST00000588030, ENST00000588090, ENST00000588230, ENST00000589235, ENST00000589660, ENST00000589686, ENST00000589710, ENST00000591935, ENST00000413636, ENST00000590188,	ENST00000607150, ENST00000291547, ENST00000432907,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	12 X 7 X 6=504	13 X 10 X 6=780
	# samples	13	15
	** MAII score	log2(13/504*10)=-1.95491211047146 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(15/780*10)=-2.37851162325373 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: CIRBP [Title/Abstract] AND PKNOX1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	CIRBP(1271411)-PKNOX1(44450156), # samples:1
Anticipated loss of major functional domain due to fusion event.	CIRBP-PKNOX1 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. CIRBP-PKNOX1 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. CIRBP-PKNOX1 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. CIRBP-PKNOX1 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. CIRBP-PKNOX1 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF. CIRBP-PKNOX1 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	CIRBP	GO:0009411	response to UV	11574538
Hgene	CIRBP	GO:0045727	positive regulation of translation	11574538
Hgene	CIRBP	GO:0048255	mRNA stabilization	11574538

Fusion gene breakpoints across CIRBP (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 PKNOX1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Top

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
ChiTaRS5.0	N/A	DA500684	CIRBP	chr19	1271411	+	PKNOX1	chr21	44450156	+

Top

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)
ENST00000588030	CIRBP	chr19	1271411	+	ENST00000432907	PKNOX1	chr21	44450156	+	810	525	26	601	191
ENST00000589660	CIRBP	chr19	1271411	+	ENST00000432907	PKNOX1	chr21	44450156	+	605	320	55	396	113
ENST00000588090	CIRBP	chr19	1271411	+	ENST00000432907	PKNOX1	chr21	44450156	+	761	476	118	552	144
ENST00000591935	CIRBP	chr19	1271411	+	ENST00000432907	PKNOX1	chr21	44450156	+	620	335	46	411	121
ENST00000589710	CIRBP	chr19	1271411	+	ENST00000432907	PKNOX1	chr21	44450156	+	697	412	132	488	118
ENST00000588230	CIRBP	chr19	1271411	+	ENST00000432907	PKNOX1	chr21	44450156	+	635	350	64	426	120
ENST00000586472	CIRBP	chr19	1271411	+	ENST00000432907	PKNOX1	chr21	44450156	+	635	350	64	426	120
ENST00000589686	CIRBP	chr19	1271411	+	ENST00000432907	PKNOX1	chr21	44450156	+	696	411	131	487	118
ENST00000444172	CIRBP	chr19	1271411	+	ENST00000432907	PKNOX1	chr21	44450156	+	525	240	125	316	63
ENST00000587323	CIRBP	chr19	1271411	+	ENST00000432907	PKNOX1	chr21	44450156	+	630	345	59	421	120
ENST00000320936	CIRBP	chr19	1271411	+	ENST00000432907	PKNOX1	chr21	44450156	+	630	345	59	421	120
ENST00000587896	CIRBP	chr19	1271411	+	ENST00000432907	PKNOX1	chr21	44450156	+	621	336	11	412	133
ENST00000589235	CIRBP	chr19	1271411	+	ENST00000432907	PKNOX1	chr21	44450156	+	617	332	46	408	120
ENST00000585630	CIRBP	chr19	1271411	+	ENST00000432907	PKNOX1	chr21	44450156	+	618	333	53	409	118
ENST00000586773	CIRBP	chr19	1271411	+	ENST00000432907	PKNOX1	chr21	44450156	+	599	314	34	390	118

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
ENST00000588030	ENST00000432907	CIRBP	chr19	1271411	+	PKNOX1	chr21	44450156	+	0.46627837	0.5337217
ENST00000589660	ENST00000432907	CIRBP	chr19	1271411	+	PKNOX1	chr21	44450156	+	0.3026048	0.6973952
ENST00000588090	ENST00000432907	CIRBP	chr19	1271411	+	PKNOX1	chr21	44450156	+	0.52368414	0.47631583
ENST00000591935	ENST00000432907	CIRBP	chr19	1271411	+	PKNOX1	chr21	44450156	+	0.5232948	0.4767052
ENST00000589710	ENST00000432907	CIRBP	chr19	1271411	+	PKNOX1	chr21	44450156	+	0.46131095	0.538689
ENST00000588230	ENST00000432907	CIRBP	chr19	1271411	+	PKNOX1	chr21	44450156	+	0.4540677	0.5459323
ENST00000586472	ENST00000432907	CIRBP	chr19	1271411	+	PKNOX1	chr21	44450156	+	0.4540677	0.5459323
ENST00000589686	ENST00000432907	CIRBP	chr19	1271411	+	PKNOX1	chr21	44450156	+	0.43979123	0.5602088
ENST00000444172	ENST00000432907	CIRBP	chr19	1271411	+	PKNOX1	chr21	44450156	+	0.882474	0.11752604
ENST00000587323	ENST00000432907	CIRBP	chr19	1271411	+	PKNOX1	chr21	44450156	+	0.45305884	0.54694116
ENST00000320936	ENST00000432907	CIRBP	chr19	1271411	+	PKNOX1	chr21	44450156	+	0.45305884	0.54694116
ENST00000587896	ENST00000432907	CIRBP	chr19	1271411	+	PKNOX1	chr21	44450156	+	0.4769931	0.5230069
ENST00000589235	ENST00000432907	CIRBP	chr19	1271411	+	PKNOX1	chr21	44450156	+	0.43894953	0.5610505
ENST00000585630	ENST00000432907	CIRBP	chr19	1271411	+	PKNOX1	chr21	44450156	+	0.3642256	0.6357744
ENST00000586773	ENST00000432907	CIRBP	chr19	1271411	+	PKNOX1	chr21	44450156	+	0.36507106	0.63492894

Top

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

>16835_16835_1_CIRBP-PKNOX1_CIRBP_chr19_1271411_ENST00000320936_PKNOX1_chr21_44450156_ENST00000432907_length(amino acids)=120AA_BP=96
MPDSVAAMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKGGRGFFRGGRGRG

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

>16835_16835_2_CIRBP-PKNOX1_CIRBP_chr19_1271411_ENST00000444172_PKNOX1_chr21_44450156_ENST00000432907_length(amino acids)=63AA_BP=39

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

>16835_16835_3_CIRBP-PKNOX1_CIRBP_chr19_1271411_ENST00000585630_PKNOX1_chr21_44450156_ENST00000432907_length(amino acids)=118AA_BP=94
MPQAAMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKGGRGFFRGGRGRGRG

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

>16835_16835_4_CIRBP-PKNOX1_CIRBP_chr19_1271411_ENST00000586472_PKNOX1_chr21_44450156_ENST00000432907_length(amino acids)=120AA_BP=96
MPDSVAAMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKGGRGFFRGGRGRG

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

>16835_16835_5_CIRBP-PKNOX1_CIRBP_chr19_1271411_ENST00000586773_PKNOX1_chr21_44450156_ENST00000432907_length(amino acids)=118AA_BP=94
MPQAAMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKGGRGFFRGGRGRGRG

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

>16835_16835_6_CIRBP-PKNOX1_CIRBP_chr19_1271411_ENST00000587323_PKNOX1_chr21_44450156_ENST00000432907_length(amino acids)=120AA_BP=96
MPDSVAAMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKGGRGFFRGGRGRG

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

>16835_16835_7_CIRBP-PKNOX1_CIRBP_chr19_1271411_ENST00000587896_PKNOX1_chr21_44450156_ENST00000432907_length(amino acids)=133AA_BP=109
MWCAVFPLASGTCPTQCVAAMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGK

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

>16835_16835_8_CIRBP-PKNOX1_CIRBP_chr19_1271411_ENST00000588030_PKNOX1_chr21_44450156_ENST00000432907_length(amino acids)=191AA_BP=167
MPACFVAWAGPWPPQDLPVWGRRDHQLSPATGVGDSHSATPTCSPSWSLTSVWLAAGRSPGRLGGPRTPQGTLGWQAAMASDEGKLFVGG
LSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKGGRGFFRGGRGRGRGFSRGPLPTSAGWSWRTV

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

>16835_16835_9_CIRBP-PKNOX1_CIRBP_chr19_1271411_ENST00000588090_PKNOX1_chr21_44450156_ENST00000432907_length(amino acids)=144AA_BP=120
MRPPVGTQDRGEIPGSHGCSQTQLTPEAQAAMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDD

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

>16835_16835_10_CIRBP-PKNOX1_CIRBP_chr19_1271411_ENST00000588230_PKNOX1_chr21_44450156_ENST00000432907_length(amino acids)=120AA_BP=96
MPDSVAAMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKGGRGFFRGGRGRG

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

>16835_16835_11_CIRBP-PKNOX1_CIRBP_chr19_1271411_ENST00000589235_PKNOX1_chr21_44450156_ENST00000432907_length(amino acids)=120AA_BP=96
MPDSVAAMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKGGRGFFRGGRGRG

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

>16835_16835_12_CIRBP-PKNOX1_CIRBP_chr19_1271411_ENST00000589660_PKNOX1_chr21_44450156_ENST00000432907_length(amino acids)=113AA_BP=89
MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKGGRGFFRGGRGRGRGFSRGP

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

>16835_16835_13_CIRBP-PKNOX1_CIRBP_chr19_1271411_ENST00000589686_PKNOX1_chr21_44450156_ENST00000432907_length(amino acids)=118AA_BP=94
MPQAAMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKGGRGFFRGGRGRGRG

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

>16835_16835_14_CIRBP-PKNOX1_CIRBP_chr19_1271411_ENST00000589710_PKNOX1_chr21_44450156_ENST00000432907_length(amino acids)=118AA_BP=94
MPQAAMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKGGRGFFRGGRGRGRG

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

>16835_16835_15_CIRBP-PKNOX1_CIRBP_chr19_1271411_ENST00000591935_PKNOX1_chr21_44450156_ENST00000432907_length(amino acids)=121AA_BP=97
MTPEAQAAMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKGGRGFFRGGRGR

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

Top

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/chr19:1271411/chr21:44450156)
- 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
CIRBP Q14011	.
FUNCTION: Cold-inducible mRNA binding protein that plays a protective role in the genotoxic stress response by stabilizing transcripts of genes involved in cell survival. Acts as a translational activator. Seems to play an essential role in cold-induced suppression of cell proliferation. Binds specifically to the 3'-untranslated regions (3'-UTRs) of stress-responsive transcripts RPA2 and TXN. Acts as a translational repressor (By similarity). Promotes assembly of stress granules (SGs), when overexpressed. {ECO:0000250, ECO:0000269\|PubMed:11574538, ECO:0000269\|PubMed:16513844}.	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.

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

PKNOX1

chr19:1271411

chr21:44450156

ENST00000291547

259_321

437.0

DNA binding

Homeobox%3B TALE-type

- 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

CIRBP

chr19:1271411

chr21:44450156

ENST00000320936

92_158

173.0

Compositional bias

Note=Gly-rich

Hgene

CIRBP

chr19:1271411

chr21:44450156

ENST00000585630

92_158

173.0

Compositional bias

Note=Gly-rich

Hgene

CIRBP

chr19:1271411

chr21:44450156

ENST00000586472

92_158

173.0

Compositional bias

Note=Gly-rich

Hgene

CIRBP

chr19:1271411

chr21:44450156

ENST00000588030

92_158

173.0

Compositional bias

Note=Gly-rich

Hgene

CIRBP

chr19:1271411

chr21:44450156

ENST00000588090

92_158

173.0

Compositional bias

Note=Gly-rich

Hgene

CIRBP

chr19:1271411

chr21:44450156

ENST00000589660

92_158

173.0

Compositional bias

Note=Gly-rich

Hgene

CIRBP

chr19:1271411

chr21:44450156

ENST00000320936

6_84

173.0

Domain

RRM

Hgene

CIRBP

chr19:1271411

chr21:44450156

ENST00000585630

6_84

173.0

Domain

RRM

Hgene

CIRBP

chr19:1271411

chr21:44450156

ENST00000586472

6_84

173.0

Domain

RRM

Hgene

CIRBP

chr19:1271411

chr21:44450156

ENST00000588030

6_84

173.0

Domain

RRM

Hgene

CIRBP

chr19:1271411

chr21:44450156

ENST00000588090

6_84

173.0

Domain

RRM

Hgene

CIRBP

chr19:1271411

chr21:44450156

ENST00000589660

6_84

173.0

Domain

RRM

Top

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
CIRBP
PKNOX1

- 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

Top

Related Drugs to CIRBP-PKNOX1

Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to CIRBP-PKNOX1

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