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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:LSM7-IQGAP1 (FusionGDB2 ID:49978)

Fusion Gene Summary for LSM7-IQGAP1

check button Fusion gene summary
Fusion gene informationFusion gene name: LSM7-IQGAP1
Fusion gene ID: 49978
HgeneTgene
Gene symbol

LSM7

IQGAP1

Gene ID

51690

8826

Gene nameLSM7 homolog, U6 small nuclear RNA and mRNA degradation associatedIQ motif containing GTPase activating protein 1
SynonymsYNL147WHUMORFA01|SAR1|p195
Cytomap

19p13.3

15q26.1

Type of geneprotein-codingprotein-coding
DescriptionU6 snRNA-associated Sm-like protein LSm7LSM7 U6 small nuclear RNA and mRNA degradation associatedLSM7 homolog, U6 small nuclear RNA associatedras GTPase-activating-like protein IQGAP1RasGAP-like with IQ motifs
Modification date2020031320200327
UniProtAcc.

P46940

Ensembl transtripts involved in fusion geneENST00000252622, ENST00000589532, 
ENST00000268182, ENST00000560738, 
ENST00000560020, 
Fusion gene scores* DoF score3 X 3 X 3=2717 X 15 X 7=1785
# samples 419
** MAII scorelog2(4/27*10)=0.567040592723894
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(19/1785*10)=-3.23185275058551
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LSM7 [Title/Abstract] AND IQGAP1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLSM7(2328386)-IQGAP1(91030186), # 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
HgeneLSM7

GO:0000398

mRNA splicing, via spliceosome

28781166

TgeneIQGAP1

GO:0071277

cellular response to calcium ion

18567582


check buttonFusion gene breakpoints across LSM7 (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 IQGAP1 (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
ChimerDB4Non-CancerERR315349LSM7chr19

2328386

-IQGAP1chr15

91030186

+


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Fusion Gene ORF analysis for LSM7-IQGAP1

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-frameENST00000252622ENST00000268182LSM7chr19

2328386

-IQGAP1chr15

91030186

+
In-frameENST00000252622ENST00000560738LSM7chr19

2328386

-IQGAP1chr15

91030186

+
5CDS-intronENST00000252622ENST00000560020LSM7chr19

2328386

-IQGAP1chr15

91030186

+
intron-3CDSENST00000589532ENST00000268182LSM7chr19

2328386

-IQGAP1chr15

91030186

+
intron-3CDSENST00000589532ENST00000560738LSM7chr19

2328386

-IQGAP1chr15

91030186

+
intron-intronENST00000589532ENST00000560020LSM7chr19

2328386

-IQGAP1chr15

91030186

+

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)
ENST00000252622LSM7chr192328386-ENST00000268182IQGAP1chr1591030186+3236151271100357
ENST00000252622LSM7chr192328386-ENST00000560738IQGAP1chr1591030186+1364151271100357

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
ENST00000252622ENST00000268182LSM7chr192328386-IQGAP1chr1591030186+0.0002263780.9997737
ENST00000252622ENST00000560738LSM7chr192328386-IQGAP1chr1591030186+0.0017112210.9982888

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Fusion Genomic Features for LSM7-IQGAP1


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)
LSM7chr192328385-IQGAP1chr1591030185+1.26E-050.99998736
LSM7chr192328385-IQGAP1chr1591030185+1.26E-050.99998736

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 LSM7-IQGAP1


check button Go to

FGviewer for the breakpoints of chr19:2328386-chr15:91030186

.
- 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
.IQGAP1

P46940

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: Plays a crucial role in regulating the dynamics and assembly of the actin cytoskeleton. Binds to activated CDC42 but does not stimulate its GTPase activity. It associates with calmodulin. Could serve as an assembly scaffold for the organization of a multimolecular complex that would interface incoming signals to the reorganization of the actin cytoskeleton at the plasma membrane. May promote neurite outgrowth (PubMed:15695813). May play a possible role in cell cycle regulation by contributing to cell cycle progression after DNA replication arrest (PubMed:20883816). {ECO:0000269|PubMed:15695813, ECO:0000269|PubMed:20883816}.

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

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneIQGAP1chr19:2328386chr15:91030186ENST0000026818230381004_12371341.33333333333331658.0DomainRas-GAP
TgeneIQGAP1chr19:2328386chr15:91030186ENST00000268182303844_1591341.33333333333331658.0DomainCalponin-homology (CH)
TgeneIQGAP1chr19:2328386chr15:91030186ENST000002681823038679_7121341.33333333333331658.0DomainWW
TgeneIQGAP1chr19:2328386chr15:91030186ENST000002681823038745_7741341.33333333333331658.0DomainIQ 1
TgeneIQGAP1chr19:2328386chr15:91030186ENST000002681823038775_8041341.33333333333331658.0DomainIQ 2
TgeneIQGAP1chr19:2328386chr15:91030186ENST000002681823038805_8341341.33333333333331658.0DomainIQ 3
TgeneIQGAP1chr19:2328386chr15:91030186ENST000002681823038835_8641341.33333333333331658.0DomainIQ 4
TgeneIQGAP1chr19:2328386chr15:91030186ENST0000026818230381276_16571341.33333333333331658.0RegionNote=C2
TgeneIQGAP1chr19:2328386chr15:91030186ENST000002681823038956_12741341.33333333333331658.0RegionNote=C1


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Fusion Gene Sequence for LSM7-IQGAP1


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.
>In-frame_ENST00000252622_ENST00000268182_ERR315349_LSM7_chr19_2328386_-_IQGAP1_chr15_91030186_length(transcript)=3236nt_BP=151nt
GGGAGGTCAAAGGGCGCGGGGCGGTGCCTGCGAAGAGCCACACGGCGCGACAAGATGGCGGATAAGGAGAAGAAGAAAAAGGAGAGCATC
TTGGACTTGTCCAAGTACATCGACAAGACGATCCGGGTAAAGTTCCAGGGAGGCCGCGAAGGGGAAAGCTCTGGCAATTTAAATGACCCA
AATAAGGAGGCACTGGCTAAGACGGAAGTGTCTCTCACCCTGACCAACAAGTTCGACGTGCCTGGAGATGAGAATGCAGAAATGGATGCT
CGAACCATCTTACTGAATACAAAACGTTTAATTGTGGATGTCATCCGGTTCCAGCCAGGAGAGACCTTGACTGAAATCCTAGAAACACCA
GCCACCAGTGAACAGGAAGCAGAACATCAGAGAGCCATGCAGAGACGTGCTATCCGTGATGCCAAAACACCTGACAAGATGAAAAAGTCA
AAATCTGTAAAGGAAGACAGCAACCTCACTCTTCAAGAGAAGAAAGAGAAGATCCAGACAGGTTTAAAGAAGCTAACAGAGCTTGGAACC
GTGGACCCAAAGAACAAATACCAGGAACTGATCAACGACATTGCCAGGGATATTCGGAATCAGCGGAGGTACCGACAGAGGAGAAAGGCC
GAACTAGTGAAACTGCAACAGACATACGCTGCTCTGAACTCTAAGGCCACCTTTTATGGGGAGCAGGTGGATTACTATAAAAGCTATATC
AAAACCTGCTTGGATAACTTAGCCAGCAAGGGCAAAGTCTCCAAAAAGCCTAGGGAAATGAAAGGAAAGAAAAGCAAAAAGATTTCTCTG
AAATATACAGCAGCAAGACTACATGAAAAAGGAGTTCTTCTGGAAATTGAGGACCTGCAAGTGAATCAGTTTAAAAATGTTATATTTGAA
ATCAGTCCAACAGAAGAAGTTGGAGACTTCGAAGTGAAAGCCAAATTCATGGGAGTTCAAATGGAGACTTTTATGTTACATTATCAGGAC
CTGCTGCAGCTACAGTATGAAGGAGTTGCAGTCATGAAATTATTTGATAGAGCTAAAGTAAATGTCAACCTCCTGATCTTCCTTCTCAAC
AAAAAGTTCTACGGGAAGTAATTGATCGTTTGCTGCCAGCCCAGAAGGATGAAGGAAAGAAGCACCTCACAGCTCCTTTCTAGGTCCTTC
TTTCCTCATTGGAAGCAAAGACCTAGCCAACAACAGCACCTCAATCTGATACACTCCCGATGCCACATTTTTAACTCCTCTCGCTCTGAT
GGGACATTTGTTACCCTTTTTTCATAGTGAAATTGTGTTTCAGGCTTAGTCTGACCTTTCTGGTTTCTTCATTTTCTTCCATTACTTAGG
AAAGAGTGGAAACTCCACTAAAATTTCTCTGTGTTGTTACAGTCTTAGAGGTTGCAGTACTATATTGTAAGCTTTGGTGTTTGTTTAATT
AGCAATAGGGATGGTAGGATTCAAATGTGTGTCATTTAGAAGTGGAAGCTATTAGCACCAATGACATAAATACATACAAGACACACAACT
AAAATGTCATGTTATTAACAGTTATTAGGTTGTCATTTAAAAATAAAGTTCCTTTATATTTCTGTCCCATCAGGAAAACTGAAGGATATG
GGGAATCATTGGTTATCTTCCATTGTGTTTTTCTTTATGGACAGGAGCTAATGGAAGTGACAGTCATGTTCAAAGGAAGCATTTCTAGAA
AAAAGGAGATAATGTTTTTAAATTTCATTATCAAACTTGGGCAATTCTGTTTGTGTAACTCCCCGACTAGTGGATGGGAGAGTCCCATTG
CTAAAATTCAGCTACTCAGATAAATTCAGAATGGGTCAAGGCACCTGCCTGTTTTTGTTGGTGCACAGAGATTGACTTGATTCAGAGAGA
CAATTCACTCCATCCCTATGGCAGAGGAATGGGTTAGCCCTAATGTAGAATGTCATTGTTTTTAAAACTGTTTTATATCTTAAGAGTGCC
TTATTAAAGTATAGATGTATGTCTTAAAATGTGGGTGATAGGAATTTTAAAGATTTATATAATGCATCAAAAGCCTTAGAATAAGAAAAG
CTTTTTTTAAATTGCTTTATCTGTATATCTGAACTCTTGAAACTTATAGCTAAAACACTAGGATTTATCTGCAGTGTTCAGGGAGATAAT
TCTGCCTTTAATTGTCTAAAACAAAAACAAAACCAGCCAACCTATGTTACACGTGAGATTAAAACCAATTTTTTCCCCATTTTTTCTCCT
TTTTTCTCTTGCTGCCCACATTGTGCCTTTATTTTATGAGCCCCAGTTTTCTGGGCTTAGTTTAAAAAAAAAATCAAGTCTAAACATTGC
ATTTAGAAAGCTTTTGTTCTTGGATAAAAAGTCATACACTTTAAAAAAAAAAAAAACTTTTTCCAGGAAAATATATTGAAATCATGCTGC
TGAGCCTCTATTTTCTTTCTTTGATGTTTTGATTCAGTATTCTTTTATCATAAATTTTTAGCATTTAAAAATTCACTGATGTACATTAAG
CCAATAAACTGCTTTAATGAATAACAAACTATGTAGTGTGTCCCTATTATAAATGCATTGGAGAAGTATTTTTATGAGACTCTTTACTCA
GGTGCATGGTTACAGCCCACAGGGAGGCATGGAGTGCCATGGAAGGATTCGCCACTACCCAGACCTTGTTTTTTGTTGTATTTTGGAAGA
CAGGTTTTTTAAAGAAACATTTTCCTCAGATTAAAAGATGATGCTATTACAACTAGCATTGCCTCAAAAACTGGGACCAACCAAAGTGTG
TCAACCCTGTTTCCTTAAAAGAGGCTATGAATCCCAAAGGCCACATCCAAGACAGGCAATAATGAGCAGAGTTTACAGCTCCTTTAATAA
AATGTGTCAGTAATTTTAAGGTTTATAGTTCCCTCAACACAATTGCTAATGCAGAATAGTGTAAAATGCGCTTCAAGAATGTTGATGATG
ATGATATAGAATTGTGGCTTTAGTAGCACAGAGGATGCCCCAACAAACTCATGGCGTTGAAACCACACAGTTCTCATTACTGTTATTTAT
TAGCTGTAGCATTCTCTGTCTCCTCTCTCTCCTCCTTTGACCTTCTCCTCGACCAGCCATCATGACATTTACCATGAATTTACTTCCTCC

>In-frame_ENST00000252622_ENST00000268182_ERR315349_LSM7_chr19_2328386_-_IQGAP1_chr15_91030186_length(amino acids)=357AA_start in transcript=27_stop in transcript=1100
MRRATRRDKMADKEKKKKESILDLSKYIDKTIRVKFQGGREGESSGNLNDPNKEALAKTEVSLTLTNKFDVPGDENAEMDARTILLNTKR
LIVDVIRFQPGETLTEILETPATSEQEAEHQRAMQRRAIRDAKTPDKMKKSKSVKEDSNLTLQEKKEKIQTGLKKLTELGTVDPKNKYQE
LINDIARDIRNQRRYRQRRKAELVKLQQTYAALNSKATFYGEQVDYYKSYIKTCLDNLASKGKVSKKPREMKGKKSKKISLKYTAARLHE

--------------------------------------------------------------
>In-frame_ENST00000252622_ENST00000560738_ERR315349_LSM7_chr19_2328386_-_IQGAP1_chr15_91030186_length(transcript)=1364nt_BP=151nt
GGGAGGTCAAAGGGCGCGGGGCGGTGCCTGCGAAGAGCCACACGGCGCGACAAGATGGCGGATAAGGAGAAGAAGAAAAAGGAGAGCATC
TTGGACTTGTCCAAGTACATCGACAAGACGATCCGGGTAAAGTTCCAGGGAGGCCGCGAAGGGGAAAGCTCTGGCAATTTAAATGACCCA
AATAAGGAGGCACTGGCTAAGACGGAAGTGTCTCTCACCCTGACCAACAAGTTCGACGTGCCTGGAGATGAGAATGCAGAAATGGATGCT
CGAACCATCTTACTGAATACAAAACGTTTAATTGTGGATGTCATCCGGTTCCAGCCAGGAGAGACCTTGACTGAAATCCTAGAAACACCA
GCCACCAGTGAACAGGAAGCAGAACATCAGAGAGCCATGCAGAGACGTGCTATCCGTGATGCCAAAACACCTGACAAGATGAAAAAGTCA
AAATCTGTAAAGGAAGACAGCAACCTCACTCTTCAAGAGAAGAAAGAGAAGATCCAGACAGGTTTAAAGAAGCTAACAGAGCTTGGAACC
GTGGACCCAAAGAACAAATACCAGGAACTGATCAACGACATTGCCAGGGATATTCGGAATCAGCGGAGGTACCGACAGAGGAGAAAGGCC
GAACTAGTGAAACTGCAACAGACATACGCTGCTCTGAACTCTAAGGCCACCTTTTATGGGGAGCAGGTGGATTACTATAAAAGCTATATC
AAAACCTGCTTGGATAACTTAGCCAGCAAGGGCAAAGTCTCCAAAAAGCCTAGGGAAATGAAAGGAAAGAAAAGCAAAAAGATTTCTCTG
AAATATACAGCAGCAAGACTACATGAAAAAGGAGTTCTTCTGGAAATTGAGGACCTGCAAGTGAATCAGTTTAAAAATGTTATATTTGAA
ATCAGTCCAACAGAAGAAGTTGGAGACTTCGAAGTGAAAGCCAAATTCATGGGAGTTCAAATGGAGACTTTTATGTTACATTATCAGGAC
CTGCTGCAGCTACAGTATGAAGGAGTTGCAGTCATGAAATTATTTGATAGAGCTAAAGTAAATGTCAACCTCCTGATCTTCCTTCTCAAC
AAAAAGTTCTACGGGAAGTAATTGATCGTTTGCTGCCAGCCCAGAAGGATGAAGGAAAGAAGCACCTCACAGCTCCTTTCTAGGTCCTTC
TTTCCTCATTGGAAGCAAAGACCTAGCCAACAACAGCACCTCAATCTGATACACTCCCGATGCCACATTTTTAACTCCTCTCGCTCTGAT
GGGACATTTGTTACCCTTTTTTCATAGTGAAATTGTGTTTCAGGCTTAGTCTGACCTTTCTGGTTTCTTCATTTTCTTCCATTACTTAGG

>In-frame_ENST00000252622_ENST00000560738_ERR315349_LSM7_chr19_2328386_-_IQGAP1_chr15_91030186_length(amino acids)=357AA_start in transcript=27_stop in transcript=1100
MRRATRRDKMADKEKKKKESILDLSKYIDKTIRVKFQGGREGESSGNLNDPNKEALAKTEVSLTLTNKFDVPGDENAEMDARTILLNTKR
LIVDVIRFQPGETLTEILETPATSEQEAEHQRAMQRRAIRDAKTPDKMKKSKSVKEDSNLTLQEKKEKIQTGLKKLTELGTVDPKNKYQE
LINDIARDIRNQRRYRQRRKAELVKLQQTYAALNSKATFYGEQVDYYKSYIKTCLDNLASKGKVSKKPREMKGKKSKKISLKYTAARLHE

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Fusion Gene PPI Analysis for LSM7-IQGAP1


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 LSM7-IQGAP1


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 LSM7-IQGAP1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneIQGAP1C0006118Brain Neoplasms1CTD_human
TgeneIQGAP1C0023893Liver Cirrhosis, Experimental1CTD_human
TgeneIQGAP1C0043094Weight Gain1CTD_human
TgeneIQGAP1C0153633Malignant neoplasm of brain1CTD_human
TgeneIQGAP1C0496899Benign neoplasm of brain, unspecified1CTD_human
TgeneIQGAP1C0750974Brain Tumor, Primary1CTD_human
TgeneIQGAP1C0750977Recurrent Brain Neoplasm1CTD_human
TgeneIQGAP1C0750979Primary malignant neoplasm of brain1CTD_human
TgeneIQGAP1C1527390Neoplasms, Intracranial1CTD_human
TgeneIQGAP1C2239176Liver carcinoma1CTD_human