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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:GRAMD1A-KRTDAP (FusionGDB2 ID:HG57655TG388533)

Fusion Gene Summary for GRAMD1A-KRTDAP

check button Fusion gene summary
Fusion gene informationFusion gene name: GRAMD1A-KRTDAP
Fusion gene ID: hg57655tg388533
HgeneTgene
Gene symbol

GRAMD1A

KRTDAP

Gene ID

57655

388533

Gene nameGRAM domain containing 1Akeratinocyte differentiation associated protein
SynonymsKIAA1533KDAP|UNQ467
Cytomap('GRAMD1A')('KRTDAP')

19q13.11

19q13.12

Type of geneprotein-codingprotein-coding
Descriptionprotein Aster-AGRAM domain-containing protein 1Akeratinocyte differentiation-associated proteinKIPV467
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000598073, ENST00000317991, 
ENST00000411896, ENST00000424536, 
ENST00000599564, ENST00000504615, 
Fusion gene scores* DoF score5 X 3 X 5=751 X 1 X 1=1
# samples 61
** MAII scorelog2(6/75*10)=-0.321928094887362
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(1/1*10)=3.32192809488736
Context

PubMed: GRAMD1A [Title/Abstract] AND KRTDAP [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGRAMD1A(35500233)-KRTDAP(35978661), # samples:3
Anticipated loss of major functional domain due to fusion event.GRAMD1A-KRTDAP 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.
GRAMD1A-KRTDAP 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.
* 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 GRAMD1A (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure
check buttonFusion gene breakpoints across KRTDAP (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check button Fusion gene information
* 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
ChimerDB4LUADTCGA-L9-A8F4-01AGRAMD1Achr19

35500233

-KRTDAPchr19

35978661

-
ChimerDB4LUADTCGA-L9-A8F4-01AGRAMD1Achr19

35500233

+KRTDAPchr19

35978661

-
ChimerDB4LUADTCGA-L9-A8F4GRAMD1Achr19

35500233

+KRTDAPchr19

35978661

-


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Fusion Gene ORF analysis for GRAMD1A-KRTDAP

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
3UTR-3CDSENST00000598073ENST00000484218GRAMD1Achr19

35500233

+KRTDAPchr19

35978661

-
3UTR-5UTRENST00000598073ENST00000338897GRAMD1Achr19

35500233

+KRTDAPchr19

35978661

-
3UTR-5UTRENST00000598073ENST00000479340GRAMD1Achr19

35500233

+KRTDAPchr19

35978661

-
5CDS-5UTRENST00000317991ENST00000338897GRAMD1Achr19

35500233

+KRTDAPchr19

35978661

-
5CDS-5UTRENST00000317991ENST00000479340GRAMD1Achr19

35500233

+KRTDAPchr19

35978661

-
5CDS-5UTRENST00000411896ENST00000338897GRAMD1Achr19

35500233

+KRTDAPchr19

35978661

-
5CDS-5UTRENST00000411896ENST00000479340GRAMD1Achr19

35500233

+KRTDAPchr19

35978661

-
5CDS-5UTRENST00000424536ENST00000338897GRAMD1Achr19

35500233

+KRTDAPchr19

35978661

-
5CDS-5UTRENST00000424536ENST00000479340GRAMD1Achr19

35500233

+KRTDAPchr19

35978661

-
5CDS-5UTRENST00000599564ENST00000338897GRAMD1Achr19

35500233

+KRTDAPchr19

35978661

-
5CDS-5UTRENST00000599564ENST00000479340GRAMD1Achr19

35500233

+KRTDAPchr19

35978661

-
5UTR-3CDSENST00000504615ENST00000484218GRAMD1Achr19

35500233

+KRTDAPchr19

35978661

-
5UTR-5UTRENST00000504615ENST00000338897GRAMD1Achr19

35500233

+KRTDAPchr19

35978661

-
5UTR-5UTRENST00000504615ENST00000479340GRAMD1Achr19

35500233

+KRTDAPchr19

35978661

-
In-frameENST00000317991ENST00000484218GRAMD1Achr19

35500233

+KRTDAPchr19

35978661

-
In-frameENST00000411896ENST00000484218GRAMD1Achr19

35500233

+KRTDAPchr19

35978661

-
In-frameENST00000424536ENST00000484218GRAMD1Achr19

35500233

+KRTDAPchr19

35978661

-
In-frameENST00000599564ENST00000484218GRAMD1Achr19

35500233

+KRTDAPchr19

35978661

-

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)
ENST00000599564GRAMD1Achr1935500233+ENST00000484218KRTDAPchr1935978661-74255153637194
ENST00000317991GRAMD1Achr1935500233+ENST00000484218KRTDAPchr1935978661-60241139497152
ENST00000411896GRAMD1Achr1935500233+ENST00000484218KRTDAPchr1935978661-4632725358117
ENST00000424536GRAMD1Achr1935500233+ENST00000484218KRTDAPchr1935978661-43324223328101

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
ENST00000599564ENST00000484218GRAMD1Achr1935500233+KRTDAPchr1935978661-0.104996420.89500356
ENST00000317991ENST00000484218GRAMD1Achr1935500233+KRTDAPchr1935978661-0.080666670.91933334
ENST00000411896ENST00000484218GRAMD1Achr1935500233+KRTDAPchr1935978661-0.1229086440.87709135
ENST00000424536ENST00000484218GRAMD1Achr1935500233+KRTDAPchr1935978661-0.12010340.87989664

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Fusion Genomic Features for GRAMD1A-KRTDAP


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)

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.
genomic feature

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Fusion Protein Features for GRAMD1A-KRTDAP


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr19:35500233/chr19:35978661)
- 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.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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
HgeneGRAMD1Achr19:35500233chr19:35978661ENST00000317991+220367_53873725.0DomainVASt
HgeneGRAMD1Achr19:35500233chr19:35978661ENST00000317991+22091_15873725.0DomainGRAM
HgeneGRAMD1Achr19:35500233chr19:35978661ENST00000411896+218367_53873714.0DomainVASt
HgeneGRAMD1Achr19:35500233chr19:35978661ENST00000411896+21891_15873714.0DomainGRAM
HgeneGRAMD1Achr19:35500233chr19:35978661ENST00000317991+220610_63073725.0TransmembraneHelical
HgeneGRAMD1Achr19:35500233chr19:35978661ENST00000411896+218610_63073714.0TransmembraneHelical


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Fusion Gene Sequence for GRAMD1A-KRTDAP


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.
>34575_34575_1_GRAMD1A-KRTDAP_GRAMD1A_chr19_35500233_ENST00000317991_KRTDAP_chr19_35978661_ENST00000484218_length(transcript)=602nt_BP=411nt
GTCGCTGACGCCGCGGCGGCCTCCGGCGGCTCCGGCCTTTTGTGCGGGCGGTTGGGTCGGGTGGGGGCGGCGGCCGCGGAAGGCCAGGCC
GGTGCCCTGCGGGGACGCCCAGCGCAGCCCAGCCCCGCGCAGCCCAGCCCTGCCCTGCCCTGCCCTGCCCTGCGCCCGGGGCGCGCCCAC
CGCGCCGCATCCATGTTCGACACCACACCCCACTCTGGCCGGAGCACGCCAAGCAGCTCCCCATCGCTCCGGAAACGGCTGCAGCTCCTG
CCCCCAAGCCGGCCCCCACCTGAGCCAGAACCAGGCACCATGGTGGAGAAGGGATCAGATAGCTCCTCAGAGAAGGGTGGGGTGCCTGGG
ACCCCCAGCACCCAGAGCCTAGGCAGCCGGAACTTCATCCGCAACAGCAAGTCTATCAAAAGGAAACTTCCTTTCCTCAACTGGGATGCC
TTTCCTAAGCTGAAAGGACTGAGGAGCGCAACTCCTGATGCCCAGTGACCATGACCTCCACTGGAAGAGGGGGCTAGCGTGAGCGCTGAT

>34575_34575_1_GRAMD1A-KRTDAP_GRAMD1A_chr19_35500233_ENST00000317991_KRTDAP_chr19_35978661_ENST00000484218_length(amino acids)=152AA_BP=61
MCGRLGRVGAAAAEGQAGALRGRPAQPSPAQPSPALPCPALRPGRAHRAASMFDTTPHSGRSTPSSSPSLRKRLQLLPPSRPPPEPEPGT

--------------------------------------------------------------
>34575_34575_2_GRAMD1A-KRTDAP_GRAMD1A_chr19_35500233_ENST00000411896_KRTDAP_chr19_35978661_ENST00000484218_length(transcript)=463nt_BP=272nt
CTGCCCTGCCCTGCCCTGCCCTGCGCCCGGGGCGCGCCCACCGCGCCGCATCCATGTTCGACACCACACCCCACTCTGGCCGGAGCACGC
CAAGCAGCTCCCCATCGCTCCGGAAACGGCTGCAGCTCCTGCCCCCAAGCCGGCCCCCACCTGAGCCAGAACCAGGCACCATGGTGGAGA
AGGGATCAGATAGCTCCTCAGAGAAGGGTGGGGTGCCTGGGACCCCCAGCACCCAGAGCCTAGGCAGCCGGAACTTCATCCGCAACAGCA
AGTCTATCAAAAGGAAACTTCCTTTCCTCAACTGGGATGCCTTTCCTAAGCTGAAAGGACTGAGGAGCGCAACTCCTGATGCCCAGTGAC
CATGACCTCCACTGGAAGAGGGGGCTAGCGTGAGCGCTGATTCTCAACCTACCATAACTCTTTCCTGCCTCAGGAACTCCAATAAAACAT

>34575_34575_2_GRAMD1A-KRTDAP_GRAMD1A_chr19_35500233_ENST00000411896_KRTDAP_chr19_35978661_ENST00000484218_length(amino acids)=117AA_BP=26
MPCPALRPGRAHRAASMFDTTPHSGRSTPSSSPSLRKRLQLLPPSRPPPEPEPGTMVEKGSDSSSEKGGVPGTPSTQSLGSRNFIRNSKS

--------------------------------------------------------------
>34575_34575_3_GRAMD1A-KRTDAP_GRAMD1A_chr19_35500233_ENST00000424536_KRTDAP_chr19_35978661_ENST00000484218_length(transcript)=433nt_BP=242nt
GGCGCGCCCACCGCGCCGCATCCATGTTCGACACCACACCCCACTCTGGCCGGAGCACGCCAAGCAGCTCCCCATCGCTCCGGAAACGGC
TGCAGCTCCTGCCCCCAAGCCGGCCCCCACCTGAGCCAGAACCAGGCACCATGGTGGAGAAGGGATCAGATAGCTCCTCAGAGAAGGGTG
GGGTGCCTGGGACCCCCAGCACCCAGAGCCTAGGCAGCCGGAACTTCATCCGCAACAGCAAGTCTATCAAAAGGAAACTTCCTTTCCTCA
ACTGGGATGCCTTTCCTAAGCTGAAAGGACTGAGGAGCGCAACTCCTGATGCCCAGTGACCATGACCTCCACTGGAAGAGGGGGCTAGCG

>34575_34575_3_GRAMD1A-KRTDAP_GRAMD1A_chr19_35500233_ENST00000424536_KRTDAP_chr19_35978661_ENST00000484218_length(amino acids)=101AA_BP=10
MFDTTPHSGRSTPSSSPSLRKRLQLLPPSRPPPEPEPGTMVEKGSDSSSEKGGVPGTPSTQSLGSRNFIRNSKSIKRKLPFLNWDAFPKL

--------------------------------------------------------------
>34575_34575_4_GRAMD1A-KRTDAP_GRAMD1A_chr19_35500233_ENST00000599564_KRTDAP_chr19_35978661_ENST00000484218_length(transcript)=742nt_BP=551nt
AAGTCTGAATGCTGTGTGGACAGAGGAGGAGGACCCAATAAGAGACCACACCGCTGTTCCAGACCCTCTCCATGGATGATGTCCTGCCCC
TGATGCCTTGGGAGACCCTGTTGGCACAGGGCAGTCCCCAGGGCTCGCCTGACCTCCCAGCAGGGCAGCGGAAGCAGCAGCCACAGGGTG
ACAGGGCCCAGGGCCTGGCCTCTGAGTCCTGGAAGCTCCTGGAGGTGCCCATCATTCACATAACGCCATCCAGTGATGGGGAGTCCCCCG
CCTGCACCCCAACCCCCCGACGCCGGCAGCAGCAGAGGATGCCAGACCCGCAGAGTCTGTCCCAGGACAGCACCACACCCCACTCTGGCC
GGAGCACGCCAAGCAGCTCCCCATCGCTCCGGAAACGGCTGCAGCTCCTGCCCCCAAGCCGGCCCCCACCTGAGCCAGAACCAGGCACCA
TGGTGGAGAAGGGATCAGATAGCTCCTCAGAGAAGGGTGGGGTGCCTGGGACCCCCAGCACCCAGAGCCTAGGCAGCCGGAACTTCATCC
GCAACAGCAAGTCTATCAAAAGGAAACTTCCTTTCCTCAACTGGGATGCCTTTCCTAAGCTGAAAGGACTGAGGAGCGCAACTCCTGATG
CCCAGTGACCATGACCTCCACTGGAAGAGGGGGCTAGCGTGAGCGCTGATTCTCAACCTACCATAACTCTTTCCTGCCTCAGGAACTCCA

>34575_34575_4_GRAMD1A-KRTDAP_GRAMD1A_chr19_35500233_ENST00000599564_KRTDAP_chr19_35978661_ENST00000484218_length(amino acids)=194AA_BP=103
MFQTLSMDDVLPLMPWETLLAQGSPQGSPDLPAGQRKQQPQGDRAQGLASESWKLLEVPIIHITPSSDGESPACTPTPRRRQQQRMPDPQ
SLSQDSTTPHSGRSTPSSSPSLRKRLQLLPPSRPPPEPEPGTMVEKGSDSSSEKGGVPGTPSTQSLGSRNFIRNSKSIKRKLPFLNWDAF

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

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Fusion Gene PPI Analysis for GRAMD1A-KRTDAP


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 GRAMD1A-KRTDAP


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 GRAMD1A-KRTDAP


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource