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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 30243

FusionGeneSummary for RAI1_LRRC4C

check button Fusion gene summary
Fusion gene informationFusion gene name: RAI1_LRRC4C
Fusion gene ID: 30243
HgeneTgene
Gene symbol

RAI1

LRRC4C

Gene ID

10743

57689

Gene nameretinoic acid induced 1leucine rich repeat containing 4C
SynonymsSMCR|SMSNGL-1|NGL1
Cytomap

17p11.2

11p12

Type of geneprotein-codingprotein-coding
Descriptionretinoic acid-induced protein 1Smith-Magenis syndrome chromosome regionleucine-rich repeat-containing protein 4Cnetrin-G1 ligand
Modification date2018052320180522
UniProtAcc

Q7Z5J4

Q9HCJ2

Ensembl transtripts involved in fusion geneENST00000353383, ENST00000489697, 
ENST00000261641, 
ENST00000528697, 
ENST00000530763, ENST00000534577, 
ENST00000278198, ENST00000527150, 
Fusion gene scores* DoF score17 X 9 X 11=16835 X 4 X 5=100
# samples 185
** MAII scorelog2(18/1683*10)=-3.22496636500027
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(5/100*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RAI1 [Title/Abstract] AND LRRC4C [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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
HgeneRAI1

GO:0045893

positive regulation of transcription, DNA-templated

22578325

TgeneLRRC4C

GO:0050770

regulation of axonogenesis

14595443


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVHNSCTCGA-P3-A6T6-01ARAI1chr17

17707163

+LRRC4Cchr11

40669828

-
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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
5CDS-5UTRENST00000353383ENST00000528697RAI1chr17

17707163

+LRRC4Cchr11

40669828

-
5CDS-5UTRENST00000353383ENST00000530763RAI1chr17

17707163

+LRRC4Cchr11

40669828

-
5CDS-5UTRENST00000353383ENST00000534577RAI1chr17

17707163

+LRRC4Cchr11

40669828

-
5CDS-intronENST00000353383ENST00000278198RAI1chr17

17707163

+LRRC4Cchr11

40669828

-
5CDS-intronENST00000353383ENST00000527150RAI1chr17

17707163

+LRRC4Cchr11

40669828

-
intron-5UTRENST00000489697ENST00000528697RAI1chr17

17707163

+LRRC4Cchr11

40669828

-
intron-5UTRENST00000489697ENST00000530763RAI1chr17

17707163

+LRRC4Cchr11

40669828

-
intron-5UTRENST00000489697ENST00000534577RAI1chr17

17707163

+LRRC4Cchr11

40669828

-
intron-intronENST00000489697ENST00000278198RAI1chr17

17707163

+LRRC4Cchr11

40669828

-
intron-intronENST00000489697ENST00000527150RAI1chr17

17707163

+LRRC4Cchr11

40669828

-
intron-5UTRENST00000261641ENST00000528697RAI1chr17

17707163

+LRRC4Cchr11

40669828

-
intron-5UTRENST00000261641ENST00000530763RAI1chr17

17707163

+LRRC4Cchr11

40669828

-
intron-5UTRENST00000261641ENST00000534577RAI1chr17

17707163

+LRRC4Cchr11

40669828

-
intron-intronENST00000261641ENST00000278198RAI1chr17

17707163

+LRRC4Cchr11

40669828

-
intron-intronENST00000261641ENST00000527150RAI1chr17

17707163

+LRRC4Cchr11

40669828

-

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FusionProtFeatures for RAI1_LRRC4C


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
RAI1

Q7Z5J4

LRRC4C

Q9HCJ2

Transcriptional regulator of the circadian clockcomponents: CLOCK, ARNTL/BMAL1, ARNTL2/BMAL2, PER1/3, CRY1/2,NR1D1/2 and RORA/C. Positively regulates the transcriptionalactivity of CLOCK a core component of the circadian clock.Regulates transcription through chromatin remodeling byinteracting with other proteins in chromatin as well as proteinsin the basic transcriptional machinery. May be important forembryonic and postnatal development. May be involved in neuronaldifferentiation. {ECO:0000269|PubMed:22578325}. May promote neurite outgrowth of developing thalamicneurons. {ECO:0000269|PubMed:14595443}.

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


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FusionGeneSequence for RAI1_LRRC4C


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for RAI1_LRRC4C


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
RAI1PIN1, TESC, DDIT3, GATA1, GLI1, LZTR1, MAML3, ZNF496, MAPK8IP2, GSK3B, CASP2, RPS6KA5, CDKN1A, TTR, GADD45A, SIRT7, HECW2, HIST1H2BG, DAXX, TCF20, CDK2AP1, HMG20A, NAGK, NR3C1, ARLRRC4CNTNG1, CREB3L4, LRRC4B, LRRC4, VLDLR, SULF1, SULF2, DVL2, SBF1, UBE2S, NCOA5, DOLK, NOB1, FSTL1, SLC39A11, BTBD1, MTMR1, NOP9, LRP5, CNPY3, PKP2, BRI3BP, DNAJB9, FRAS1


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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RelatedDrugs for RAI1_LRRC4C


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for RAI1_LRRC4C


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneRAI1C0795864Smith-Magenis syndrome12CTD_human;ORPHANET
HgeneRAI1C0028754Obesity2CTD_human;HPO
HgeneRAI1C0003469Anxiety Disorders1CTD_human
HgeneRAI1C0018273Growth Disorders1CTD_human
HgeneRAI1C0025202melanoma1CTD_human
HgeneRAI1C0036341Schizophrenia1PSYGENET
HgeneRAI1C0376634Craniofacial Abnormalities1CTD_human
HgeneRAI1C0525041Neurobehavioral Manifestations1CTD_human
HgeneRAI1C0700201Dyssomnias1CTD_human
HgeneRAI1C1510586Autism Spectrum Disorders1CTD_human
HgeneRAI1C1970482Potocki-Lupski syndrome1CTD_human
HgeneRAI1C3714756Intellectual Disability1CTD_human;HPO
HgeneRAI1C3887612Psychomotor Agitation1CTD_human