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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: 3644

FusionGeneSummary for AVL9_LRAT

check button Fusion gene summary
Fusion gene informationFusion gene name: AVL9_LRAT
Fusion gene ID: 3644
HgeneTgene
Gene symbol

AVL9

LRAT

Gene ID

23080

9227

Gene nameAVL9 cell migration associatedlecithin retinol acyltransferase
SynonymsKIAA0241LCA14
Cytomap

7p14.3

4q32.1

Type of geneprotein-codingprotein-coding
Descriptionlate secretory pathway protein AVL9 homologAVL9 homolog (S. cerevisiase)lecithin retinol acyltransferaselecithin retinol acyltransferase (phosphatidylcholine--retinol O-acyltransferase)
Modification date2018052320180519
UniProtAcc

Q8NBF6

O95237

Ensembl transtripts involved in fusion geneENST00000404479, ENST00000318709, 
ENST00000459629, ENST00000409301, 
ENST00000500890, ENST00000507827, 
ENST00000336356, 
Fusion gene scores* DoF score6 X 6 X 3=1083 X 2 X 3=18
# samples 73
** MAII scorelog2(7/108*10)=-0.625604485218502
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: AVL9 [Title/Abstract] AND LRAT [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
HgeneAVL9

GO:0016477

cell migration

22595670

TgeneLRAT

GO:0042572

retinol metabolic process

10819989


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
ChiTaRS3.1BX093249AVL9chr7

32800442

+LRATchr4

155672877

+
* 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
intron-intronENST00000404479ENST00000500890AVL9chr7

32800442

+LRATchr4

155672877

+
intron-intronENST00000404479ENST00000507827AVL9chr7

32800442

+LRATchr4

155672877

+
intron-3UTRENST00000404479ENST00000336356AVL9chr7

32800442

+LRATchr4

155672877

+
intron-intronENST00000318709ENST00000500890AVL9chr7

32800442

+LRATchr4

155672877

+
intron-intronENST00000318709ENST00000507827AVL9chr7

32800442

+LRATchr4

155672877

+
intron-3UTRENST00000318709ENST00000336356AVL9chr7

32800442

+LRATchr4

155672877

+
intron-intronENST00000459629ENST00000500890AVL9chr7

32800442

+LRATchr4

155672877

+
intron-intronENST00000459629ENST00000507827AVL9chr7

32800442

+LRATchr4

155672877

+
intron-3UTRENST00000459629ENST00000336356AVL9chr7

32800442

+LRATchr4

155672877

+
intron-intronENST00000409301ENST00000500890AVL9chr7

32800442

+LRATchr4

155672877

+
intron-intronENST00000409301ENST00000507827AVL9chr7

32800442

+LRATchr4

155672877

+
intron-3UTRENST00000409301ENST00000336356AVL9chr7

32800442

+LRATchr4

155672877

+

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FusionProtFeatures for AVL9_LRAT


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
AVL9

Q8NBF6

LRAT

O95237

Functions in cell migration.{ECO:0000269|PubMed:22595670}. Transfers the acyl group from the sn-1 position ofphosphatidylcholine to all-trans retinol, producing all-transretinyl esters. Retinyl esters are storage forms of vitamin A.LRAT plays a critical role in vision. It provides the all-transretinyl ester substrates for the isomerohydrolase which processesthe esters into 11-cis-retinol in the retinal pigment epithelium;due to a membrane-associated alcohol dehydrogenase, 11 cis-retinolis oxidized and converted into 11-cis-retinaldehyde which is thechromophore for rhodopsin and the cone photopigments.{ECO:0000269|PubMed:9920938}.

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 AVL9_LRAT


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 AVL9_LRAT


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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RelatedDrugs for AVL9_LRAT


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneLRATO95237DB00162Vitamin ALecithin retinol acyltransferasesmall moleculeapproved|nutraceutical|vet_approved

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RelatedDiseases for AVL9_LRAT


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneAVL9C3495559Juvenile arthritis1CTD_human
TgeneLRATC0917796Optic Atrophy, Hereditary, Leber2CTD_human
TgeneLRATC0015398Eye Diseases, Hereditary1CTD_human
TgeneLRATC0023893Liver Cirrhosis, Experimental1CTD_human
TgeneLRATC0042842Vitamin A Deficiency1CTD_human
TgeneLRATC0339527Leber Congenital Amaurosis1CTD_human;ORPHANET
TgeneLRATC2750063Leber Congenital Amaurosis 141CTD_human;UNIPROT
TgeneLRATC4277682Chemical and Drug Induced Liver Injury1CTD_human