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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: 19767

FusionGeneSummary for LINC00312_ATF4

check button Fusion gene summary
Fusion gene informationFusion gene name: LINC00312_ATF4
Fusion gene ID: 19767
HgeneTgene
Gene symbol

LINC00312

ATF4

Gene ID

29931

468

Gene namelong intergenic non-protein coding RNA 312activating transcription factor 4
SynonymsERR-10|ERR10|LMCD1DN|LOH3CR2A|NAG-7|NAG7|NCRNA00312CREB-2|CREB2|TAXREB67|TXREB
Cytomap

3p25.3

22q13.1

Type of genencRNAprotein-coding
DescriptionLMCD1 downstream neighborestrogen receptor repressor 10loss of heterozygosity, 3, chromosomal region 2, gene Anasopharyngeal carcinoma candidate 7cyclic AMP-dependent transcription factor ATF-4DNA-binding protein TAXREB67cAMP response element-binding protein 2cAMP-dependent transcription factor ATF-4cAMP-responsive element-binding protein 2cyclic AMP-responsive element-binding protein 2tax-re
Modification date2018052720180523
UniProtAcc

P18848

Ensembl transtripts involved in fusion geneENST00000442796, ENST00000404241, 
ENST00000337304, ENST00000396680, 
Fusion gene scores* DoF score1 X 1 X 1=12 X 2 X 1=4
# samples 12
** MAII scorelog2(1/1*10)=3.32192809488736log2(2/4*10)=2.32192809488736
Context

PubMed: LINC00312 [Title/Abstract] AND ATF4 [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
TgeneATF4

GO:0034976

response to endoplasmic reticulum stress

19061639

TgeneATF4

GO:0045893

positive regulation of transcription, DNA-templated

15775988|18940792

TgeneATF4

GO:0045944

positive regulation of transcription by RNA polymerase II

11478948|15775988|18940792

TgeneATF4

GO:1990440

positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress

12871976


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
ChiTaRS3.1BC055409LINC00312chr3

8615220

+ATF4chr22

39918548

+
* 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
3UTR-3CDSENST00000442796ENST00000404241LINC00312chr3

8615220

+ATF4chr22

39918548

+
3UTR-3CDSENST00000442796ENST00000337304LINC00312chr3

8615220

+ATF4chr22

39918548

+
3UTR-3CDSENST00000442796ENST00000396680LINC00312chr3

8615220

+ATF4chr22

39918548

+

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FusionProtFeatures for LINC00312_ATF4


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
LINC00312

ATF4

P18848

Lectin that binds to various sugars: galactose > mannose= fucose > N-acetylglucosamine > N-acetylgalactosamine(PubMed:10224141). Acts as a chemoattractant, probably involved inthe regulation of cell migration (PubMed:28301481).{ECO:0000269|PubMed:10224141, ECO:0000269|PubMed:28301481}. Transcriptional activator. Binds the cAMP responseelement (CRE) (consensus: 5'-GTGACGT[AC][AG]-3'), a sequencepresent in many viral and cellular promoters. Cooperates withFOXO1 in osteoblasts to regulate glucose homeostasis throughsuppression of beta-cell production and decrease in insulinproduction (By similarity). It binds to a Tax-responsive enhancerelement in the long terminal repeat of HTLV-I. Regulates theinduction of DDIT3/CHOP and asparagine synthetase (ASNS) inresponse to endoplasmic reticulum (ER) stress. In concert withDDIT3/CHOP, activates the transcription of TRIB3 and promotes ERstress-induced neuronal apoptosis by regulating thetranscriptional induction of BBC3/PUMA. Activates transcription ofSIRT4. Regulates the circadian expression of the core clockcomponent PER2 and the serotonin transporter SLC6A4. Binds in acircadian time-dependent manner to the cAMP response elements(CRE) in the SLC6A4 and PER2 promoters and periodically activatesthe transcription of these genes. During ER stress response,activates the transcription of NLRP1, possibly in concert withother factors (PubMed:26086088). {ECO:0000250,ECO:0000269|PubMed:15775988, ECO:0000269|PubMed:16682973,ECO:0000269|PubMed:18940792, ECO:0000269|PubMed:26086088}.

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 LINC00312_ATF4


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 LINC00312_ATF4


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 LINC00312_ATF4


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 LINC00312_ATF4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneATF4C0005586Bipolar Disorder2PSYGENET
TgeneATF4C0011570Mental Depression1PSYGENET
TgeneATF4C0011581Depressive disorder1PSYGENET
TgeneATF4C0027540Necrosis1CTD_human
TgeneATF4C0036341Schizophrenia1PSYGENET
TgeneATF4C0242184Hypoxia1CTD_human
TgeneATF4C1134719Invasive Ductal Breast Carcinoma1CTD_human