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ATGpr specifications

Information


Unique identifier OMICS_09989
Name ATGpr
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for ATGpr

ATGpr citations

 (26)
library_books

The long non coding RNA MYCNOS 01 regulates MYCN protein levels and affects growth of MYCN amplified rhabdomyosarcoma and neuroblastoma cells

2018
BMC Cancer
PMCID: 5822637
PMID: 29466962
DOI: 10.1186/s12885-018-4129-8

[…] Translation prediction for the MYCNOS-01 transcript sequence was carried out using the ExPASy translate tool (http://web.expasy.org/translate/) [] and Kozak sequence prediction was carried out using ATGpr (http://atgpr.dbcls.jp/) []. […]

library_books

Allele specific repression of Sox2 through the long non coding RNA Sox2ot

2018
Sci Rep
PMCID: 5762901
PMID: 29321583
DOI: 10.1038/s41598-017-18649-4

[…] c exon 1 (Fig. ). We analyzed the cDNA sequences for the presence of open reading frames (ORFs) through Coding Potential Calculator, NCBI’s ORFfinder, and a translation initiation prediction program (ATGpr) but the outcome underscored the non-coding nature of all Sox2otb and Sox2otc splice variants (Supplementary Fig. ). To test whether the transcripts can be translated into a polypeptide we perfo […]

library_books

Unique N terminal sequences in two Runx1 isoforms are dispensable for Runx1 function

2017
BMC Dev Biol
PMCID: 5648507
PMID: 29047338
DOI: 10.1186/s12861-017-0156-y

[…] he truncated protein would lack the first two amino acids of the Runt-domain. In addition, the sequence around AUG (+73) was predicted to be closer to Kozak sequences than AUG (+151) according to the ATGpr program []. We therefore propose that the position of the non-canonical downstream AUG is at +73. Interestingly, we found that the amount of truncated P2-Runx1 isoform in Runx1 ΔP1:P2TAA/ ΔP1:P2 […]

library_books

LincIN, a novel NF90 binding long non coding RNA, is overexpressed in advanced breast tumors and involved in metastasis

2017
PMCID: 5450112
PMID: 28558830
DOI: 10.1186/s13058-017-0853-2

[…] detected in poly(A)- enriched RNA fractions (Additional file : Figure S2).Based on a BLASTX analysis of all possible reading frames identified by the open reading frame (ORF) finder from the NCBI and ATGpr (http://atgpr.dbcls.jp/), LincIN lacks the potential to encode any recognizable protein domains. As described previously [], we further examined the coding potential of LincIN using a bioinforma […]

library_books

X linked primary ciliary dyskinesia due to mutations in the cytoplasmic axonemal dynein assembly factor PIH1D3

2017
Nat Commun
PMCID: 5309803
PMID: 28176794
DOI: 10.1038/ncomms14279

[…] erefore escape NMD and a shorter in-frame PIH1D3 protein could be expressed. Such an alternative ATG indeed exists in exon 4 (codon 61) and it contains a good Kozak consensus sequence as predicted by ATGpr (score of 0.15 versus 0.16 for the usual ATG initiation codon).We investigated PIH1D3-mutated cilia motility using high-speed video microscopy imaging. All affected individuals had immotile cili […]

library_books

Characterization of Alstrom Syndrome 1 (ALMS1) Transcript Variants in Hodgkin Lymphoma Cells

2017
PLoS One
PMCID: 5279758
PMID: 28135309
DOI: 10.1371/journal.pone.0170694

[…] ranslation start site prediction tools [,] indicated that the corresponding ATG codon in exon 3 can serve as start codon (NetStart 1.0 [] prediction scores for exon 1: 0.890, score for exon 3: 0.518; ATGpr [] reliability for exon 1: 0.60, for exon 3: 0.13). Alternatively, an additional exon upstream of exon one might exist which can provide a splice donor site. Until now, we were not able to ident […]

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ATGpr institution(s)
Helix Research Institute, Kisarazu-shi, Chiba-ken, Japan

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