ATGpr statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool ATGpr
info

Tool usage distribution map

This map represents all the scientific publications referring to ATGpr per scientific context
info info

Associated diseases

This word cloud represents ATGpr usage per disease context
info

Popular tool citations

chevron_left Translation initiation site prediction chevron_right
Want to access the full stats & trends on this tool?

Protocols

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 […]


Want to access the full list of citations?
ATGpr institution(s)
Helix Research Institute, Kisarazu-shi, Chiba-ken, Japan

ATGpr reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review ATGpr