(Q33429974)

26 July 2017

title

Evolutionary conservation of orthoretroviral long terminal repeats (LTRs) and ab initio detection of single LTRs in genomic data (English)

1 reference

26 July 2017

8

Jonas Blomberg

0 references

Samuel Kaski

7

object named as

Samuel Kaski

1 reference

26 July 2017

Patric Jern

2

0 references

author name string

Farid Benachenhou

1

1 reference

26 July 2017

Merja Oja

3

1 reference

26 July 2017

Göran Sperber

4

1 reference

26 July 2017

Vidar Blikstad

5

1 reference

26 July 2017

Panu Somervuo

6

1 reference

26 July 2017

language of work or name

English

0 references

publication date

13 April 2009

1 reference

26 July 2017

1 reference

26 July 2017

volume

4

1 reference

26 July 2017

issue

4

1 reference

26 July 2017

page(s)

e5179

1 reference

Creative Commons Attribution 4.0 International

26 July 2017

copyright license

start time

13 April 2009

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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14 July 2018

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Bidirectional transcription is an inherent feature of Giardia lamblia promoters and contributes to an abundance of sterile antisense transcripts throughout the genome

14 July 2018

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14 July 2018

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Human Immunodeficiency Virus-Type 1 LTR DNA contains an intrinsic gene producing antisense RNA and protein products

14 July 2018

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HTLV-I antisense transcripts initiating in the 3'LTR are alternatively spliced and polyadenylated

14 July 2018

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Identification of transposable elements using multiple alignments of related genomes

14 July 2018

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Functional human endogenous retroviral LTR transcription start sites are located between the R and U5 regions

14 July 2018

1 reference

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Transcription of two human genes from a bidirectional endogenous retrovirus promoter

14 July 2018

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Transcriptional activation by bidirectional RNA polymerase II elongation over a silent promoter

14 July 2018

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Combined evidence annotation of transposable elements in genome sequences

14 July 2018

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Repbase Update, a database of eukaryotic repetitive elements

14 July 2018

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Use of endogenous retroviral sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy

14 July 2018

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14 July 2018

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De novo identification of repeat families in large genomes

14 July 2018

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14 July 2018

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Sobo, a recently amplified satellite repeat of potato, and its implications for the origin of tandemly repeated sequences

14 July 2018

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Sequence variability, gene structure, and expression of full-length human endogenous retrovirus H.

14 July 2018

1 reference

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14 July 2018

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Automated de novo identification of repeat sequence families in sequenced genomes

14 July 2018

1 reference

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Immunolocalization studies of an antisense protein in HIV-1-infected cells and viral particles

14 July 2018

1 reference

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Resolution of the early placental mammal radiation using Bayesian phylogenetics

14 July 2018

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14 July 2018

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Functional characterization of a piscine retroviral promoter

14 July 2018

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Replication of Mus dunni endogenous retrovirus depends on promoter activation followed by enhancer multimerization.

14 July 2018

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R region sequences in the long terminal repeat of a murine retrovirus specifically increase expression of unspliced RNAs.

14 July 2018

1 reference

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Diversity of human endogenous retrovirus class II-like sequences

14 July 2018

1 reference

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14 July 2018

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Proviral structure, chromosomal location, and expression of HERV-K-T47D, a novel human endogenous retrovirus derived from T47D particles.

14 July 2018

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The secondary structure of the R region of a murine leukemia virus is important for stimulation of long terminal repeat-driven gene expression.

14 July 2018

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The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664473

Mechanism and regulation of mRNA polyadenylation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664473

A novel method to develop highly specific models for regulatory units detects a new LTR in GenBank which contains a functional promoter

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664473

Comparative analyses of LTRs of the ERV-H family of primate-specific retrovirus-like elements isolated from marmoset, African green monkey, and man.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664473

Identification of endogenous retroviral sequences based on modular organization: proviral structure at the SSAV1 locus

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664473

Common modular structure of lentivirus LTRs.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664473

MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664473

The promoter activity of long terminal repeats of the HERV-H family of human retrovirus-like elements is critically dependent on Sp1 family proteins interacting with a GC/GT box located immediately 3' to the TATA box

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664473

A mouse mammary tumor virus promoter element near the transcription initiation site

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664473

Hidden Markov models in computational biology. Applications to protein modeling

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664473

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664473

Transcription termination and polyadenylation in retroviruses

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664473

Maximum entropy weighting of aligned sequences of proteins or DNA

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664473

Nucleotide sequences of the retroviral long terminal repeats and their adjacent regions

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664473

Sequences flanking the repeat arrays of human minisatellites: association with tandem and dispersed repeat elements.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664473

Polyadenylation function and sequence variability of the long terminal repeats of the human endogenous retrovirus-like family RTVL-H.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664473

Functional analysis of the long terminal repeats of intracisternal A-particle genes: sequences within the U3 region determine both the efficiency and direction of promoter activity

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664473

Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664473

Sequence logos: a new way to display consensus sequences

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664473

Functional heterogeneity of a large family of human LTR-like promoters and enhancers

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664473

The HTLV-I rex response element mediates a novel form of mRNA polyadenylation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664473

Transcriptional initiation and postinitiation effects of murine leukemia virus long terminal repeat R-region sequences

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664473

Identification of regulatory elements within the minimal promoter region of the human endogenous ERV9 proviruses: accurate transcription initiation is controlled by an Inr-like element

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664473

LTR_STRUC: a novel search and identification program for LTR retrotransposons

14 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0005179

Efficient algorithms and software for detection of full-length LTR retrotransposons.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0005179

A tutorial on hidden Markov models and selected applications in speech recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0005179

Self-organizing map-based discovery and visualization of human endogenous retroviral sequence groups

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0005179

Definition and variation of human endogenous retrovirus H.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0005179

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0005179

Subfamilies and nearest-neighbour dendrogram for the LTRs of human endogenous retroviruses HERV-K mapped on human chromosome 19: physical neighbourhood does not correlate with identity level.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0005179

Solitary HERV-K LTRs possess bi-directional promoter activity and contain a negative regulatory element in the U5 region

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19365549

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The transcriptional activity of HERV-I LTR is negatively regulated by its cis-elements and wild type p53 tumor suppressor protein

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19365549

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0005179

1 reference

26 July 2017

0 references

1 reference

26 July 2017

1 reference