RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts (Q34946799)

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English	RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts	scientific article

Statements

scholarly article

1 reference

Europe PubMed Central

5 August 2017

RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts (English)

1 reference

Europe PubMed Central

5 August 2017

Plasmodium falciparum

0 references

ATP-dependent RNA helicase DDX23, putative

1 reference

10 September 2018

small nuclear ribonucleoprotein Sm D3, putative

1 reference

11 September 2018

U6 snRNA-associated Sm-like protein LSm5, putative

1 reference

12 September 2018

pre-mRNA-splicing factor SLU7, putative

0 references

small nuclear ribonucleoprotein Sm D2, putative

0 references

pre-mRNA-processing protein 45, putative

0 references

pre-mRNA-processing factor 19, putative

0 references

splicing factor 3B subunit 1, putative

0 references

pre-mRNA-splicing factor RDS3, putative

0 references

pre-mRNA-splicing factor CEF1, putative

0 references

U6 snRNA-associated Sm-like protein LSm7, putative

0 references

pre-mRNA-splicing factor CWC15, putative

0 references

U5 small nuclear ribonucleoprotein 40 kDa protein, putative

0 references

small nuclear ribonucleoprotein G, putative

0 references

U6 snRNA-associated Sm-like protein LSm3, putative

0 references

U4/U6.U5 small nuclear ribonucleoprotein, putative

0 references

small nuclear ribonucleoprotein Sm D3, putative

0 references

splicing factor 3A subunit 3, putative

0 references

small nuclear ribonucleoprotein Sm D1, putative

0 references

13 kDa ribonucleoprotein-associated protein, putative

0 references

pre-mRNA-processing factor 6, putative

0 references

U6 snRNA-associated Sm-like protein LSm4, putative

0 references

pre-mRNA-splicing factor CLF1, putative

0 references

pre-mRNA-processing-splicing factor 8, putative

0 references

U4/U6 small nuclear ribonucleoprotein PRP31, putative

0 references

splicing factor 3B subunit 4, putative

0 references

small nuclear ribonucleoprotein-associated protein B, putative

0 references

splicing factor 3A subunit 2, putative

0 references

splicing factor 3B subunit 5, putative

0 references

U1 small nuclear ribonucleoprotein 70 kDa homolog, putative

0 references

transformer-2 protein homolog beta, putative

0 references

U5 small nuclear ribonucleoprotein component, putative

0 references

U4/U6.U5 tri-snRNP-associated protein 1, putative

0 references

U6 snRNA-associated Sm-like protein LSm2, putative

0 references

pre-mRNA-splicing factor BUD31, putative

0 references

splicing factor 3A subunit 1, putative

0 references

U6 snRNA-associated Sm-like protein LSm5, putative

0 references

splicing factor 3B subunit 2, putative

0 references

pre-mRNA-splicing factor ISY1, putative

0 references

U6 snRNA-associated Sm-like protein LSm6, putative

0 references

regulator of nonsense transcripts 3B, putative

0 references

U4/U6 small nuclear ribonucleoprotein PRP4, putative

0 references

small nuclear ribonucleoprotein E, putative

0 references

intron-binding protein aquarius, putative

0 references

U4/U6 small nuclear ribonucleoprotein PRP3, putative

0 references

U4/U6.U5 tri-snRNP-associated protein 2, putative

0 references

pre-mRNA-splicing factor SLU7, putative

0 references

U1 small nuclear ribonucleoprotein C, putative

0 references

splicing factor 3B subunit 3, putative

0 references

pre-mRNA-splicing factor SYF1, putative

0 references

small nuclear ribonucleoprotein Sm D2, putative

0 references

pre-mRNA-processing protein 45, putative

0 references

pre-mRNA-processing factor 19, putative

0 references

splicing factor 3B subunit 1, putative

0 references

pre-mRNA-splicing factor RDS3, putative

0 references

pre-mRNA-splicing factor CEF1, putative

0 references

U6 snRNA-associated Sm-like protein LSm7, putative

0 references

pre-mRNA-splicing factor CWC15, putative

0 references

U5 small nuclear ribonucleoprotein 40 kDa protein, putative

0 references

small nuclear ribonucleoprotein G, putative

0 references

U6 snRNA-associated Sm-like protein LSm3, putative

0 references

U4/U6.U5 small nuclear ribonucleoprotein, putative

0 references

small nuclear ribonucleoprotein Sm D3, putative

0 references

splicing factor 3A subunit 3, putative

0 references

U6 snRNA-associated Sm-like protein LSm4, putative

0 references

pre-mRNA-processing factor 6, putative

0 references

13 kDa ribonucleoprotein-associated protein, putative

0 references

small nuclear ribonucleoprotein Sm D1, putative

0 references

pre-mRNA-splicing factor CLF1, putative

0 references

pre-mRNA-processing-splicing factor 8, putative

0 references

U4/U6 small nuclear ribonucleoprotein PRP31, putative

0 references

splicing factor 3B subunit 4, putative

0 references

small nuclear ribonucleoprotein-associated protein B, putative

0 references

splicing factor 3A subunit 2, putative

0 references

splicing factor 3B subunit 5, putative

0 references

U1 small nuclear ribonucleoprotein 70 kDa homolog, putative

0 references

transformer-2 protein homolog beta, putative

0 references

U5 small nuclear ribonucleoprotein component, putative

0 references

U4/U6.U5 tri-snRNP-associated protein 1, putative

0 references

U6 snRNA-associated Sm-like protein LSm2, putative

0 references

pre-mRNA-splicing factor BUD31, putative

0 references

splicing factor 3A subunit 1, putative

0 references

U6 snRNA-associated Sm-like protein LSm5, putative

0 references

splicing factor 3B subunit 2, putative

0 references

pre-mRNA-splicing factor ISY1, putative

0 references

U6 snRNA-associated Sm-like protein LSm6, putative

0 references

regulator of nonsense transcripts 3B, putative

0 references

U4/U6 small nuclear ribonucleoprotein PRP4, putative

0 references

small nuclear ribonucleoprotein E, putative

0 references

intron-binding protein aquarius, putative

0 references

U4/U6 small nuclear ribonucleoprotein PRP3, putative

0 references

U4/U6.U5 tri-snRNP-associated protein 2, putative

0 references

U1 small nuclear ribonucleoprotein C, putative

0 references

splicing factor 3B subunit 3, putative

0 references

pre-mRNA-splicing factor SYF1, putative

0 references

small nuclear ribonucleoprotein Sm D2, putative

0 references

pre-mRNA-processing protein 45, putative

0 references

pre-mRNA-processing factor 19, putative

0 references

splicing factor 3B subunit 1, putative

0 references

U4/U6.U5 tri-snRNP-associated protein 1, putative

0 references

pre-mRNA-splicing factor CLF1, putative

0 references

pre-mRNA-processing-splicing factor 8, putative

0 references

U4/U6 small nuclear ribonucleoprotein PRP31, putative

0 references

U6 snRNA-associated Sm-like protein LSm2, putative

0 references

pre-mRNA-splicing factor BUD31, putative

0 references

pre-mRNA-splicing factor SLU7, putative

0 references

splicing factor 3A subunit 2, putative

0 references

pre-mRNA-splicing factor CWC15, putative

0 references

U1 small nuclear ribonucleoprotein C, putative

0 references

U4/U6.U5 small nuclear ribonucleoprotein, putative

0 references

U6 snRNA-associated Sm-like protein LSm3, putative

0 references

small nuclear ribonucleoprotein G, putative

0 references

U5 small nuclear ribonucleoprotein 40 kDa protein, putative

0 references

splicing factor 3A subunit 3, putative

0 references

transformer-2 protein homolog beta, putative

0 references

transformer-2 protein homolog beta, putative

0 references

U5 small nuclear ribonucleoprotein component, putative

0 references

pre-mRNA-splicing factor RDS3, putative

0 references

pre-mRNA-splicing factor CEF1, putative

0 references

U6 snRNA-associated Sm-like protein LSm4, putative

0 references

pre-mRNA-processing factor 6, putative

0 references

13 kDa ribonucleoprotein-associated protein, putative

0 references

small nuclear ribonucleoprotein Sm D1, putative

0 references

U6 snRNA-associated Sm-like protein LSm7, putative

0 references

splicing factor 3B subunit 3, putative

0 references

pre-mRNA-splicing factor SYF1, putative

0 references

U4/U6 small nuclear ribonucleoprotein PRP3, putative

0 references

U4/U6.U5 tri-snRNP-associated protein 2, putative

0 references

U6 snRNA-associated Sm-like protein LSm6, putative

0 references

regulator of nonsense transcripts 3B, putative

0 references

U4/U6 small nuclear ribonucleoprotein PRP4, putative

0 references

small nuclear ribonucleoprotein E, putative

0 references

intron-binding protein aquarius, putative

0 references

splicing factor 3B subunit 5, putative

0 references

U1 small nuclear ribonucleoprotein 70 kDa homolog, putative

0 references

small nuclear ribonucleoprotein-associated protein B, putative

0 references

splicing factor 3B subunit 4, putative

0 references

splicing factor 3B subunit 2, putative

0 references

pre-mRNA-splicing factor ISY1, putative

0 references

splicing factor 3A subunit 1, putative

0 references

1 reference

based on heuristic

inferred from title

1 reference

based on heuristic

inferred from title

alternative mRNA splicing, via spliceosome

1 reference

based on heuristic

inferred from title

1 reference

based on heuristic

inferred from title

Katherine Lontok

object named as

Katherine Sorber

1

0 references

author name string

Michelle T Dimon

2

1 reference

Europe PubMed Central

5 August 2017

Joseph L DeRisi

3

1 reference

Europe PubMed Central

5 August 2017

language of work or name

0 references

publication date

17 January 2011

1 reference

Europe PubMed Central

5 August 2017

Nucleic Acids Research

1 reference

Europe PubMed Central

5 August 2017

39

1 reference

Europe PubMed Central

5 August 2017

9

1 reference

Europe PubMed Central

5 August 2017

3820-3835

1 reference

Europe PubMed Central

5 August 2017

copyright license

Creative Commons Attribution-NonCommercial 2.5 Generic

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

0 references

HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089446

8 July 2018

Deciphering the splicing code

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089446

8 July 2018

New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089446

8 July 2018

SF2/ASF autoregulation involves multiple layers of post-transcriptional and translational control

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089446

8 July 2018

A global view of the nonprotein-coding transcriptome in Plasmodium falciparum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089446

8 July 2018

Regulatory roles of natural antisense transcripts

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089446

8 July 2018

A Plasmodium falciparum FcB1-schizont-EST collection providing clues to schizont specific gene structure and polymorphism

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8 July 2018

TopHat: discovering splice junctions with RNA-Seq

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8 July 2018

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

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8 July 2018

The SR protein family of splicing factors: master regulators of gene expression

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The long march: a sample preparation technique that enhances contig length and coverage by high-throughput short-read sequencing

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8 July 2018

Isolation and characterization of Plasmodium falciparum UAP56 homolog: evidence for the coupling of RNA binding and splicing activity by site-directed mutations

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3089446

8 July 2018

Multiple and specific mRNA processing targets for the major human hnRNP proteins

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8 July 2018

The transmembrane isoform of Plasmodium falciparum MAEBL is essential for the invasion of Anopheles salivary glands

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Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

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Computational screen for spliceosomal RNA genes aids in defining the phylogenetic distribution of major and minor spliceosomal components

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8 July 2018

Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis

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cDNA sequences reveal considerable gene prediction inaccuracy in the Plasmodium falciparum genome.

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Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle

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8 July 2018

Different levels of alternative splicing among eukaryotes

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8 July 2018

Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species

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8 July 2018

What are DNA sequence motifs?

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8 July 2018

Reverse transcriptase template switching and false alternative transcripts.

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8 July 2018

A suboptimal 5' splice site downstream of HIV-1 splice site A1 is required for unspliced viral mRNA accumulation and efficient virus replication

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8 July 2018

Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts

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8 July 2018

Antisense transcription in the mammalian transcriptome

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8 July 2018

Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation

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8 July 2018

Nonsense-mediated mRNA decay: molecular insights and mechanistic variations across species

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8 July 2018

WebLogo: A Sequence Logo Generator

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8 July 2018

The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosome

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8 July 2018

Definition of a spliceosome interaction domain in yeast Prp2 ATPase

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8 July 2018

The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum

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Discovery of gene function by expression profiling of the malaria parasite life cycle

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8 July 2018

Multiple splice variants encode a novel adenylyl cyclase of possible plastid origin expressed in the sexual stage of the malaria parasite Plasmodium falciparum

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8 July 2018

Gene discovery in the apicomplexa as revealed by EST sequencing and assembly of a comparative gene database

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8 July 2018

Taq DNA polymerase slippage mutation rates measured by PCR and quasi-likelihood analysis: (CA/GT)n and (A/T)n microsatellites

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Genome sequence of the human malaria parasite Plasmodium falciparum

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The generic genome browser: a building block for a model organism system database

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BLAT—The BLAST-Like Alignment Tool

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PfPK6, a novel cyclin-dependent kinase/mitogen-activated protein kinase-related protein kinase from Plasmodium falciparum

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tRNA ligase is required for regulated mRNA splicing in the unfolded protein response

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Demonstration of alternative splicing of a pre-mRNA expressed in the blood stage form of Plasmodium falciparum

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Genome-wide identification of genes upregulated at the onset of gametocytogenesis in Plasmodium falciparum

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21 January 2018

A screen for conserved sequences with biased base composition identifies noncoding RNAs in the A-T rich genome of Plasmodium falciparum.

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21 January 2018

Cyclic nucleotide-specific phosphodiesterases of Plasmodium falciparum: PfPDEalpha, a non-essential cGMP-specific PDE that is an integral membrane protein.

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21 January 2018

A small-scale systematic analysis of alternative splicing in Plasmodium falciparum.

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21 January 2018

Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction.

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RNA polymerase II synthesizes antisense RNA in Plasmodium falciparum

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21 January 2018

Choosing BLAST options for better detection of orthologs as reciprocal best hits.

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21 January 2018

Isolation of an active step I spliceosome and composition of its RNP core.

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21 January 2018

Release of SF3 from the intron branchpoint activates the first step of pre-mRNA splicing

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21 January 2018

Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs

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21 January 2018

Categorization and characterization of transcript-confirmed constitutively and alternatively spliced introns and exons from human

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21 January 2018

Widespread distribution of antisense transcripts in the Plasmodium falciparum genome

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21 January 2018

PlasmoDB: An integrative database of the Plasmodium falciparum genome. Tools for accessing and analyzing finished and unfinished sequence data. The Plasmodium Genome Database Collaborative

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mutations in a yeast intron demonstrate the importance of specific conserved nucleotides for the two stages of nuclear mRNA splicing

1 reference

https://pubmed.ncbi.nlm.nih.gov/21245033

12 December 2020

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10.1093/NAR/GKQ1223

1 reference

Europe PubMed Central

5 August 2017

1 reference

Europe PubMed Central

5 August 2017

1 reference

Europe PubMed Central

5 August 2017

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