RBPmap protocols

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RBPmap specifications

Information


Unique identifier OMICS_06127
Name RBPmap
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Invertebrates
    • Drosophila melanogaster
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Maintainer


  • person_outline Yael Mandel-Gutfreund <>

Publication for RBPmap

RBPmap in pipelines

 (2)
2016
PMCID: 4778320
PMID: 26939613
DOI: 10.1186/s12864-016-2521-9

[…] were then mapped to the genome by blat [] and visualized by igv []. the annotation of transcript sequence and the structure of 5’ utr sequence of prickle1 were retrieved from ucsc genome browser []. rbpmap [] was then used to predict the rbp binding sites in the prickle1 5’ utr region., the expression pattern of prickle1 transcript of uc001rnl.2 and uc010skw.1 was profiled, and two […]

2016
PMCID: 4931246
PMID: 27350239
DOI: 10.1038/ncomms12060

[…] for 21 human splicing factors and 95 rna-binding proteins were then predicted for each exon and its adjacent intronic/intergenic sequences with two folds of exon lengths using online tools sfmap and rbpmap, respectively. the binding density was then calculated as the percentage of binding sites in the whole length of the sequence for prediction. for each subset of exons, such binding densities […]


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RBPmap in publications

 (21)
PMCID: 5871876
PMID: 29593233
DOI: 10.1038/s41598-018-23730-7

[…] though partial mutants lack only few nucleotides of the 16–31 region, the deletion of the whole 16–31 region is necessary to fully recover the translation of the main orf in the 1b-vdac mrna., the rbpmap server (http://rbpmap.technion.ac.il/) was used to identify the presence of rna motif(s) able to bind known rna-binding proteins (rbps). using as a query the 1a- or 1b-5′ utr sequences, […]

PMCID: 5899436
PMID: 29581274
DOI: 10.1073/pnas.1714573115

[…] 4) showed a larger increase in exon 14 inclusion relative to sh-tdp43 or sh-srsf3 alone, consistent with our previous results (). we thereafter predicted tdp43- and srsf3-binding motifs using the rbpmap website and identified putative target sequences for srsf3 and tdp43 located in the syngap1 exon 14 (blue in , upper) and intron 14 (red in , upper), respectively. this indicated that tdp43 […]

PMCID: 5819218
PMID: 29458410
DOI: 10.1186/s13104-018-3250-8

[…] forms stable ribonucleoproteins (rnps) with hnrnpl. these possibilities are being explored., to better understand the protein binding repertoire of ebv-sisrna-1 and ebv-sisrna-2, we used the program rbpmap [] to predict human host rna binding proteins (rbps) that might directly interact. both type 1 (nc_007605) and type 2 (nc_009334) ebv sequences were analyzed using a sequence fragment […]

PMCID: 5855702
PMID: 29415469
DOI: 10.3390/ijms19020480

[…] reading absorbance at 580 nm 24 h, 48 h, 72 h and 96 h after transfection., rbp binding site predictions within circsmarca5 sequence were done by providing the circsmarca5 fasta sequence as input in rbpmap [], attract (https://attract.cnic.es/index) and catrapid (http://service.tartaglialab.com/page/catrapid_group) online tools, respectively. inverted repeats were retrieved using emboss […]

PMCID: 5766645
PMID: 29358943
DOI: 10.3389/fgene.2017.00227

[…] together and published in several databases, including the protein–rna interface database (pridb) (lewis et al., ), the nucleic acid–protein interaction database (npidb) (kirsanov et al., ), and rbpmap (paz et al., ). a comprehensive understanding of the characteristic rna–protein interacting regions is especially important in the field of molecular biology, and a comparison […]


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RBPmap institution(s)
Department of Biology, Technion - Israel Institute of Technology, Technion City, Haifa, Israel
RBPmap funding source(s)
Israel United States Binational Science Foundation (BSF)

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