The DOI matches its Crossref record; 22 of the 22 references it cites were found in a registry or an index.
SFmap: a web server for motif analysis and prediction of splicing factor binding sites
Open accessAbstract
Alternative splicing (AS) is a post-transcriptional process considered to be responsible for the huge diversity of proteins in higher eukaryotes. AS events are regulated by different splicing factors (SFs) that bind to sequence elements on the RNA. SFmap is a web server for predicting putative SF binding sites in genomic data (http://sfmap.technion.ac.il). SFmap implements the COS(WR) algorithm, which computes similarity scores for a given regulatory motif based on information derived from its sequence environment and its evolutionary conservation. Input for SFmap is a human genomic sequence or a list of sequences in FASTA format that can either be uploaded from a file or pasted into a window. SFmap searches within a given sequence for significant hits of binding motifs that are either stored in our database or defined by the user. SFmap results are provided both as a text file and as a graphical web interface.
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“binding sites for many splice factors, including YB-1, SRp20, Sam68, SLM2, SRp40, and multiple hnRNPs (including hnRNP K), were predicted in the near vicinity of the junction site by SpliceAid 2 (30) and SFmap (version 1.8; ref. 31; Fig. 1C).”
From Discovery of a Novel CIP2A Variant (NOCIVA) with Clinical Relevance in Predicting TKI Resistance in Myeloid Leukemias (2021) · cites this paper as [31]
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Cites
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
The UCSC Genome Browser database: update 2011
Fujita, P. A., Rhead, B., Zweig, A. S., Hinrichs, A. S., Karolchik, D., Cline, M., Goldman, M. J., Barber, G. P., Clawson, H., Coelho, A., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq963 · Cited by 1,843
ESEfinder: a web resource to identify exonic splicing enhancers
Cartegni, L. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg616 · Cited by 1,593
Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches
Chen, M., & Manley, J. L. (2009) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2777 · Cited by 1,284
Cooper, T. A., Wan, L., & Dreyfuss, G. (2009) · Cell · doi:10.1016/j.cell.2009.02.011 · Cited by 1,198
Splicing regulation: From a parts list of regulatory elements to an integrated splicing code
Wang, Z., & Burge, C. B. (2008) · RNA · doi:10.1261/rna.876308 · Cited by 1,127
Systematic Identification and Analysis of Exonic Splicing Silencers
Wang, Z., Rolish, M. E., Yeo, G. W.-M., Tung, V., Mawson, M., & Burge, C. B. (2004) · Cell · doi:10.1016/j.cell.2004.11.010 · Cited by 678
Smith, P. J., Zhang, C., Wang, J., Chew, S. L., Zhang, M. Q., & Krainer, A. R. (2006) · Human Molecular Genetics · doi:10.1093/hmg/ddl171 · Cited by 514
Multiple roles of TDP-43 in gene expression, splicing regulation, and human disease
Buratti, E. (2007) · Frontiers in bioscience · doi:10.2741/2727 · Cited by 493
The UCSC Genome Browser Database: update 2009
Kuhn, R. M., Karolchik, D., Zweig, A. S., Wang, T., Smith, K. E., Rosenbloom, K. R., Rhead, B., Raney, B. J., Pohl, A., Pheasant, M., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn875 · Cited by 388
SC35 autoregulates its expression by promoting splicing events that destabilize its mRNAs
Sureau, A., Gattoni, R., Dooghe, Y., Ste'venin, J., & Soret, J. (2001) · EMBO Journal · doi:10.1093/emboj/20.7.1785 · Cited by 347
Goren, A., Ram, O., Amit, M., Keren, H., Lev-Maor, G., Vig, I., Pupko, T., & Ast, G. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.05.008 · Cited by 301
RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons
Fairbrother, W. G., Yeo, G. W.-M., Yeh, R., Goldstein, P., Mawson, M., Sharp, P. A., & Burge, C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh393 · Cited by 288
RegRNA: an integrated web server for identifying regulatory RNA motifs and elements
Huang, H.-L., Chien, C.-H., Jen, K.-H., & Huang, H. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl333 · Cited by 242
Finding signals that regulate alternative splicing in the post-genomic era.
Ladd, A. N., & Cooper, T. A. (2002) · Genome biology · doi:10.1186/gb-2002-3-11-reviews0008 · Cited by 219
Chasin, L. A. (2007) · Advances in experimental medicine and biology · doi:10.1007/978-0-387-77374-2_6 · Cited by 143
Exon Inclusion Is Dependent on Predictable Exonic Splicing Enhancers
Zhang, X. H.-F., Kangsamaksin, T., Chao, M. S. P., Banerjee, J. K., & Chasin, L. A. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.16.7323-7332.2005 · Cited by 117
Yamauchi, F. (2004) · Nucleic Acids Research · doi:10.1093/nar/gnh176 · Cited by 101
SROOGLE: webserver for integrative, user-friendly visualization of splicing signals
Schwartz, S., Hall, E., & Ast, G. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp320 · Cited by 86
A computational approach for genome-wide mapping of splicing factor binding sites
Akerman, M., David-Eden, H., Pinter, R. Y., & Mandel‐Gutfreund, Y. (2009) · Genome biology · doi:10.1186/gb-2009-10-3-r30 · Cited by 73
Self-citationAntagonistic factors control the unproductive splicing of SC35 terminal intron
Dreumont, N., Hardy, S., Behm‐Ansmant, I., Kister, L., Branlant, C., Stévenin, J., & Bourgeois, C. F. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp1086 · Cited by 48
Co-occupancy of two Pumilio molecules on a single hunchback NRE
Gupta, Y. K., Lee, T. H., Edwards, T. A., Escalante, C. R., Kadyrova, L. Y., Wharton, R. P., & Aggarwal, A. K. (2009) · RNA · doi:10.1261/rna.1327609 · Cited by 26
Research works printed but not linked: 1
- 2009, Nucleic Acids Research, 38, 1353
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Function of alternative splicing
Stamm, S., Ben‐Ari, S., Rafalska, I., Tang, Y., Zhang, Z., Toiber, D., Thanaraj, T. A., & Soreq, H. (2004) · Gene · doi:10.1016/j.gene.2004.10.022 · Cited by 1,398
Function of alternative splicing
Kelemen, O., Convertini, P., Zhang, Z., Wen, Y., Shen, M., Falaleeva, M., & Stamm, S. (2013) · Gene · doi:10.1016/j.gene.2012.07.083 · Cited by 743
RBPmap: a web server for mapping binding sites of RNA-binding proteins
Paz, I., Kosti, I., Ares, M., Cline, M., & Mandel‐Gutfreund, Y. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku406 · Cited by 581
Self-citationHunt, R., Simhadri, V. L., Iandoli, M., Sauna, Z. E., & Kimchi‐Sarfaty, C. (2014) · Trends in Genetics · doi:10.1016/j.tig.2014.04.006 · Cited by 397
Comprehensive identification of internal structure and alternative splicing events in circular RNAs
Gao, Y., Wang, J., Zheng, Y., Zhang, J., Chen, S., & Zhao, F. (2016) · Nature Communications · doi:10.1038/ncomms12060 · Cited by 290
Metadata
- Authors
- Paz, I., Akerman, M., Dror, I., Kosti, I., & Mandel-Gutfreund, Y.
- Affiliations
- Technion – Israel Institute of Technology (IL)
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-05-25
- Volume
- 38
- Issue
- Web Server
- Pages
- W281-W285
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC2896136
- OpenAlex
- W1988971922
- Cited by
- 102
- References
- 22
- Citations by year
- 2025: 2 · 2023: 4 · 2022: 6 · 2021: 4 · 2020: 3 · 2019: 9 · 2018: 5 · 2017: 9 · 2016: 10 · 2015: 11 · 2014: 16 · 2013: 6 · 2012: 9
- FWCI
- 2.73
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
- HighWire Press Open Archive (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- alternative splicing, evolutionary conservation, human genome sequence, web server
- MeSH terms
- Algorithms, Binding Sites, Humans, Software, User-Computer Interface, Genome, Human, RNA-Binding Proteins, Alternative Splicing, Sequence Analysis, RNA, Internet
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