Enhancing the GABI-Kat Arabidopsis thaliana T-DNA insertion mutant database by incorporating Araport11 annotation
Kleinbölting N, Huep G, Weisshaar B (2017)
Plant and Cell Physiology 58(1): e7.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
Download
![Open access file OA](https://pub.uni-bielefeld.de/images/access_open.png)
Einrichtung
Abstract / Bemerkung
SimpleSearch provides access to a database containing information about T-DNA insertion lines of the GABI-Kat collection of Arabidopsis thaliana mutants. These mutants are an important tool for reverse genetics, and GABI-Kat is the second largest collection of such T-DNA insertion mutants. Insertion sites were deduced from flanking sequence tags (FSTs), and the database contains information about mutant plant lines as well as insertion alleles. Here, we describe improvements within the interface (available at http://www.gabi-kat.de/db/genehits.php) and with regard to the database content that have been realized in the last five years. These improvements include the integration of the Araport11 genome sequence annotation data containing the recently updated A. thaliana structural gene descriptions, an updated visualization component that displays groups of insertions with very similar insertion positions, mapped confirmation sequences, and primers. The visualization component provides a quick way to identify insertions of interest, and access to improved data about the exact structure of confirmed insertion alleles. In addition, the database content has been extended by incorporating additional insertion alleles that were detected during the confirmation process, as well as by adding new FSTs that have been produced during continued efforts to complement gaps in FST availability. Finally, the current database content regarding predicted and confirmed insertion alleles as well as primer sequences has been made available as downloadable flat files.
Erscheinungsjahr
2017
Zeitschriftentitel
Plant and Cell Physiology
Band
58
Ausgabe
1
Art.-Nr.
e7
ISSN
0032-0781, 1471-9053
Page URI
https://pub.uni-bielefeld.de/record/2907696
Zitieren
Kleinbölting N, Huep G, Weisshaar B. Enhancing the GABI-Kat Arabidopsis thaliana T-DNA insertion mutant database by incorporating Araport11 annotation. Plant and Cell Physiology. 2017;58(1): e7.
Kleinbölting, N., Huep, G., & Weisshaar, B. (2017). Enhancing the GABI-Kat Arabidopsis thaliana T-DNA insertion mutant database by incorporating Araport11 annotation. Plant and Cell Physiology, 58(1), e7. doi:10.1093/pcp/pcw205
Kleinbölting, Nils, Huep, Gunnar, and Weisshaar, Bernd. 2017. “Enhancing the GABI-Kat Arabidopsis thaliana T-DNA insertion mutant database by incorporating Araport11 annotation”. Plant and Cell Physiology 58 (1): e7.
Kleinbölting, N., Huep, G., and Weisshaar, B. (2017). Enhancing the GABI-Kat Arabidopsis thaliana T-DNA insertion mutant database by incorporating Araport11 annotation. Plant and Cell Physiology 58:e7.
Kleinbölting, N., Huep, G., & Weisshaar, B., 2017. Enhancing the GABI-Kat Arabidopsis thaliana T-DNA insertion mutant database by incorporating Araport11 annotation. Plant and Cell Physiology, 58(1): e7.
N. Kleinbölting, G. Huep, and B. Weisshaar, “Enhancing the GABI-Kat Arabidopsis thaliana T-DNA insertion mutant database by incorporating Araport11 annotation”, Plant and Cell Physiology, vol. 58, 2017, : e7.
Kleinbölting, N., Huep, G., Weisshaar, B.: Enhancing the GABI-Kat Arabidopsis thaliana T-DNA insertion mutant database by incorporating Araport11 annotation. Plant and Cell Physiology. 58, : e7 (2017).
Kleinbölting, Nils, Huep, Gunnar, and Weisshaar, Bernd. “Enhancing the GABI-Kat Arabidopsis thaliana T-DNA insertion mutant database by incorporating Araport11 annotation”. Plant and Cell Physiology 58.1 (2017): e7.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Copyright Statement:
Dieses Objekt ist durch das Urheberrecht und/oder verwandte Schutzrechte geschützt. [...]
Volltext(e)
Name
201701_NKl-GHu_GKat-DB_PCP.pdf
637.75 KB
Access Level
![Open access file OA](https://pub.uni-bielefeld.de/images/access_open.png)
Zuletzt Hochgeladen
2019-09-06T09:18:42Z
MD5 Prüfsumme
4fbc677e293d07b330c0958740bc6d1c
Daten bereitgestellt von European Bioinformatics Institute (EBI)
2 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
Highly efficient heritable targeted deletions of gene clusters and non-coding regulatory regions in Arabidopsis using CRISPR/Cas9.
Durr J, Papareddy R, Nakajima K, Gutierrez-Marcos J., Sci Rep 8(1), 2018
PMID: 29535386
Durr J, Papareddy R, Nakajima K, Gutierrez-Marcos J., Sci Rep 8(1), 2018
PMID: 29535386
Editorial: Plant and Cell Physiology's 2017 Database Issue.
Ohyanagi H, Obayashi T, Yano K., Plant Cell Physiol 58(1), 2017
PMID: 28158372
Ohyanagi H, Obayashi T, Yano K., Plant Cell Physiol 58(1), 2017
PMID: 28158372
41 References
Daten bereitgestellt von Europe PubMed Central.
Genome-wide insertional mutagenesis of Arabidopsis thaliana.
Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen H, Shinn P, Stevenson DK, Zimmerman J, Barajas P, Cheuk R, Gadrinab C, Heller C, Jeske A, Koesema E, Meyers CC, Parker H, Prednis L, Ansari Y, Choy N, Deen H, Geralt M, Hazari N, Hom E, Karnes M, Mulholland C, Ndubaku R, Schmidt I, Guzman P, Aguilar-Henonin L, Schmid M, Weigel D, Carter DE, Marchand T, Risseeuw E, Brogden D, Zeko A, Crosby WL, Berry CC, Ecker JR., Science 301(5633), 2003
PMID: 12893945
Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen H, Shinn P, Stevenson DK, Zimmerman J, Barajas P, Cheuk R, Gadrinab C, Heller C, Jeske A, Koesema E, Meyers CC, Parker H, Prednis L, Ansari Y, Choy N, Deen H, Geralt M, Hazari N, Hom E, Karnes M, Mulholland C, Ndubaku R, Schmidt I, Guzman P, Aguilar-Henonin L, Schmid M, Weigel D, Carter DE, Marchand T, Risseeuw E, Brogden D, Zeko A, Crosby WL, Berry CC, Ecker JR., Science 301(5633), 2003
PMID: 12893945
Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
The Arabidopsis information resource: Making and mining the "gold standard" annotated reference plant genome.
Berardini TZ, Reiser L, Li D, Mezheritsky Y, Muller R, Strait E, Huala E., Genesis 53(8), 2015
PMID: 26201819
Berardini TZ, Reiser L, Li D, Mezheritsky Y, Muller R, Strait E, Huala E., Genesis 53(8), 2015
PMID: 26201819
GABI-DUPLO: a collection of double mutants to overcome genetic redundancy in Arabidopsis thaliana.
Bolle C, Huep G, Kleinbolting N, Haberer G, Mayer K, Leister D, Weisshaar B., Plant J. 75(1), 2013
PMID: 23573814
Bolle C, Huep G, Kleinbolting N, Haberer G, Mayer K, Leister D, Weisshaar B., Plant J. 75(1), 2013
PMID: 23573814
Perspectives on Systematic Analyses of Gene Function in Arabidopsis thaliana: New Tools, Topics and Trends.
Bolle C, Schneider A, Leister D., Curr. Genomics 12(1), 2011
PMID: 21886450
Bolle C, Schneider A, Leister D., Curr. Genomics 12(1), 2011
PMID: 21886450
BLAST+: architecture and applications
Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K.., 2009
Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K.., 2009
Araport11: a complete reannotation of the Arabidopsis thaliana reference genome
Cheng C-Y., Krishnakumar V., Chan A., Thibaud-Nissen F., Schobel S., Town C.D.., 2016
Cheng C-Y., Krishnakumar V., Chan A., Thibaud-Nissen F., Schobel S., Town C.D.., 2016
Multiplex genome engineering using CRISPR/Cas systems.
Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F., Science 339(6121), 2013
PMID: 23287718
Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F., Science 339(6121), 2013
PMID: 23287718
ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering
Gaj T., Gersbach C.A., Barbas C.F.r.., 2013
Gaj T., Gersbach C.A., Barbas C.F.r.., 2013
The introduction and expression of transgenes in plants
Gelvin SB., Curr. Opin. Biotechnol. 9(2), 1998
PMID: 9664052
Gelvin SB., Curr. Opin. Biotechnol. 9(2), 1998
PMID: 9664052
AGROBACTERIUM AND PLANT GENES INVOLVED IN T-DNA TRANSFER AND INTEGRATION.
Gelvin SB., Annu. Rev. Plant Physiol. Plant Mol. Biol. 51(), 2000
PMID: 15012192
Gelvin SB., Annu. Rev. Plant Physiol. Plant Mol. Biol. 51(), 2000
PMID: 15012192
Finding a way to the nucleus
Gelvin S.B.., 2010
Gelvin S.B.., 2010
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
Haas B.J., Delcher A.L., Mount S.M., Wortman J.R., Smith R.K., Hannick L.I.., 2003
Haas B.J., Delcher A.L., Mount S.M., Wortman J.R., Smith R.K., Hannick L.I.., 2003
An easy-to-use primer design tool to address paralogous loci and T-DNA insertion sites in the genome of Arabidopsis thaliana
Huep G., Kleinboelting N., Weisshaar B.., 2014
Huep G., Kleinboelting N., Weisshaar B.., 2014
Genome-wide analysis of Agrobacterium T-DNA integration sites in the Arabidopsis genome generated under non-selective conditions.
Kim SI, Veena , Gelvin SB., Plant J. 51(5), 2007
PMID: 17605756
Kim SI, Veena , Gelvin SB., Plant J. 51(5), 2007
PMID: 17605756
The Structural Features of Thousands of T-DNA Insertion Sites Are Consistent with a Double-Strand Break Repair-Based Insertion Mechanism.
Kleinboelting N, Huep G, Appelhagen I, Viehoever P, Li Y, Weisshaar B., Mol Plant 8(11), 2015
PMID: 26343971
Kleinboelting N, Huep G, Appelhagen I, Viehoever P, Li Y, Weisshaar B., Mol Plant 8(11), 2015
PMID: 26343971
GABI-Kat SimpleSearch: new features of the Arabidopsis thaliana T-DNA mutant database.
Kleinboelting N, Huep G, Kloetgen A, Viehoever P, Weisshaar B., Nucleic Acids Res. 40(Database issue), 2011
PMID: 22080561
Kleinboelting N, Huep G, Kloetgen A, Viehoever P, Weisshaar B., Nucleic Acids Res. 40(Database issue), 2011
PMID: 22080561
Araport: the Arabidopsis information portal.
Krishnakumar V, Hanlon MR, Contrino S, Ferlanti ES, Karamycheva S, Kim M, Rosen BD, Cheng CY, Moreira W, Mock SA, Stubbs J, Sullivan JM, Krampis K, Miller JR, Micklem G, Vaughn M, Town CD., Nucleic Acids Res. 43(Database issue), 2014
PMID: 25414324
Krishnakumar V, Hanlon MR, Contrino S, Ferlanti ES, Karamycheva S, Kim M, Rosen BD, Cheng CY, Moreira W, Mock SA, Stubbs J, Sullivan JM, Krampis K, Miller JR, Micklem G, Vaughn M, Town CD., Nucleic Acids Res. 43(Database issue), 2014
PMID: 25414324
T-DNA as an insertional mutagen in Arabidopsis.
Krysan PJ, Young JC, Sussman MR., Plant Cell 11(12), 1999
PMID: 10590158
Krysan PJ, Young JC, Sussman MR., Plant Cell 11(12), 1999
PMID: 10590158
Phenome analysis in plant species using loss-of-function and gain-of-function mutants.
Kuromori T, Takahashi S, Kondou Y, Shinozaki K, Matsui M., Plant Cell Physiol. 50(7), 2009
PMID: 19502383
Kuromori T, Takahashi S, Kondou Y, Shinozaki K, Matsui M., Plant Cell Physiol. 50(7), 2009
PMID: 19502383
Arabidopsis database and stock resources.
Li D, Dreher K, Knee E, Brkljacic J, Grotewold E, Berardini TZ, Lamesch P, Garcia-Hernandez M, Reiser L, Huala E., Methods Mol. Biol. 1062(), 2014
PMID: 24057361
Li D, Dreher K, Knee E, Brkljacic J, Grotewold E, Berardini TZ, Lamesch P, Garcia-Hernandez M, Reiser L, Huala E., Methods Mol. Biol. 1062(), 2014
PMID: 24057361
GABI-Kat SimpleSearch: a flanking sequence tag (FST) database for the identification of T-DNA insertion mutants in Arabidopsis thaliana.
Li Y, Rosso MG, Strizhov N, Viehoever P, Weisshaar B., Bioinformatics 19(11), 2003
PMID: 12874060
Li Y, Rosso MG, Strizhov N, Viehoever P, Weisshaar B., Bioinformatics 19(11), 2003
PMID: 12874060
Analysis of T-DNA insertion site distribution patterns in Arabidopsis thaliana reveals special features of genes without insertions.
Li Y, Rosso MG, Ulker B, Weisshaar B., Genomics 87(5), 2006
PMID: 16488113
Li Y, Rosso MG, Ulker B, Weisshaar B., Genomics 87(5), 2006
PMID: 16488113
GABI-Kat SimpleSearch: an Arabidopsis thaliana T-DNA mutant database with detailed information for confirmed insertions.
Li Y, Rosso MG, Viehoever P, Weisshaar B., Nucleic Acids Res. 35(Database issue), 2006
PMID: 17062622
Li Y, Rosso MG, Viehoever P, Weisshaar B., Nucleic Acids Res. 35(Database issue), 2006
PMID: 17062622
Activation tagging, a novel tool to dissect the functions of a gene family.
Nakazawa M, Ichikawa T, Ishikawa A, Kobayashi H, Tsuhara Y, Kawashima M, Suzuki K, Muto S, Matsui M., Plant J. 34(5), 2003
PMID: 12787254
Nakazawa M, Ichikawa T, Ishikawa A, Kobayashi H, Tsuhara Y, Kawashima M, Suzuki K, Muto S, Matsui M., Plant J. 34(5), 2003
PMID: 12787254
Linking genotype to phenotype using the Arabidopsis unimutant collection.
O'Malley RC, Ecker JR., Plant J. 61(6), 2010
PMID: 20409268
O'Malley RC, Ecker JR., Plant J. 61(6), 2010
PMID: 20409268
Functional genomics in Arabidopsis: large-scale insertional mutagenesis complements the genome sequencing project.
Parinov S, Sundaresan V., Curr. Opin. Biotechnol. 11(2), 2000
PMID: 10753770
Parinov S, Sundaresan V., Curr. Opin. Biotechnol. 11(2), 2000
PMID: 10753770
T-DNA border sequences required for crown gall tumorigenesis
Peralta E.G., Ream L.W.., 1985
Peralta E.G., Ream L.W.., 1985
An Arabidopsis thaliana T-DNA mutagenized population (GABI-Kat) for flanking sequence tag-based reverse genetics.
Rosso MG, Li Y, Strizhov N, Reiss B, Dekker K, Weisshaar B., Plant Mol. Biol. 53(1-2), 2003
PMID: 14756321
Rosso MG, Li Y, Strizhov N, Reiss B, Dekker K, Weisshaar B., Plant Mol. Biol. 53(1-2), 2003
PMID: 14756321
Seed and molecular resources for Arabidopsis.
Scholl RL, May ST, Ware DH., Plant Physiol. 124(4), 2000
PMID: 11115863
Scholl RL, May ST, Ware DH., Plant Physiol. 124(4), 2000
PMID: 11115863
Use of mutants from T-DNA insertion populations generated by high-throughput screening
Stracke R., Huep G., Weisshaar B.., 2010
Stracke R., Huep G., Weisshaar B.., 2010
High-throughput generation of sequence indexes from T-DNA mutagenized Arabidopsis thaliana lines
Strizhov N., Li Y., Rosso M.G., Viehoever P., Dekker K.A., Weisshaar B.., 2003
Strizhov N., Li Y., Rosso M.G., Viehoever P., Dekker K.A., Weisshaar B.., 2003
Distribution of 1000 sequenced T-DNA tags in the Arabidopsis genome.
Szabados L, Kovacs I, Oberschall A, Abraham E, Kerekes I, Zsigmond L, Nagy R, Alvarado M, Krasovskaja I, Gal M, Berente A, Redei GP, Haim AB, Koncz C., Plant J. 32(2), 2002
PMID: 12383088
Szabados L, Kovacs I, Oberschall A, Abraham E, Kerekes I, Zsigmond L, Nagy R, Alvarado M, Krasovskaja I, Gal M, Berente A, Redei GP, Haim AB, Koncz C., Plant J. 32(2), 2002
PMID: 12383088
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
Arabidopsis Genome Initiative., Nature 408(6814), 2000
PMID: 11130711
Arabidopsis Genome Initiative., Nature 408(6814), 2000
PMID: 11130711
Agrobacterium T-DNA integration: molecules and models.
Tzfira T, Li J, Lacroix B, Citovsky V., Trends Genet. 20(8), 2004
PMID: 15262410
Tzfira T, Li J, Lacroix B, Citovsky V., Trends Genet. 20(8), 2004
PMID: 15262410
Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum.
VanBuren R, Bryant D, Edger PP, Tang H, Burgess D, Challabathula D, Spittle K, Hall R, Gu J, Lyons E, Freeling M, Bartels D, Ten Hallers B, Hastie A, Michael TP, Mockler TC., Nature 527(7579), 2015
PMID: 26560029
VanBuren R, Bryant D, Edger PP, Tang H, Burgess D, Challabathula D, Spittle K, Hall R, Gu J, Lyons E, Freeling M, Bartels D, Ten Hallers B, Hastie A, Michael TP, Mockler TC., Nature 527(7579), 2015
PMID: 26560029
Right 25 bp terminus sequence of the nopaline T-DNA is essential for and determines direction of DNA transfer from agrobacterium to the plant genome.
Wang K, Herrera-Estrella L, Van Montagu M, Zambryski P., Cell 38(2), 1984
PMID: 6467373
Wang K, Herrera-Estrella L, Van Montagu M, Zambryski P., Cell 38(2), 1984
PMID: 6467373
Annotation of the Arabidopsis genome.
Wortman JR, Haas BJ, Hannick LI, Smith RK Jr, Maiti R, Ronning CM, Chan AP, Yu C, Ayele M, Whitelaw CA, White OR, Town CD., Plant Physiol. 132(2), 2003
PMID: 12805579
Wortman JR, Haas BJ, Hannick LI, Smith RK Jr, Maiti R, Ronning CM, Chan AP, Yu C, Ayele M, Whitelaw CA, White OR, Town CD., Plant Physiol. 132(2), 2003
PMID: 12805579
CONSTANS activates SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 through FLOWERING LOCUS T to promote flowering in Arabidopsis.
Yoo SK, Chung KS, Kim J, Lee JH, Hong SM, Yoo SJ, Yoo SY, Lee JS, Ahn JH., Plant Physiol. 139(2), 2005
PMID: 16183837
Yoo SK, Chung KS, Kim J, Lee JH, Hong SM, Yoo SJ, Yoo SY, Lee JS, Ahn JH., Plant Physiol. 139(2), 2005
PMID: 16183837
A greedy aligning DNA sequences
Zhang Z., Schwartz S., Wagner L., Miller W.., 2004
Zhang Z., Schwartz S., Wagner L., Miller W.., 2004
Export
Markieren/ Markierung löschen
Markierte Publikationen
Web of Science
Dieser Datensatz im Web of Science®Quellen
PMID: 28013277
PubMed | Europe PMC
Suchen in