Morpholino Database

Search By For Use * as a wildcard character (e.g. "BMP*"). For Tips on search see Search FAQs.

For optimal performance, we recommend the following web browsers: Firefox 3.5 or higher, Safari 4.0 or higher, IE 7.0 or higher.

	MODB v1.0
	BLAST ZFIN for Morpholinos MODB Morpholino Index Advanced Search BLAST Search About MODB

Welcome to the MOrpholino DataBase!

Morpholinos are a powerful knockdown tool that have been proven to efficiently and specifically reduce translation of a target mRNA (Summerton, 1999). This knockdown technology is particularly useful in zebrafish as the system is amenable to large scale screening (Nasevicius and Ekker, 2000). Through a collaboration with Dr. Lynda Ellis we set out to identify all cotranslationally translocated genes in the zebrafish genome (Secretome/CTT-ome). Morpholinos were designed against putative secreted/CTT targets and injected into 1-4 cell stage zebrafish embryos. The embryos were observed over a 5 day period for defects in several different systems. The first screen examined 184 gene targets of which 26 demonstrated defects of interest (Pickart et al. 2006). A collaboration with the Verfaillie laboratory examined the knockdown of targets identified in a comparative microarray analysis of hematopoietic stem cells demonstrating how microarray and morpholino technologies can be used in conjunction to enrich for defects in specific developmental processes. Currently, many collaborations are underway to identify genes involved in morphological, kidney, skin, eye, pigment, vascular and hematopoietic development, lipid metabolism and more.

The generation of a large amount data from laboratories located throughout the world has necessitated the creation of a central database that would be easily accessible and searchable. MODB (MOprholino DataBase) was created to bring together the data generated from the first and subsequent morpholino screening project and has served as a central repository for data on a large number of morpholinos. We are currently in the second phase of screening and are adding more data on a daily basis. The goal of this database is to organize our data and make it available to the public. Currently, we have a publicly accessible sequence-based search that will allow general users to determine if MODB contains morpholinos targeting a particular sequence. To obtain more information on a given target or morpholino select Morpholino index or use one of the many search functions available at MODB (e.g. BLAST Search, Phenotype Browser and Anatomy Browser). For an explanation of MODB and its features see About MODB . Morpholinos can be ordered directly from Gene Tools as we do not have a license to provide morpholinos and morpholinos have a shelf life.

Use BLAST to Explore MODB

Sequence:

Tips:

Enter your nucleotide sequence in FASTA format by copying and pasting it into the given space.
Submit your sequence by selecting ‘Explore MODB’.
Results will be display if there is a match to the queried sequence. The standard length of morpholinos used in our screen is 25 nucleotides. Matches less than 24/25 may have no specific effect on gene expression depending on where the mis-matches occur.
For more information regarding a target sequence of a morpholino please contact the Ekker Laboratory. Morpholinos can be ordered directly from Gene Tools as we do not have a license to provide morpholinos and morpholinos have a shelf life. For more information regarding BLAST and FASTA format see NCBI.

	References
	Manuscript describing the initial morpholino screen for 150 genes: Pickart MA, Klee EW, Nielsen AL, Sivasubbu S, Mendenhall EM, Bill BR, Chen E, Eckfeldt CE, Knowlton M, Robu ME, Larson JD, Deng Y, Schimmenti LA, Ellis LB, Verfaillie CM, Hammerschmidt M, Farber SA, Ekker (2006). Genome-wide reverse genetics framework to identify novel functions of the vertebrate secretome. PloS One 1: e104. Full text A morpholino-based screen for hematopoietic genes: Eckfeldt CE, Mendenhall EM, Flynn CM, Wang TF, Pickart MA, Grindle SM, Ekker SC, Verfaillie CM. (2005). Functional analysis of human hematopoietic stem cell gene expression using zebrafish. PLoS Biol. 3(8): e254. Full text Common morpholino toxicity and a tool to attenuate this technical limitation for morpholino screening: Robu ME, Larson JD, Nasevicius A, Beiraghi S, Brenner C, Farber SA, Ekker SC (2007). p53 activation by knockdown technologies. PloS Genetics 3(5): e78. Full text EST-based bioinformatics pipeline for identifying members of the vertebrate secretome: Klee EW, Carlson DF, Fahrenkrug SC, Ekker SC, Ellis LB. (2004). Identifying secretomes in people, pufferfish and pigs. Nucleic Acids Res. 32(4): 1414-21. Full text Some morpholino papers derived from this screen Chen E, Larson JD, Ekker SC. (2006). Functional analysis of zebrafish microfibril-associated glycoprotein-1 (Magp1) in vivo reveals roles for microfibrils in vascular development and function. Blood 107(11): 4364-74. Full text Chen E, Stringer SE, Rusch MA, Selleck SB, Ekker SC. (2005). A unique role for 6-O sulfation modification in zebrafish vascular development. Dev Biol. 284(2): 364-76. Full text Chen E, Hermanson S, Ekker SC. (2004). Syndecan-2 is essential for angiogenic sprouting during zebrafish development. Blood 103(5): 1710-9. Full text Leung AY, Mendenhall EM, Kwan TT, Liang R, Eckfeldt C, Chen E, Hammerschmidt M, Grindley S, Ekker SC, Verfaillie CM. (2005). Characterization of expanded intermediate cell mass in zebrafish chordin morphant embryos. Dev Biol. 277(1): 235-54. Full text Original zebrafish morpholino paper Nasevicius A, Ekker SC. (2000). Effective targeted gene 'knockdown' in zebrafish. Nat Genet. 26(2): 216-20. Full text Summerton J (1999). Morpholino antisense oligomers: the case for an RNase H-independent structural type. Biochim Biophys Acta. 1489(1):141-58. Full text