MaizeGDB Docs: Maize Gene Discovery Project: RescueMu Library Plates: Sequences

Project Documentation & Protocols: Maize Gene Discovery Project: RescueMu Library Plates: Sequences

Sequences from initial Grid G rows that have a highly significant BLAST score.

Items recovered multiple times are likely to be germinal insertions. Items recovered >20 times are likely to be parental insertions (pre-existing insertions segregating in the population that slipped through our screen against them). Given the large differences in base composition between introns and exons, some plasmids sequence well to the right or to the left, but not in both directions.

Organism	Match	Recovery (X)	Recovery (Y)	Example 1	Example 2
Arabidopsis thaliana	Arabidopsis thaliana chromosome 1 BAC F13M7 sequence, complete sequence	1	0	1006002D09.x2	1006002D09.x2
Arabidopsis thaliana	Arabidopsis thaliana chromosome 1 BAC T8K14 sequence, complete	1	1	1006004B10.x1	1006004B10.y2
Arabidopsis thaliana	Arabidopsis thaliana chromosome I BAC T14N5 genomic sequence, complete	0	1	1006008E01.y1	1006008E01.y1
Arabidopsis thaliana	Arabidopsis thaliana chromosome II section 190 of 255 of the complete	0	1	1006002H03.y1	1006002H03.y1
Arabidopsis thaliana	Arabidopsis thaliana chromosome III BAC F18C1 genomic sequence,	2	0	1006003B08.x2	1006003G01.x2
Arabidopsis thaliana	Arabidopsis thaliana chromosome III BAC F3L24 genomic sequence,	0	1	1006004G05.y2	1006004G05.y2
Arabidopsis thaliana	Arabidopsis thaliana chromosome III BAC F7O18 genomic sequence,	0	55	1006001B07.y1	1006014G09.y1
Arabidopsis thaliana	Arabidopsis thaliana DNA chromosome 4, BAC clone F8L21 (ESSA project)	0	1	1006003D03.y2	1006003D03.y2
Bovine T-protein	Bovine T-protein mRNA, complete cds	0	1	1006002D05.y2	1006002D05.y2
Cloning vector	Cloning vector pTurbo-Cre, complete sequence	1	0	1006006H02.x1	1006006H02.x1
Drosophila melanogaster	Drosophila melanogaster retinal homeobox protein (Rx) mRNA sequence	0	1	1006002C08.y1	1006002C08.y1
Genomic Sequence	Genomic Sequence For Oryza sativa, Nipponbare strain, Clone	0	1	1006001G05.y2	1006001G05.y2
Hordeum vulgare	Hordeum vulgare genomic DNA fragment; clone MWG2067.rev	4	0	1006005G12.x1	1006007B09.x1
Hordeum vulgare	Hordeum vulgare genomic DNA fragment; clone MWG2067.uni	0	3	1006005G12.y1	1006013H08.y1
Hordeum vulgare	Hordeum vulgare lipoxygenase (LoxB) mRNA, complete cds	0	1	1006003A07.y2	1006003A07.y2
Hyparrhenia hirta	Hyparrhenia hirta maturase (matK) gene, complete cds; chloroplast	0	1	1006014A03.y1	1006014A03.y1
Litomosoides sigmodontis	Litomosoides sigmodontis microfilarial sheath protein SHP3a (shp3a) and	0	1	1006001H09.y1	1006001H09.y1
Maize (Zea	Maize (Zea mays) histone H4 gene (H4C14), complete cds	0	1	1006014F03.y1	1006014F03.y1
Maize DNA	Maize DNA for Ds(bz-wm) controlling element (Ds1-related)	1	0	1006013B01.x2	1006013B01.x2
Maize Gpc1	Maize Gpc1 gene for glyceraldehyde-3-phosphate dehydrogenase (GADPH)	2	0	1006006A06.x1	1006006B01.x1
Maize oleosin	Maize oleosin KD18 (KD18; L2) gene, complete cds	1	0	1006004B04.x2	1006004B04.x2
Maize pseudo-Gpa2	Maize pseudo-Gpa2 pseudogene for glyceraldehyde-3-phosphate	1	0	1006003D03.x1	1006003D03.x1
Maize transposable	Maize transposable element Mu1 sequence	1	0	1006001H04.x3	1006001H04.x3
Oryza sativa	Oryza sativa chromosome 10 BAC OSJNBa0055O03 genomic sequence, complete	1	0	1006004G11.x1	1006004G11.x1
Oryza sativa	Oryza sativa chromosome 3 BAC OSJNBa0091J19 genomic sequence, complete	1	1	1006001G05.x1	1006013G05.y1
Oryza sativa	Oryza sativa clone LS101 50S ribosomal protein L5 (rpl5) mRNA,	0	1	1006003D01.y1	1006003D01.y1
Oryza sativa	Oryza sativa complete chloroplast genome	0	1	1006004E02.y2	1006004E02.y2
Oryza sativa	Oryza sativa gene for ovp2, complete cds	0	1	1006001H11.y1	1006001H11.y1
Oryza sativa	Oryza sativa genomic DNA, chromosome 1, clone:P0708G02	1	0	1006004G06.x3	1006004G06.x3
Oryza sativa	Oryza sativa genomic DNA, chromosome 1, clone:P0711E10	0	1	1006002E08.y2	1006002E08.y2
Oryza sativa	Oryza sativa genomic DNA, chromosome 1, PAC clone:P0410E03	1	0	1006013G04.x2	1006013G04.x2
Oryza sativa	Oryza sativa genomic DNA, chromosome 1, PAC clone:P0435H01, complete	1	1	1006004H07.x2	1006004H07.y1
Oryza sativa	Oryza sativa genomic DNA, chromosome 1, PAC clone:P0443E07, complete	1	1	1006013B05.x3	1006013B05.y1
Oryza sativa	Oryza sativa genomic DNA, chromosome 1, PAC clone:P0445D12, complete	0	1	1006014F09.y1	1006014F09.y1
Oryza sativa	Oryza sativa genomic DNA, chromosome 1, PAC clone:P0451C06	0	2	1006002B03.y2	1006002H12.y2
Oryza sativa	Oryza sativa genomic DNA, chromosome 1, PAC clone:P0498A12, complete	0	1	1006004E12.y2	1006004E12.y2
Oryza sativa	Oryza sativa genomic DNA, chromosome 1, PAC clone:P0686E09, complete	1	1	1006003B01.x2	1006003B01.y1
Oryza sativa	Oryza sativa genomic DNA, chromosome 1, PAC clone:P0710E05	1	0	1006004D08.x2	1006004D08.x2
Oryza sativa	Oryza sativa genomic DNA, chromosome 6, BAC clone:OSJNBa0035I03,	0	1	1006001F07.y2	1006001F07.y2
Oryza sativa	Oryza sativa genomic DNA, chromosome 6, BAC clone:OSJNBa0075G19,	0	1	1006001C11.y2	1006001C11.y2
Oryza sativa	Oryza sativa genomic DNA, chromosome 6, PAC clone:P0541H01	1	0	1006006G11.x2	1006006G11.x2
Oryza sativa	Oryza sativa genomic DNA, chromosome 6, PAC clone:P0644B06	0	1	1006004D03.y1	1006004D03.y1
Oryza sativa	Oryza sativa genomic DNA, chromosome 8, clone:P0026F07	0	1	1006002F10.y2	1006002F10.y2
Oryza sativa	Oryza sativa microsatellite MRG2490 containing (CT)X24, genomic	1	0	1006014B04.x1	1006014B04.x1
Oryza sativa	Oryza sativa microsatellite MRG5092 containing (CCT)X11, closest to	0	1	1006003C06.y2	1006003C06.y2
Oryza sativa	Oryza sativa microsatellite MRG5171 containing (CGG)X8, closest to	0	2	1006014G08.y1	1006014H08.y1
Oryza sativa	Oryza sativa microsatellite MRG5403 containing (GAG)X8, genomic	0	3	1006003A11.y2	1006003F11.y1
Oryza sativa	Oryza sativa microsatellite MRG5554 containing (GGA)X8, closest to	0	4	1006001B09.y2	1006002F02.y2
Oryza sativa	Oryza sativa nucleotide pyrophosphatase precursor, mRNA, complete	1	1	1006004E09.x1	1006004E09.y1
Panax ginseng	Panax ginseng mRNA for 60S ribosomal protein L27a, complete cds	1	0	1006001D07.x1	1006001D07.x1
Pseudomonas aeruginosa	Pseudomonas aeruginosa PA01, section 272 of 529 of the complete	1	0	1006002A02.x2	1006002A02.x2
Rhizobium meliloti	Rhizobium meliloti nodP and nodQ genes for host-specific nodule	0	1	1006008F12.y1	1006008F12.y1
Rhizobium meliloti	Rhizobium meliloti nodulation protein (nodP and nodQ) genes, complete	1	0	1006006A02.x1	1006006A02.x1
Shuttle vector	Shuttle vector pBHad, complete plasmid sequence	1	0	1006005A09.x1	1006005A09.x1
Solanum tuberosum	Solanum tuberosum apoprotein 2 (Lhca3.St.1) gene, partial cds; and	1	0	1006002E09.x1	1006002E09.x1
Spinacia oleracea	Spinacia oleracea complete chloroplast genome	1	0	1006014H02.x1	1006014H02.x1
Triticum aestivum	Triticum aestivum poly(A)-binding protein (wheatpab) mRNA, complete	0	1	1006008B03.y1	1006008B03.y1
Volvox carteri	Volvox carteri f. nagariensis somatic regenerator RegA (regA) gene,	0	1	1006014D03.y1	1006014D03.y1
Wheat ubiquitin	Wheat ubiquitin carrier protein (UBC1) mRNA, complete cds	1	0	1006005A10.x1	1006005A10.x1
Z.diploperennis	Z.diploperennis DNA for Grande1-4 retrotransposon	1	0	1006013E09.x1	1006013E09.x1
Z.diploperennis	Z.diploperennis Grande1 gene	0	1	1006013F07.y1	1006013F07.y1
Z.mays	Z.mays GapC2 gene	0	1	1006002C09.y2	1006002C09.y2
Z.mays	Z.mays gene for polygalacturonase	1	0	1006003F03.x1	1006003F03.x1
Z.mays	Z.mays PK1 gene for receptor-like protein kinase	0	2	1006014A10.y1	1006014E01.y1
Zea mays	Zea mays 22-kDa alpha zein gene cluster, complete sequence	0	4	1006001C01.y2	1006014C10.y1
Zea mays	Zea mays 6-phosphogluconate dehydrogenase isoenzyme A gene, partial	1	0	1006002A07.x2	1006002A07.x2
Zea mays	Zea mays alcohol dehydrogenase 1 (adh1) gene, adh1-F allele, complete	4	8	1006002F09.y2	1006014H11.y1
Zea mays	Zea mays alcohol dehydrogenase 1 (adh1) gene, adh1-F allele, complete cds	0	4	1006001D08.y2	1006003G04.y2
Zea mays	Zea mays Ama gene encoding single-subunit RNA polymerase	0	2	1006002E07.y2	1006004B07.y1
Zea mays	Zea mays anthocyanin regulatory C1 (c1) gene, C1-1162 allele,	0	1	1006014G10.y1	1006014G10.y1
Zea mays	Zea mays auxin-binding protein (abp4) gene, exons 1-5 and complete	0	1	1006003F10.y2	1006003F10.y2
Zea mays	Zea mays beta-D-glucosidase (glu1) gene, intron 10 transposon 2,	1	0	1006014B10.x1	1006014B10.x1
Zea mays	Zea mays cell wall invertase Incw1 gene, complete cds	0	1	1006004H06.y2	1006004H06.y2
Zea mays	Zea mays chloroplast trnC gene, rpoB gene, rpoC1 gene, rpoC2 gene and	0	1	1006003A05.y2	1006003A05.y2
Zea mays	Zea mays chromosome 4 22 kDa zein-associated intercluster region,	1	0	1006013H01.x1	1006013H01.x1
Zea mays	Zea mays complete chloroplast genome	8	3	1006001D05.y2	1006014E09.y1
Zea mays	Zea mays copia-type retroelement PREM-2 gag gene, complete cds	1	1	1006008B06.y1	1006014H01.x1
Zea mays	Zea mays cosmid II.2E10 22-kDa alpha zein gene cluster, complete	2	1	1006002H08.y2	1006013D08.x3
Zea mays	Zea mays cosmid IV.1E1 22-kDa alpha zein protein 21 (sz22-21) gene,	2	0	1006014F08.x1	1006014G04.x1
Zea mays	Zea mays eIF-5 gene, exons 1-2	2	0	1006014A05.x1	1006014D02.x1
Zea mays	Zea mays flowering-time protein isoforms alpha and beta (ZmLD) gene,	1	0	1006002A03.x1	1006002A03.x1
Zea mays	Zea mays glutathione S-transferase GST 16 mRNA, complete cds	0	1	1006003E01.y2	1006003E01.y2
Zea mays	Zea mays glyceraldehyde-3-phosphate dehydrogenase (GapC4) gene,	0	1	1006003C02.y2	1006003C02.y2
Zea mays	Zea mays glyceraldehyde-3-phosphate dehydrogenase (gpc4) gene,	0	1	1006003C03.y2	1006003C03.y2
Zea mays	Zea mays hexose transporter (pGlcT) mRNA, partial cds; nuclear gene	1	1	1006014F12.x1	1006014F12.y1
Zea mays	Zea mays hox1a and trap genes	2	0	1006013E06.x1	1006013G12.x1
Zea mays	Zea mays indole-3-glycerol phosphate lyase (Igl) gene, complete cds;	1	0	1006001H10.x3	1006001H10.x3
Zea mays	Zea mays kinesin-like calmodulin binding protein (KCBP) gene,	1	0	1006002G09.x1	1006002G09.x1
Zea mays	Zea mays ldh and pdc pseudogenes, complete sequence	1	0	1006002D08.x1	1006002D08.x1
Zea mays	Zea mays lethal leaf-spot 1 (lls1) gene, partial cds	5	0	1006001A08.x1	1006007E04.x1
Zea mays	Zea mays mfs14 gene, exons 1-2	0	1	1006001A05.y2	1006001A05.y2
Zea mays	Zea mays miniature inverted-repeat transposable element Hbr10	1	0	1006004G09.x2	1006004G09.x2
Zea mays	Zea mays miniature inverted-repeat transposable element Hbr22	2	0	1006007G10.x1	1006013C05.x3
Zea mays	Zea mays miniature inverted-repeat transposable element Hbr36	1	0	1006003G09.x2	1006003G09.x2
Zea mays	Zea mays miniature inverted-repeat transposable element Hbr43	82	0	1006001F04.x3	1006014G09.x1
Zea mays	Zea mays mRNA for mitochondrial phosphate transporter, complete cds	0	2	1006013B12.y1	1006013H11.y1
Zea mays	Zea mays mRNA for phospholipase D, complete cds	2	1	1006001F10.x3	1006014C02.y1
Zea mays	Zea mays mus2 gene, exons 1-16	0	1	1006013C03.y1	1006013C03.y1
Zea mays	Zea mays nitrate reductase (NR1) gene, complete cds	0	1	1006003G12.y2	1006003G12.y2
Zea mays	Zea mays nitrate reductase gene, complete cds	0	1	1006014F01.y1	1006014F01.y1
Zea mays	Zea mays P2 protein (P2) gene, complete cds	0	1	1006002B08.y2	1006002B08.y2
Zea mays	Zea mays PAO gene for flavin containing polyamine oxidase, exons 1-8	1	0	1006005H12.x1	1006005H12.x1
Zea mays	Zea mays pao gene for polyamine oxidase, exons 1-8, clone pMPAO2	6	0	1006003B11.x2	1006007F11.x1
Zea mays	Zea mays plastid, complete genome	0	5	1006002A09.y2	1006014H02.y1
Zea mays	Zea mays putative matrix attachment region sequence	1	0	1006011A01.x1	1006011A01.x1
Zea mays	Zea mays putative tryptophan synthase alpha (TSAlike) mRNA,	0	1	1006001H10.y1	1006001H10.y1
Zea mays	Zea mays RACA small GTP binding protein mRNA, complete cds	0	1	1006001B05.y2	1006001B05.y2
Zea mays	Zea mays RACC small GTP binding protein mRNA, complete cds	2	0	1006004B08.x3	1006004H10.x1
Zea mays	Zea mays RAD51 homolog RAD51A (rad51A) mRNA, complete cds	2	0	1006003C07.x2	1006003D09.x1
Zea mays	Zea mays retrotransposon Cinful prpol mRNA, partial cds	0	2	1006002B04.y1	1006002B09.y2
Zea mays	Zea mays retrotransposon Cinful-1, complete sequence	2	5	1006002E04.y2	1006014H06.y1
Zea mays	Zea mays retrotransposon Huck-1 5' LTR, partial sequence	0	1	1006002H05.y2	1006002H05.y2
Zea mays	Zea mays retrotransposon Huck-2 3' LTR, partial sequence	1	0	1006004D03.x2	1006004D03.x2
Zea mays	Zea mays retrotransposon Huck-2 5' LTR and primer binding site DNA	0	1	1006002G06.y2	1006002G06.y2
Zea mays	Zea mays starch branching enzyme 2a gene, partial cds	0	1	1006004H12.y2	1006004H12.y2
Zea mays	Zea mays starch branching enzyme IIb (ae) gene, complete cds	0	1	1006003H03.y2	1006003H03.y2
Zea mays	Zea mays subsp. huehuetenangensis isolate Beadle s.n. b gene,	2	0	1006001C10.x3	1006001C11.x3
Zea mays	Zea mays subsp. mays Grande retrotransposon DNA, partial LTR, clone	1	0	1006014C09.x1	1006014C09.x1
Zea mays	Zea mays superoxide dismutase 4A (sod4A) gene, complete cds	3	0	1006001D10.x3	1006001H02.x1
Zea mays	Zea mays T cytoplasm male sterility restorer factor 2 (rf2) gene,	1	1	1006002C12.x2	1006014H04.y1
Zea mays	Zea mays transposable element Mu1.7	1	0	1006008F12.x1	1006008F12.x1
Zea mays	Zea mays W-22 clone PREM-1B retroelement PREM-1, partial sequence	1	0	1006003F04.x2	1006003F04.x2
Zea mays	Zea mays zinc finger protein ID1 (id1) mRNA, complete cds	0	2	1006002C04.y2	1006002G07.y2
Zea mays	Zea mays ZMPMS2 gene for 19 kDa zein protein	1	0	1006001D01.x3	1006001D01.x3

Sequencing Templates Production

Plasmids were prepared by ligating pieces of genomic DNA generated from a double-digest using BamHI and BglII. The DNA concentration was low to insure that most ligation was "self-ligation" of the ends of a single piece of linear DNA. Circularization occurs at the cohesive overhangs generated by the two enzymes. Sequencing from the right end of RescueMu up to the ligation site yields the genomic DNA that we know was next to the transposon in vivo. Sequence beyond the ligation site most likely comes from the "left" side of the RescueMu transposon in vivo. Thus sequencing through the ligation site generates sequence that comes from two different places in the genome and is in two different directions. The sequences before and after a predicted ligation site were therefore separated and submitted under their own identification (ID) numbers to the GSS database at Genbank.

Below is a detailed explanation of the situation.

Restriction Enzyme Digestion Strategy Generates Two Types of Ligation Sites

The recognition site for BamHI is

5'-G GATCC-3'

3'-CCTAG G-5'

and the recognition site for BglII is

5'-A GATCT-3'

3'-TCTAG A-5'

Same Enzyme Ligation: If the ligation joined two ends where both were cut by BglII or both were cut by BamHI, the restriction site would have been recreated. Finding one of the two restrictions sites during sequencing is therefore a good indication that we have found the ligation site. There is a slight chance for some restriction sites to be missed during the double-digest so this is not a 100 percent sure prediction.

Mixed Site Ligation: If the ligation joined two ends where one was cut by BglII and the other by BamHI, then we would end up with one of the two junction ligation sequences below:

5'-GGATCT-3'

3'-CCTAGA-5'

Because these ligation sequences are not restriction sites, they could have been present in the genomic DNA (assuming a random distribution, every 4⁶ bases) and therefore not represent the true ligation site.

Identification Numbers in GenBank

If a possible ligation site (a BamHI or BglII restriction site or either of the two junction ligation sites) was found during sequencing, the sequence before the ligation site was submitted as normal with its plate id, well number, direction, and run number. The sequence after the ligation site, if it was at least 30 bases, was submitted with an ID based on the original sequence ID as follows:

Ligation Site Type

Original Sequence ID

Post-ligation Sequence ID

1 enzyme both ends

1006001A01.x1

1006001A01.1EL_x1

2 enzymes

1006001A01.x1

1006001A01.2EL_x1

In this way, the post-ligation sequence is tied back to the original sequence ID and indicates the ligation type. The comment field in the Genbank record describes what was done for each sequence, too.

Return to Documentation Index | Return to Maize Gene Discovery Project index | Return to Homepage

If you have some comments about this page, or about the site in general, fill out our easy to use feedback form without leaving this page!

Be sure to cite us!