Experiment no.

4:

rolA=transferred TL-DNA genes involved in the pathogenesis of hairyroot disease [Agrobacterium rhizogenes, Ri plasmid A4, mRNA Plasmid Partial, 103 nt]
GenBank: S74256.1 FASTA Graphics Go to: LOCUS 1995 DEFINITION S74256 103 bp mRNA linear BCT 16-MAR-

rolA=transferred TL-DNA genes involved in the pathogenesis of hairy-root disease [Agrobacterium rhizogenes, Ri plasmid A4, mRNA Plasmid Partial, 103 nt]. ACCESSION S74256 VERSION S74256.1 GI:710464 KEYWORDS . SOURCE Agrobacterium rhizogenes (Rhizobium rhizogenes) ORGANISM Agrobacterium rhizogenes Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium. REFERENCE 1 (bases 1 to 103) AUTHORS Magrelli,A., Langenkemper,K., Dehio,C., Schell,J. and Spena,A. TITLE Splicing of the rolA transcript of Agrobacterium rhizogenes in Arabidopsis JOURNAL Science 266 (5193), 1986-1988 (1994) PUBMED 7528444 REMARK GenBank staff at the National Library of Medicine created this entry [NCBI gibbsq 157725] from the original journal article. FEATURES Location/Qualifiers source 1..103 /organism="Agrobacterium rhizogenes" /plasmid="" /mol_type="mRNA" /db_xref="taxon:359" gene 1..103 /gene="rolA" /note="transferred TL-DNA genes involved in the pathogenesis of hairy-root disease" CDS 101..103 /gene="rolA" /note="only initation codon shown" /codon_start=1 ORIGIN 1 aacgcttcaa tacggtgagt gtggttgtag gttcaattat tactattttt gaagctgtgt 61 atttcccttt ttctaatatg cacctatttc atgtttcaga atg //

Experiment no.3:

rolA=transferred TL-DNA genes involved in the pathogenesis of hairyroot disease [Agrobacterium rhizogenes, Ri plasmid A4, mRNA Plasmid Partial, 103 nt]
GenBank: S74256.1
GenBank Graphics >gi|710464|gb|S74256.1| rolA=transferred TL-DNA genes involved in the pathogenesis of hairy-root disease [Agrobacterium rhizogenes, Ri plasmid A4, mRNA Plasmid Partial, 103 nt] AACGCTTCAATACGGTGAGTGTGGTTGTAGGTTCAATTATTACTATTTTTGAAGCTGTGTATTTCCCTTTTTCTAAT ATGCACCTATTTCATGTTTCAGAATG

Experiment no.5:

gi|710464|gb|S74256.1| rolA=transferred TL-DNA

Graphic Summary
Distribution of 8 Blast Hits on the Query Sequence
An overview of the database sequences aligned to the query sequence is shown. The score of each alignment is indicated by one of five different colors, which divides the range of scores into five groups. Multiple alignments on the same database sequence are connected by a striped line. Mousing over a hit sequence causes the definition and score to be shown in the window at the top, clicking on a hit sequence takes the user to the associated alignments. New: This graphic is an overview of database sequences aligned to the query sequence. Alignments are color-coded by score, within one of five score ranges. Multiple alignments on the same database sequence are connected by a dashed line. Mousing over an alignment shows the alignment definition and score in the box at the top. Clicking an alignment displays the alignment detail.
Mouse-over to show defline and scores, click to show alignments

Legend for links to other resources: UniGene GEO Gene Structure PubChem BioAssay Sequences producing significant alignments: Max Total Query Accession Description score score coverage Catharanthus roseus isolate CrT1 DQ852611.1 191 191 100% cultivar Prabal, genomic sequence Catharanthus roseus isolate CrT2 cultivar Prabal putative rolA protein, tyrosine phosphatase RolB, cytokinin DQ852612.1 191 191 100% beta glucosidase RolC, and hypothetical proteins genes, complete cds Synthetic construct RolA mRNA, AF442735.1 191 191 100% complete cds Synthetic construct RolA gene, AF442734.1 191 191 100% complete cds rolA=transferred TL-DNA genes involved in the pathogenesis of hairyS74256.1 root disease [Agrobacterium 191 191 100% rhizogenes, Ri plasmid A4, mRNA Plasmid Partial, 103 nt] X76001.1 A.thaliana rolA gene (10null1-1) 191 191 100% Integrated Ri plasmid agropine (A. rhizogenes strain A4) complete TLK03313.1 191 191 100% DNA and flanking plant (Convolvulus arvensis) DNA Agrobacterium rhizogenes Ri plasmid X12579.1 191 191 100% rolA gene

Map Viewer

E Max Links value ident 7e-46 100%

7e-46 100%

7e-46 100% 7e-46 100%

7e-46 100%

7e-46 100% 7e-46 100%

7e-46 100%

gb|DQ852611.1| genomic sequence Length=12562

Catharanthus roseus isolate CrT1 cultivar Prabal,

Score = 191 bits (103), Expect = 7e-46 Identities = 103/103 (100%), Gaps = 0/103 (0%) Strand=Plus/Plus Query Sbjct 4690 Query Sbjct 1 4631 61 4691 AACGCTTCAATACGGTGAGTGTGGTTGTAGGTTCAATTATTACTATTTTTGAAGCTGTGT |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| AACGCTTCAATACGGTGAGTGTGGTTGTAGGTTCAATTATTACTATTTTTGAAGCTGTGT ATTTCCCTTTTTCTAATATGCACCTATTTCATGTTTCAGAATG ||||||||||||||||||||||||||||||||||||||||||| ATTTCCCTTTTTCTAATATGCACCTATTTCATGTTTCAGAATG 103 4733 60

> gb|DQ852612.1| Catharanthus roseus isolate CrT2 cultivar Prabal putative rolA protein, tyrosine phosphatase RolB, cytokinin beta glucosidase RolC, and hypothetical proteins genes, complete cds Length=8196 Score = 191 bits (103), Expect = 7e-46 Identities = 103/103 (100%), Gaps = 0/103 (0%) Strand=Plus/Plus Query Sbjct Query Sbjct 1 265 61 325 AACGCTTCAATACGGTGAGTGTGGTTGTAGGTTCAATTATTACTATTTTTGAAGCTGTGT |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| AACGCTTCAATACGGTGAGTGTGGTTGTAGGTTCAATTATTACTATTTTTGAAGCTGTGT ATTTCCCTTTTTCTAATATGCACCTATTTCATGTTTCAGAATG ||||||||||||||||||||||||||||||||||||||||||| ATTTCCCTTTTTCTAATATGCACCTATTTCATGTTTCAGAATG 103 367 60 324

> gb|AF442735.1| Length=831

Synthetic construct RolA mRNA, complete cds

Score = 191 bits (103), Expect = 7e-46 Identities = 103/103 (100%), Gaps = 0/103 (0%) Strand=Plus/Plus Query Sbjct Query Sbjct 1 208 61 268 AACGCTTCAATACGGTGAGTGTGGTTGTAGGTTCAATTATTACTATTTTTGAAGCTGTGT |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| AACGCTTCAATACGGTGAGTGTGGTTGTAGGTTCAATTATTACTATTTTTGAAGCTGTGT ATTTCCCTTTTTCTAATATGCACCTATTTCATGTTTCAGAATG ||||||||||||||||||||||||||||||||||||||||||| ATTTCCCTTTTTCTAATATGCACCTATTTCATGTTTCAGAATG 103 310 60 267

> gb|AF442734.1| Length=831

Synthetic construct RolA gene, complete cds

Score = 191 bits (103), Expect = 7e-46 Identities = 103/103 (100%), Gaps = 0/103 (0%) Strand=Plus/Plus Query Sbjct Query Sbjct 1 208 61 268 AACGCTTCAATACGGTGAGTGTGGTTGTAGGTTCAATTATTACTATTTTTGAAGCTGTGT |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| AACGCTTCAATACGGTGAGTGTGGTTGTAGGTTCAATTATTACTATTTTTGAAGCTGTGT ATTTCCCTTTTTCTAATATGCACCTATTTCATGTTTCAGAATG ||||||||||||||||||||||||||||||||||||||||||| ATTTCCCTTTTTCTAATATGCACCTATTTCATGTTTCAGAATG 103 310 60 267

> gb|S74256.1| rolA=transferred TL-DNA genes involved in the pathogenesis of hairy-root disease [Agrobacterium rhizogenes, Ri plasmid A4, mRNA Plasmid Partial, 103 nt] Length=103 Score = 191 bits (103), Expect = 7e-46 Identities = 103/103 (100%), Gaps = 0/103 (0%) Strand=Plus/Plus Query Sbjct Query Sbjct 1 1 61 61 AACGCTTCAATACGGTGAGTGTGGTTGTAGGTTCAATTATTACTATTTTTGAAGCTGTGT |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| AACGCTTCAATACGGTGAGTGTGGTTGTAGGTTCAATTATTACTATTTTTGAAGCTGTGT ATTTCCCTTTTTCTAATATGCACCTATTTCATGTTTCAGAATG ||||||||||||||||||||||||||||||||||||||||||| ATTTCCCTTTTTCTAATATGCACCTATTTCATGTTTCAGAATG 103 103 60 60

> emb|X76001.1| Length=700

A.thaliana rolA gene (10null1-1)

Score = 191 bits (103), Expect = 7e-46 Identities = 103/103 (100%), Gaps = 0/103 (0%) Strand=Plus/Plus Query Sbjct Query Sbjct 1 31 61 91 AACGCTTCAATACGGTGAGTGTGGTTGTAGGTTCAATTATTACTATTTTTGAAGCTGTGT |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| AACGCTTCAATACGGTGAGTGTGGTTGTAGGTTCAATTATTACTATTTTTGAAGCTGTGT ATTTCCCTTTTTCTAATATGCACCTATTTCATGTTTCAGAATG ||||||||||||||||||||||||||||||||||||||||||| ATTTCCCTTTTTCTAATATGCACCTATTTCATGTTTCAGAATG 103 133 60 90

> gb|K03313.1|RIATL A4) complete

Integrated Ri plasmid agropine (A. rhizogenes strain

TL-DNA and flanking plant (Convolvulus arvensis) DNA Length=21126 Score = 191 bits (103), Expect = 7e-46 Identities = 103/103 (100%), Gaps = 0/103 (0%) Strand=Plus/Plus Query Sbjct 9704 Query Sbjct 1 9645 61 9705 AACGCTTCAATACGGTGAGTGTGGTTGTAGGTTCAATTATTACTATTTTTGAAGCTGTGT |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| AACGCTTCAATACGGTGAGTGTGGTTGTAGGTTCAATTATTACTATTTTTGAAGCTGTGT ATTTCCCTTTTTCTAATATGCACCTATTTCATGTTTCAGAATG ||||||||||||||||||||||||||||||||||||||||||| ATTTCCCTTTTTCTAATATGCACCTATTTCATGTTTCAGAATG 103 9747 60

> emb|X12579.1| Length=720

Agrobacterium rhizogenes Ri plasmid rolA gene

Score = 191 bits (103), Expect = 7e-46 Identities = 103/103 (100%), Gaps = 0/103 (0%) Strand=Plus/Plus Query Sbjct Query Sbjct 1 139 61 199 AACGCTTCAATACGGTGAGTGTGGTTGTAGGTTCAATTATTACTATTTTTGAAGCTGTGT |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| AACGCTTCAATACGGTGAGTGTGGTTGTAGGTTCAATTATTACTATTTTTGAAGCTGTGT ATTTCCCTTTTTCTAATATGCACCTATTTCATGTTTCAGAATG ||||||||||||||||||||||||||||||||||||||||||| ATTTCCCTTTTTCTAATATGCACCTATTTCATGTTTCAGAATG 103 241 60 198

Experiment no.7:
CLUSTAL 2.1 Multiple Sequence Alignments Sequence type explicitly set to DNA Sequence format is Pearson Sequence 1: 1 103 bp Sequence 2: 2 183 bp Sequence 3: 3 136 bp Sequence 4: 4 150 bp Start of Pairwise alignments Aligning... Sequences (1:2) Aligned. Score: 28.1553 Sequences (1:3) Aligned. Score: 21.3592 Sequences (1:4) Aligned. Score: 25.2427 Sequences (2:3) Aligned. Score: 25.7353 Sequences (2:4) Aligned. Score: 21.3333 Sequences (3:4) Aligned. Score: 21.3235 Guide tree file created: [clustalw.dnd] There are 3 groups Start of Multiple Alignment Aligning... Group 1: Delayed Group 2: Delayed Group 3: Delayed Alignment Score 865 CLUSTAL-Alignment file created [clustalw.aln]

clustalw.aln CLUSTAL 2.1 multiple sequence alignment 1 -------------------------------AACGCTTCAAT-ACGGTGAGT-----GTG 2 ----------------ACTAGAACAACTTAAACGATTCCCTCATGAGGAATCCCTTGTG 3 --------------------------------------AGGCCACGCTGGTTTTGTTGTC 4 GAAAATGGCACTGTGAAATACGCAACACTTCAGACTTATGGTGACACAGTTCATACT CTG * * *

1 GTTGTA-GGTTCAATTAT----TACTATTTTTG--AAGCTGTGTATTTCCCTTTTTCTA 2 GCCGGATGGCAGAAGCACA--TTTTATTCTCACTAAACATTATCTGGGGCCGGAAATTA 3 GCTCGA-GGGACACGTGT---ACTCATAATAACCCAATGTCTTGGAATACGAGGCATTT 4 CTCTAGAGAAAGAACTACAAAGGGATATTTCTACCTGGATTCAAGGAACACCCTCA ATCG * * ** * 1 ATATGCACCTATTTCATGTTTCAGAATG-------------------------------2 ATGATCTCCCATCGCTTACTTCACGGTGGCGCAGTTGGTGGAGGTGCTGATCTTGTA GGG 3 AAGCTCTTTGCTAGCAAAGC--CACTGCCTGGGAGGGCAGATATGTTAGCGTTGTGCCT 4 AAAACCTTTTTTCAGACTCTTCCAAGAACC-----------------------------* * * 1 2 3 4 ----------------------GACGTTGACTCCACACTTTCCAG GA-------------------------------------------

clustalw.dnd ( ( 1:0.35664, 4:0.39093) :0.02446, 2:0.35431, 3:0.38834);

Experiment no.8:

Experiment no.6:

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5'3' Frame 1 N A S I R Stop V W L Stop V Q L L L F L K L C I S L F L I C T Y F Met F Q N 5'3' Frame 2 T L Q Y G E C G C R F N Y Y Y F Stop S C V F P F F Stop Y A P I S C F R Met 5'3' Frame 3 R F N T V S V V V G S I I T I F E A V Y F P F S N Met H L F H V S E 3'5' Frame 1 H S E T Stop N R C I L E K G K Y T A S K I V I I E P T T T L T V L K R 3'5' Frame 2 I L K H E I G A Y Stop K K G N T Q L Q K Stop Stop Stop L N L Q P H S P Y Stop S V 3'5' Frame 3 F Stop N Met K Stop V H I R K R E I H S F K N S N N Stop T Y N H T H R I E A