PDF Help

At3g04400 SYNGENTA 68274

Genomic Sequence (from TAIR)

gcttattgttaaattatttcggcccataaaataaagtccaggtcagctcacaatacatgaagaaaaccctagttcaagcgtatataaaccctct◄cggcg
ctgccattgaaactctttcaa◄ggaga►gagctgctactctgcaaccATGTCGAAGCGAGgtaaaaaaacgtttcttcatctctaattcgcttaacctaa
tctgtgtacatctcgtatgaatcatatcctgttttcgcttattttcttcatttcactttcaatgacaatggttttaccctaatttctattagtaaagctt
ctggatcatgaatattagtcttatatgtctctactttggttgatagtgtttagatctgtaacttttgtgtttgttttttgtgaatagGAAGAGGAGGAAC
CTCTGGTAACAAGTTCAGGATGTCACTGGGTCTTCCAGTGGCAGCCACTGTGAACTGTGCTGACAACACCGGAGCTAAGAACCTTTACATCATTTCGGTT
AAAGGAATCAAGGGTCGTCTTAACCGTTTGCCATCAGCGTGTGTTGGTGATATGGTTATGGCTACTGTTAAGAAAGGTAAGCCTGATCTCCGTAAGAAGG
TGCTTCCTGCTGTCATTGTTAGGCAGAGGAAGCCTTGGCGCCGAAAGGACGGTGTCTTCATGTATTTCGAAGgtaatcctttgcttttcttctctgtgat
ttgcatttcaatttctctgaagtgtgattgtctgatagaaagttttggttttgcagATAATGCTGGTGTCATTGTCAATCCCAAGGGTGAAATGAAAGgt
aagaagttgatgtttttgcttatttgttattgaattctctggtagatgtatgagttgtttatgtatgcaagttttgataacctcctgatgagttagtagt
tactagaggaagtattgtgtatctgaatttatctagaagtttgatatggggcaactcaaagccaatctcgtagtgataaatcagtagtatcatatttact
tgtagctgatgagtctgttgtgtgatgtaattagGATCTGCTATCACTGGACCAATCGGAAAGGAGTGTGCTGATCTGTGGCCAAGAATCGCAAGTGCTG
CGAACGCCATCGTTTAAgcaagcttgagatctctatgttttgtgttgaacgtttagcattatctctatttgggattgttttttgtttttgtcttagactt
ttgttatgccttaaagctgattctagttcttataagaaccttcgtttctcgtgccagtttgtcacctcagtgttttagtctatcgtaaacttgtgatttg
attcactggttcttgtgtttgttcggttttgttttaaaaaacatagaattcaagtgattcacactattttgttacgcaattagaaatatgtttagggcga
atcaattgtgtgaacagacttaagtagagcctaaaaatttgtatataactcttatattagcaagtcaattgtggatttgggaatctgtttttcaatattt
cat

Border_1 (68274_RBD)


TGCAGAGCTCGCTTGAGCTTGGATCAGATTGTCGTTTCCCGCCTTCAGTTTAAACTATCAGTGTTTATATACCCGCCTTAAGTCCATGTGTTATTCGACA
TGGTTATCAGGGCGCTGCCAAGAGGGTTTATATACGCTTGAACTAGGGTTTTCTTCATGTATTGTGAGCTGACCTGGACTTTATTTTATGGGCCGAAATA
ATTTAACAATAAGCCCAATAATGTTCTCTTTCTT

Start of BLAST Alignment:	NT < 24 / 5’ UTR
First 15 bp Perfect Match:	NT < 50 / 5’ UTR

BLAST Details:
Query Sequence: 68274_RBD 
Length: (234 letters) 
Database: TIGR AGI BAC Sequences (DNA);
                                                                     Smallest
                                                                       Sum
                                                              High  Probability
Sequences producing High-scoring Segment Pairs:              Score  P(N)      N

T27C4 60278                                                    596  9.7e-21   1
T1J8 51066                                                     146  0.88      1
MDB19 60476                                                    135  0.999     1



T27C4 60278
        Length = 71,616

  Minus Strand HSPs:

 Score = 596 (95.5 bits), Expect = 9.7e-21, P = 9.7e-21
 Identities = 132/142 (92%), Positives = 132/142 (92%), Strand = Minus / Plus

Query:   234 AAGAAAGAGAACATTATTGGGCTTATTGTTAAATTATTTCGGCCCATAAAATAAAGTCCA 175
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 12012 AAGAAAGAGAACATTATTGGGCTTATTGTTAAATTATTTCGGCCCATAAAATAAAGTCCA 12071

Query:   174 GGTCAGCTCACAATACATGAAGAAAACCCTAGTTCAAGCGTATATAAACCCTCTTGGCAG 115
             |||||||||||||||||||||||||||||||||||||||||||||||||||||| ||| |
Sbjct: 12072 GGTCAGCTCACAATACATGAAGAAAACCCTAGTTCAAGCGTATATAAACCCTCTCGGC-G 12130

Query:   114 C-GCCCT-GATAACCATGTCGA 95
             | ||| | || |||  | || |
Sbjct: 12131 CTGCCATTGA-AACTCTTTCAA 12151


T1J8 51066
        Length = 134,151

  Minus Strand HSPs:

 Score = 146 (28.0 bits), Expect = 2.1, P = 0.88
 Identities = 94/163 (57%), Positives = 94/163 (57%), Strand = Minus / Plus

Border_2 (68274_LBU)


ATTCGGCGTTAATTCAGTACATTAAAAACGTCCGCAATGTGTTATTAAGTTGTCTAAGCGTCAATTTGTTTACACCACAATATATATTGAGCTGCTACTC
TGCAACCATGTCGAAGCGAGGTAAAAAAACGTTTCTTCATCTCTAATTCGCTTAACCTAATCTGTGTACATCTCGTATGAATCATATCCTGTTTTCGGTT
ATTTTCTTCATTTCACTTTCAATGACAATGGTTTTACCCTAATTTCTATTAGTAAAGCTTCTGGATCATGAATATTAGTCTTATATGTCTCTACTTTGGT
TGATAGTGTTTAGATCTGTAACTTTTGTGTTTGTTTTTTGTGAATAGGAAGAGGAGGAACCTCTGGTAACAAGTTCAGGATGTCACTGGGTCTTCCAGGG
GCAGCCACTGTGAACTGTGCTGACAACACCGGAGCTAAGAACCTTTACATCATTTCGGTTAAAGGAATCAAGGGTCGTCTTAACCGTTTGCCATCAGCGT
GTGTTGGTGATATGGTTATGGCTACTGTTAAGAAAGGTAAGCCTGATCTCCGTAAGAAGGTGCTTCCTGCTGTCATTGTTAGGCAGAGGAAGCCTTGGCG
CCGAAAGGAC

Start of BLAST Alignment:	NT < 19 / 5’ UTR
First 15 bp Perfect Match:	NT < 19 / 5’ UTR

BLAST Details:
Query Sequence: 68274_LBU 
Length: (610 letters) 
Database: Genes from AGI, Total Genome (DNA);
                                                                     Smallest
                                                                       Sum
                                                              High  Probability
Sequences producing High-scoring Segment Pairs:              Score  P(N)      N

At3g04400 68416.t00424 60S ribosomal protein L23 (RPL23C)...  2592  1.7e-112  1
At2g33370 68415.t03782 60S ribosomal protein L23 (RPL23B)     1048  1.1e-42   1
At1g04480 68414.t00389 60S ribosomal protein L23 (RPL23A)...   980  1.1e-39   1
At1g29020 68414.t03180 calcium-binding EF hand family pro...   232  0.026     1


>At3g04400 68416.t00424 60S ribosomal protein L23 (RPL23C) similar to ribosomal
           protein L17 GB:AAA34113.1 from [Nicotiana tabacum]
        Length = 1382

  Plus Strand HSPs:

 Score = 2592 (395.0 bits), Expect = 1.7e-112, P = 1.7e-112
 Identities = 520/522 (99%), Positives = 520/522 (99%), Strand = Plus / Plus

Query:    89 GAGCTGCTACTCTGCAACCATGTCGAAGCGAGGTAAAAAAACGTTTCTTCATCTCTAATT 148
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    45 GAGCTGCTACTCTGCAACCATGTCGAAGCGAGGTAAAAAAACGTTTCTTCATCTCTAATT 104

Query:   149 CGCTTAACCTAATCTGTGTACATCTCGTATGAATCATATCCTGTTTTCGGTTATTTTCTT 208
             ||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||
Sbjct:   105 CGCTTAACCTAATCTGTGTACATCTCGTATGAATCATATCCTGTTTTCGCTTATTTTCTT 164

Query:   209 CATTTCACTTTCAATGACAATGGTTTTACCCTAATTTCTATTAGTAAAGCTTCTGGATCA 268
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   165 CATTTCACTTTCAATGACAATGGTTTTACCCTAATTTCTATTAGTAAAGCTTCTGGATCA 224

Query:   269 TGAATATTAGTCTTATATGTCTCTACTTTGGTTGATAGTGTTTAGATCTGTAACTTTTGT 328
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   225 TGAATATTAGTCTTATATGTCTCTACTTTGGTTGATAGTGTTTAGATCTGTAACTTTTGT 284

Query:   329 GTTTGTTTTTTGTGAATAGGAAGAGGAGGAACCTCTGGTAACAAGTTCAGGATGTCACTG 388
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   285 GTTTGTTTTTTGTGAATAGGAAGAGGAGGAACCTCTGGTAACAAGTTCAGGATGTCACTG 344

Query:   389 GGTCTTCCAGGGGCAGCCACTGTGAACTGTGCTGACAACACCGGAGCTAAGAACCTTTAC 448
             |||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   345 GGTCTTCCAGTGGCAGCCACTGTGAACTGTGCTGACAACACCGGAGCTAAGAACCTTTAC 404

Query:   449 ATCATTTCGGTTAAAGGAATCAAGGGTCGTCTTAACCGTTTGCCATCAGCGTGTGTTGGT 508
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   405 ATCATTTCGGTTAAAGGAATCAAGGGTCGTCTTAACCGTTTGCCATCAGCGTGTGTTGGT 464

Query:   509 GATATGGTTATGGCTACTGTTAAGAAAGGTAAGCCTGATCTCCGTAAGAAGGTGCTTCCT 568
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   465 GATATGGTTATGGCTACTGTTAAGAAAGGTAAGCCTGATCTCCGTAAGAAGGTGCTTCCT 524

Query:   569 GCTGTCATTGTTAGGCAGAGGAAGCCTTGGCGCCGAAAGGAC 610
             ||||||||||||||||||||||||||||||||||||||||||
Sbjct:   525 GCTGTCATTGTTAGGCAGAGGAAGCCTTGGCGCCGAAAGGAC 566


>At2g33370 68415.t03782 60S ribosomal protein L23 (RPL23B)
        Length = 1152

  Plus Strand HSPs:

 Score = 1048 (163.3 bits), Expect = 1.1e-42, P = 1.1e-42
 Identities = 332/452 (73%), Positives = 332/452 (73%), Strand = Plus / Plus