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At3g52380 SYNGENTA 39846

Genomic Sequence (from TAIR)

atagttgcatgagtatctacaatctaagacacaaagacatagatggatctaagggagactgaactcttgtataatggattcacaatcacaagaaacaagg
agagaaacacaaattgaacgttattatttccagcttaatggacttgaagaatgaccatcatgtttgtgcctaatctgattttctccaaattctttagaat
tctctctttgctaatcctgaccaatatgagaaattcaccatttttttgctcataggtgctatcaataacagtttcaagtttcaacaattcaccatttata
taacattaccaacagtccaacactagtaacataatcaccaaaatatattagtaataaattttcatcacagctttatatttttgtgattagaaattaggat
cttacagaaatctttcaaaaaaaaattcataacagttccattttttttggtaagattcataaaaaaattcaagttaaatgcattttataa◄aaatgtagg
aaaaactttcat◄caaaaatcgttgagaagaacatacagtatatcttatccactctcttcctcatccacgcggcaaaggcacaaacctctttagaaaaAT
GTCGTCAGCTTATTGTTCCTCCGCCGTGGCTGTATCCGCCGCAGCCACCGCTTCCTCCGCCGCTACCTTTAATCCATTACTCTCCTCCCACTCCAATTCC
CAACTCTTCTATCGCTTTACACCAAAATCCTTCAAACTCGTTGCCAATTGCCCTAATCCACTAATCCTCCACTCAAATATCCGCCGCCACCGCTTCTTCT
GCGCCGCCGAAACCGAAGCTAGTTCCGCCGATGATGAAATCCAGGCATCAGTAGAAGAAGAAGAAGAGGTAGAAGAAGAAGGAGATGAAGGTGAAGAAGA
AGTAGAGGAAGAAAAACAGACGACGCAAGCGAGTGGTGAAGAAGGGAGGCTTTACGTTGGGAATTTACCTTACACAATCACTTCTTCTGAGCTCTCTCAG
ATTTTTGGAGAAGCTGGAACTGTCGTCGATGTTCAGgttcgtctctaatcttcatacgattctatcaatcgatttggagacagtgaagcaaaattaggat
gaagattgtctaattgttagcattgttctctgttgtagATTGTTTATGATAAAGTTACTGATAGAAGCAGAGGATTTGGATTTGTAACAATGGGAAGCAT
TGAAGAAGCTAAAGAAGCGATGCAGATGTTTAACAGCTCTgtaagttcacatcatttgatcaaagatgattcagcttcagaatgtttctgatctcttgtg
tgttgagtttgtagCAAATTGGTGGTAGAACGGTGAAAGTGAACTTCCCGGAGGTGCCGAGAGGCGGTGAGAACGAAGTAATGAGAACCAAAATCCGTGA
TAATAACCGGAGTTATGTTGATAGTCCTCATAAGGTATATGCAGGAAACCTTGGTTGGAATCTAACCTCACAAGGTTTAAAGGATGCATTTGGTGATCAA
CCTGGTGTGCTTGGTGCTAAAGTTATCTATGAAAGAAATACTGGGAGGTCTAGGGGGTTTGGTTTCATCTCGTTCGAGTCAGCGGAAAATGTTCAGTCTG
CTTTGGCTACAATGAATGGCGTGgtaaggcttcttctcccttcttgtttggttgggtggtttgggttttgagactcactagttttggtttttagGAAGTT
GAAGGACGAGCGCTGAGGCTAAATTTGGCTTCAGAGAGAGAGAAACCCACTGTGTCTCCTCCTTCCGTAGAAGAAGGAGAAACCGAGGAGGCCAGTCTAG
AGAGTAACGAGGTGCTTTCGAATGTTAGTGCATGAagcagcaaaagcacaatagattccggataagtttcaga►ctgatctgctcgaggtgccaaaaatg
aaaattttgttgtctttataaatgtgttgttttgttctagtgaggctgaagaagaagacaatatatgagatagaaaacaagagattgtttgtaattttta
ttgagaatgtttttaatccataaatggtgtaatgtaacaacatatcttgattccagtaaactgcaaatttctgtcacgattaatgctagtcggtctcgtg
gtgcccggaaagcagagcatctgcagcagaatctaagtcctgagggaagaagaccctgcagaaatattgacaagccatcaagacaacgttttacgttaga
acagttcttcatatttctgtcatgaaattatgtgaaaccgaaaaagagaaaacatgcctgcaagtgttgtggtacaaggttgagctaacttgatttagat
cgccaagtcctttgtagccagccaccacttcaaggacttgcctggagaagaaaatgattgcctaagaattgttcgaagactgtatatgcttatggatttg
aca

Border_1 (39846_LBD)


TCTTAAAAACGTCCGCAATGTGTTATTAAGTTGTCTAAGCGTCAATTTGTTTACACCACAATGAAAATTTTTTTATGGATCTTATAAAATGCATTTAACT
TGAATTTTTTTGGAGCAGAACATGTCCTACATTTTTATAAAATGCATTTAACTTGAATTTTTTTATGAATCTTACCAAAAAAAATGGAACTGTTATGAAT
TTTTTTTTGAAAGATTTCTGTAAGATCCTAATTTCTAATCACAAAAATATAAAGCTGGGATGAAAATTTATTACTAATATATTTGGGGGATTATGTTACT
AGTGTTGGACTGTTGGTAATGTTATATAAATGGTGAATTGTTGAAACTTGAAACTGTTATTGATAGCACCTATGAGCAAAAAAATGGTGAATTTCTCATA
TTGGTCAGGATTAGCAAAGAGAGAATTCTAAAGAATTTGGAGAAAATCAGATTAGGCACAAACATGATGGTCATTCTTCAAGTCCATTAAGCTGGAAATA
ATAACGTTCAATTTGGGTTTCTCTCCTTGTTTCTTGGGATTGGGAATCCATTATACAAGAGTTCAGCC

Start of BLAST Alignment:	NT < 85 / 5’ UTR
First 15 bp Perfect Match:	NT < 106 / 5’ UTR

BLAST Details:
Query Sequence: 39846_LBD 
Length: (568 letters) 
Database: Genes from AGI, Total Genome (DNA);
                                                                     Smallest
                                                                       Sum
                                                              High  Probability
Sequences producing High-scoring Segment Pairs:              Score  P(N)      N

At3g52380 68416.t05354 33 kDa ribonucleoprotein, chloropl...   548  3.2e-19   1
At2g44480 68415.t05061 glycosyl hydrolase family 1 protei...   197  0.62      1
At1g01320 68414.t00039 tetratricopeptide repeat (TPR)-con...   194  0.77      1
At4g23940 68417.t03217 FtsH protease, putative contains s...   191  0.86      1


>At3g52380 68416.t05354 33 kDa ribonucleoprotein, chloroplast, putative /
           RNA-binding protein cp33, putative similar to chloroplast
           RNA-binding protein (cp33) GB:BAA06523 (Arabidopsis thaliana) (Plant
           Mol. Biol. 27 (3), 529-539 (1995)); contains InterPro entry
           IPR000504: RNA-binding region RNP-1 (RNA recognition motif) (RRM)
        Length = 1698

  Minus Strand HSPs:

 Score = 548 (88.3 bits), Expect = 3.2e-19, P = 3.2e-19
 Identities = 136/176 (77%), Positives = 136/176 (77%), Strand = Minus / Plus

Query:   250 ATATTTTTGTGATTAGAAATTAGGATCTTACAGAAATCTTTCNNNNNNNNNTTCATAACA 191
             ||||||||||||||||||||||||||||||||||||||||||         |||||||||
Sbjct:     1 ATATTTTTGTGATTAGAAATTAGGATCTTACAGAAATCTTTCAAAAAAAAATTCATAACA 60

Query:   190 GTTCCANNNNNNNNGGTAAGATTCATAAAAAAATTCAAGTTAAATGCATTTTATAAAAAT 131
             ||||||        ||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 GTTCCATTTTTTTTGGTAAGATTCATAAAAAAATTCAAGTTAAATGCATTTTATAAAAAT 120

Query:   130 GTAGGACATGTTCTGCTCCAAAAAAATTCAAGTTAA-ATGCATTTTATAAGATCCA 76
             |||||| |   | |  || ||||   || |    || || || | |||   |||||
Sbjct:   121 GTAGGAAAAACTTTCATCAAAAATCGTTGAGAAGAACATACAGTATATCTTATCCA 176

 Score = 176 (32.5 bits), Expect = 9.2, P = 0.99990
 Identities = 44/52 (84%), Positives = 44/52 (84%), Strand = Minus / Plus

Query:   111 AAAAAAATTCAAGTTAAATGCATTTTATAAGATCCATAA-AAAAATTTTCAT 61
             |||||||||||||||||||||||||||||| |    ||  ||||| ||||||
Sbjct:    87 AAAAAAATTCAAGTTAAATGCATTTTATAAAAATG-TAGGAAAAACTTTCAT 137


>At2g44480 68415.t05061 glycosyl hydrolase family 1 protein contains Pfam
           PF00232 : Glycosyl hydrolase family 1 domain; TIGRFAM TIGR01233:
           6-phospho-beta-galactosidase; similar to amygdalin hydrolase isoform
           AH I precursor (GI:16757966) [Prunus serotina]
        Length = 3355

  Minus Strand HSPs:

 Score = 197 (35.6 bits), Expect = 0.97, P = 0.62
 Identities = 141/247 (57%), Positives = 141/247 (57%), Strand = Minus / Plus

Border_2 (39846_RBU)


TGATCTACATGTTCTGATCTGCTCGAGGTGCCAAAAATGAAAATTTTGTTGTCTTTATAAATGTGTTGTTTTGTTCTAGTGAGGCTGAAGAAGAAGACAA
TATATGAGATAGAAAACAAGAGATTGTTTGTAATTTTTATTGAGAATGTTTTTAATCCATAAATGGTGTAATGTAACAACATATCTTGATTCCAGTAAAC
TGCAAATTTCTGTCACGATTAATGCTAGTCGGTCTCGTGGTGCCCGGAAAGCAGAGCATCTGCAGCAGAATCTAAGTCCTGAGGGAAGAAGACCCTGCAG
AAATATTGACAAGCCATCAAGACAACGTTTTACGTTAGAACAGTTCTTCATATTTCTGTCATGAAATTATGTGAAACCGAAAAAGAGAAAACATGCCTGC
AAGTGTTGTGGTACAAGGTTGAGCTAACTTGATTTAGATCGCCAAGTCCTTTGTAGCCAGCCACCACTTCAAGGACTTGCCTGGAGAAGAAAATGATTGC
CTAAGAATTGTTCGAAGACTGTATATGCTTATGGATTTGACAAGATTTTAATCTAGAAGCTACACTCACCTGACTAAACAAGGCTCATTACGGCCTTTGA
CAAGGGACTCTTGATCATACTTCTCTTTTTTCTTGGAAGGCCAAGTCGACTTTACAAACTTGATTCCGGCGTGTGTGTTCTTGATATCACAATATGGAGA
GTCGGTTTCGATCATCATTCTCTCTACTGGTATT

Start of BLAST Alignment:	NT > 38 / 3’ UTR
First 15 bp Perfect Match:	NT > 38 / 3’ UTR

BLAST Details:
Query Sequence: 39846_RBU 
Length: (734 letters) 
Database: Genes from AGI, Total Genome (DNA);
                                                                     Smallest
                                                                       Sum
                                                              High  Probability
Sequences producing High-scoring Segment Pairs:              Score  P(N)      N

At3g52390 68416.t05357 tatD-related deoxyribonuclease fam...  3605  1.6e-158  1
At3g52380 68416.t05354 33 kDa ribonucleoprotein, chloropl...  1005  6.5e-41   1
At4g09470 68417.t01487 hypothetical protein                    191  0.94      1
At4g30710 68417.t04038 expressed protein contains Pfam do...   185  0.9990    1


>At3g52380 68416.t05354 33 kDa ribonucleoprotein, chloroplast, putative /
           RNA-binding protein cp33, putative similar to chloroplast
           RNA-binding protein (cp33) GB:BAA06523 (Arabidopsis thaliana) (Plant
           Mol. Biol. 27 (3), 529-539 (1995)); contains InterPro entry
           IPR000504: RNA-binding region RNP-1 (RNA recognition motif) (RRM)
        Length = 1698

  Plus Strand HSPs:

 Score = 1005 (156.8 bits), Expect = 6.5e-41, P = 6.5e-41
 Identities = 201/201 (100%), Positives = 201/201 (100%), Strand = Plus / Plus

Query:    14 CTGATCTGCTCGAGGTGCCAAAAATGAAAATTTTGTTGTCTTTATAAATGTGTTGTTTTG 73
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:  1498 CTGATCTGCTCGAGGTGCCAAAAATGAAAATTTTGTTGTCTTTATAAATGTGTTGTTTTG 1557

Query:    74 TTCTAGTGAGGCTGAAGAAGAAGACAATATATGAGATAGAAAACAAGAGATTGTTTGTAA 133
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:  1558 TTCTAGTGAGGCTGAAGAAGAAGACAATATATGAGATAGAAAACAAGAGATTGTTTGTAA 1617

Query:   134 TTTTTATTGAGAATGTTTTTAATCCATAAATGGTGTAATGTAACAACATATCTTGATTCC 193
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:  1618 TTTTTATTGAGAATGTTTTTAATCCATAAATGGTGTAATGTAACAACATATCTTGATTCC 1677

Query:   194 AGTAAACTGCAAATTTCTGTC 214
             |||||||||||||||||||||
Sbjct:  1678 AGTAAACTGCAAATTTCTGTC 1698


>At4g09470 68417.t01487 hypothetical protein
        Length = 1224

  Minus Strand HSPs:

 Score = 191 (34.7 bits), Expect = 2.8, P = 0.94
 Identities = 177/301 (58%), Positives = 177/301 (58%), Strand = Minus / Plus