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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAGgtgctttgtcaacttcctctatgctggccatacacttttaagttcaaacaaataatgttcttactctgataagtagtaacaacttgttcccttttgatttactttccttccag

Basic information

species Oryza sativa
transcript LOC_Os08g41390.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g41390.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G096585_T05 (Zea mays), 5'ss of exon 7
TCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAGgt--gctttgtcaacttcctctatgctgg-ccatacacttttaagttcaaacaa---------ataatgttcttactctgataagtagtaacaacttgttcccttttgatt-tactttccttccag
||||||| |  ||||| |||||||||||  |  | |||||||||||||||||||| |||   ||||||||| |||||||||| |||||||||  |      |   |  || |||   || |  |   | | | |||  ||| ||         | |  |   | |  ||||||  ||| || ||| |||| | |||  ||| || | |  ||||||
TCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGCATGACGAA---GAGCCATTTAAATTCAAGACCGATGAAGgtaagaacatccttttgtctttatatggggctcttggcctatcagtaaaaataataattcaggaaatcgacttgatcctgatatttag-aataacatgtttcgtttgtattataatctgtttccag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|454468|gb|D28191.1|D28191
EST:     AANGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAG                         AGGAGGTCATTGATGGTATT
genomic: AAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAGgtgctttgtc ... ttccttccagAGGAGGTCATTGATGGTATT
EST: gi|58677816|gb|CK066503.1|CK066503
EST:     AAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAG                         AGGAGGTCATTGATGGTATTGACCGTGCTGTGCTAAACATGAAGAATGGCG
genomic: AAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAGgtgctttgtc ... ttccttccagAGGAGGTCATTGATGGTATTGACCGTGCTGTGCTAAACATGAAGAATGGCG
EST: gi|58673768|gb|CK062454.1|CK062454
EST:     CAGACAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAG                         AGGAGGTCATTGATGGTATTGACCGTGCTGTGCTAAACATGAAGAATGGCG
genomic: -AGA-AGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAGgtgctttgtc ... ttccttccagAGGAGGTCATTGATGGTATTGACCGTGCTGTGCTAAACATGAAGAATGGCG
EST: gi|2442986|gb|C74757.1|C74757
EST:     AAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAG                         AGGAGGTCATTGATGGTATTGACCGTGCTGTGCTAAACATGAAGAATGGCG
genomic: AAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAGgtgctttgtc ... ttccttccagAGGAGGTCATTGATGGTATTGACCGTGCTGTGCTAAACATGAAGAATGGCG
EST: gi|58695757|gb|CK084444.1|CK084444
EST:     AAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAG                         AGGAGGTCATTGATGGTATTGACCGTGCTGTGCTAAACATGAAGAATGGCG
genomic: AAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAGgtgctttgtc ... ttccttccagAGGAGGTCATTGATGGTATTGACCGTGCTGTGCTAAACATGAAGAATGGCG
EST: gi|58695816|gb|CK084503.1|CK084503
EST:     AAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAG                         AGGAGGTCATTGATGGTATTGACCGTGCTGTGCTAAACATGAAGAATGGCG
genomic: AAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAGgtgctttgtc ... ttccttccagAGGAGGTCATTGATGGTATTGACCGTGCTGTGCTAAACATGAAGAATGGCG
EST: gi|29630489|gb|CB635498.1|CB635498
EST:     AAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAG                         AGGAGGTCATTGATGGTATTGACCGTGCTGTGCTAAACATGAAGAATGGCG
genomic: AAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAGgtgctttgtc ... ttccttccagAGGAGGTCATTGATGGTATTGACCGTGCTGTGCTAAACATGAAGAATGGCG
EST: gi|58686617|gb|CK075304.1|CK075304
EST:     AAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAG                         AGGAGGTCATTGATGGTATTGACCGTGCTGTGCTAAACATGAAGAATGGCG
genomic: AAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAGgtgctttgtc ... ttccttccagAGGAGGTCATTGATGGTATTGACCGTGCTGTGCTAAACATGAAGAATGGCG
EST: gi|58682283|gb|CK070970.1|CK070970
EST:     AAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAG                         AGGAGGTCATTGATGGTATTGACCGTGCTGTGCTAAACATGAAGAATGGCG
genomic: AAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAGgtgctttgtc ... ttccttccagAGGAGGTCATTGATGGTATTGACCGTGCTGTGCTAAACATGAAGAATGGCG
EST: gi|2427305|gb|C71768.1|C71768
EST:     AAAGAAGGGGCATGATGAACCAGAGCCATTTGANTTCAAGACTGATGAAG                         AGGAGGTCATTGATGGTATTGACCGTGCTGTGCTAAACATGAAGAATGGCG
genomic: AAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAGgtgctttgtc ... ttccttccagAGGAGGTCATTGATGGTATTGACCGTGCTGTGCTAAACATGAAGAATGGCG
EST: gi|84117299|gb|CD151066.1|CD151066
EST:     AAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAG                         AGGAGGTCATTGATGGTATTGACCGTGCTGTGCTAAACATGAAGAATGGCG
genomic: AAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAGgtgctttgtc ... ttccttccagAGGAGGTCATTGATGGTATTGACCGTGCTGTGCTAAACATGAAGAATGGCG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAGgtgctttgtcaacttcctctatgctggccatacacttttaagttcaaacaaataatgttcttactctgataagtagtaacaacttgttcccttttgatttactttccttccag

- - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - -  AAGAAG