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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAGgtaaaataagtgcatgtataatatgcctctgtcagagaaaataagagaatttatccctttctttttcctttttctggttcaccag

Basic information

species Oryza sativa
transcript LOC_Os08g25734.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g25734.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G163437_T01 (Zea mays), 5'ss of exon 7
AACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAGgtaaaataagtgcatgtataatatgcctctgtcagagaaaataagagaatttatccctttctttttcctttttctggttcaccag
||||| |||||||||||||| |||||||||||||| || ||||| |||||||| || || ||||||||| | ||||| ||||| || |||||||| |||||||| ||  | || ||    ||  |  ||| ||  | ||  ||||||  | |  ||||    ||    |||||  |        
AACTGCAAGATACACCATTCTGTAGTTGGACTCCGTTCTTGCATATCTGAAGGTGCTATCATAGAGGACACTTTACTAATGGGTGCGGACTACTATGAGgtaaa-tatatacaagtg---tacactgctgccaatgcaa-caagagagctcacaccttggcgttcttcttttccag--------

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G068506_T03 (Zea mays), 5'ss of exon 7
AACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAGgtaaaataagtgcatgtata-atatgcctctgtcagagaaaataagagaatttatccctttctttttcctttttctggttcaccag
||||| |||||| ||||||| |||||||||||||| || ||||| |||||||| || || |||||||||   ||||| ||||| || |||||||| |||||||| ||  | | |  |   |||| |  ||||||  | ||  || |||  | |  |   | | ||   ||||||  |        
AACTGCAAGATAAACCATTCTGTAGTTGGACTCCGATCTTGCATATCTGAAGGTGCTATCATAGAGGACAGTTTACTAATGGGTGCGGACTACTATGAGgtaaa-tatatacgtacaagtatatactgctgtcaatgcaa-caatagagctcacacagctgtgttctttttttccag--------

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 5'ss of exon 7
lower sequence: AT5G48300.1 (Arabidopsis thaliana), 5'ss of exon 6
AACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAGgtaaaataagtgcatgtataatatgcctctgtcagagaaaataagagaatttatccctttctttttccttttt--ctggttcaccag
||||| || || || || || || ||||||||||| |||||||| || ||||| || || || || || || ||| | ||||||||||| || ||||||||||||      | || |    ||     ||  |   ||  | |     || ||     |  | ||| ||  |   || ||  | ||
AACTGCAAAATTCATCACTCTGTGGTTGGACTCCGTTCCTGCATATCAGAAGGTGCTATTATTGAAGATTCGTTATTAATGGGAGCTGATTATTACGAGgtaaaaatctgtcttgcaatcaatcttcttgctaagtaatgtcaaccttttgatgatggtggtcttctttgatgattgtttgcctag

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 5'ss of exon 7
lower sequence: PP1S76_105V6.1 (Physcomitrella patens), 5'ss of exon 7
AACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAGgtaaaataagtgcatgtataatatgcctct-gtcagagaaaataagagaatttatccctttctttttcc---tttttctggttcaccag--------------------
|||   |  ||   ||| ||||| ||||| || || || ||  | || ||||| ||  | || |||||| |  |||||||||||||||| |||||||||||||          | || ||   | |  | |    |  | || |     ||| |  |||   |||||    |||||| |  |   ||                     
AACGCAAGAATTTTCCACTCAGTGGTTGGTCTACGATCTTGGGTCTCGGAAGGTGCTGTCATTGAGGACGCTCTACTCATGGGAGCTGATTACTACGAGgtaac---------tatacaacgagtccttagatttaccagattactttgtttctatcttcgattttctaattttttcagagtagacaaatcagtattttgtgcagtga

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|89177014|gb|CI111214.1|CI111214
EST:     AAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAG                         ACTGAAGCAGACAAGAAACTCCTTGGTGAAAAAGGTGGCATTCCCATTGGT
genomic: AAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAGgtaaaataag ... ggttcaccagACTGAAGCAGACAAGAAACTCCTTGGTGAAAAAGGTGGCATTCCCATTGGT
EST: gi|29681077|gb|CB677352.1|CB677352
EST:     AAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAG                         ACTGAAGCAGACAAGAAACTCCTTGGTGAAAAAGGTGGCATTCCCATTGGT
genomic: AAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAGgtaaaataag ... ggttcaccagACTGAAGCAGACAAGAAACTCCTTGGTGAAAAAGGTGGCATTCCCATTGGT
EST: gi|58606969|gb|CK035002.1|CK035002
EST:     AAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAG                         ACTGAAGCAGACAAGAAACTCCTTGGTGAAAAAGGTGGCATTCCCATTGGT
genomic: AAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAGgtaaaataag ... ggttcaccagACTGAAGCAGACAAGAAACTCCTTGGTGAAAAAGGTGGCATTCCCATTGGT
EST: gi|33681770|gb|CF310009.1|CF310009
EST:     AAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAG                         ACTGAAGCAGACAAGAAACTCCTTGGTGAAAAAAGTGGCATTCCCATTGGT
genomic: AAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAGgtaaaataag ... ggttcaccagACTGAAGCAGACAAGAAACTCCTTGGTGAAAAAGGTGGCATTCCCATTGGT
EST: gi|86417728|gb|CI031937.1|CI031937
EST:     AAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAG                         ACTGAAGCAGACAAGAAACTCCTTGGTGAAAAAGGTGGCATTCCCATTGGT
genomic: AAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAGgtaaaataag ... ggttcaccagACTGAAGCAGACAAGAAACTCCTTGGTGAAAAAGGTGGCATTCCCATTGGT
EST: gi|29612859|gb|CB617872.1|CB617872
EST:     AAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAG                         ACTGAAGCAGACAAGAAACTCCTTGGTGAAAAAGGTGGCATTCCCATTGGT
genomic: AAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAGgtaaaataag ... ggttcaccagACTGAAGCAGACAAGAAACTCCTTGGTGAAAAAGGTGGCATTCCCATTGGT
EST: gi|38472262|gb|CF956393.1|CF956393
EST:     AAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAG                         ACTGAAGCAGACAAGAAACTCCTTGGTGAAAAAGGTGGCATTCCCATTGGT
genomic: AAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAGgtaaaataag ... ggttcaccagACTGAAGCAGACAAGAAACTCCTTGGTGAAAAAGGTGGCATTCCCATTGGT
EST: gi|29671442|gb|CB667717.1|CB667717
EST:     AAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAG                         ACTGAAGCAGACAAGAAACTCCTTGGTGAAAAAGGTGGCATTCCCATTGGT
genomic: AAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAGgtaaaataag ... ggttcaccagACTGAAGCAGACAAGAAACTCCTTGGTGAAAAAGGTGGCATTCCCATTGGT
EST: gi|86599888|gb|CI256050.1|CI256050
EST:     AAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAG                         ACTGAAGCAGACAAGAAACTCCTTGGTGAAAAAGGTGGCATTCCCATTGGT
genomic: AAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAGgtaaaataag ... ggttcaccagACTGAAGCAGACAAGAAACTCCTTGGTGAAAAAGGTGGCATTCCCATTGGT
EST: gi|29660395|gb|CB656670.1|CB656670
EST:     AAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAG                         ACTGAAGCAGACAAGAAACTCCTTGGTGAAAAAGGTGGCATTCCCATTGGT
genomic: AAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAGgtaaaataag ... ggttcaccagACTGAAGCAGACAAGAAACTCCTTGGTGAAAAAGGTGGCATTCCCATTGGT
EST: gi|2797145|gb|AA750439.1|AA750439
EST:     AAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAG                         ACTGAAGCAGACAAGAAACTCCTTGGTGAAAAAGGTGGCATTCCCATTGGT
genomic: AAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAGgtaaaataag ... ggttcaccagACTGAAGCAGACAAGAAACTCCTTGGTGAAAAAGGTGGCATTCCCATTGGT
EST: gi|29620180|gb|CB625192.1|CB625192
EST:     AAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAG                         ACTGAAGCAGACAAGAAACTCCTTGGTGAAAAAGGTGGCATTCCCATTGGT
genomic: AAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAGgtaaaataag ... ggttcaccagACTGAAGCAGACAAGAAACTCCTTGGTGAAAAAGGTGGCATTCCCATTGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTGTAAGATACACCATTCAGTAGTTGGACTCCGGTCCTGCATTTCTGAAGGCGCAATAATAGAGGACTCATTACTCATGGGAGCTGACTACTACGAGgtaaaataagtgcatgtataatatgcctctgtcagagaaaataagagaatttatccctttctttttcctttttctggttcaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA