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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATAAAGGTTTTGGCTTTGTGCGTTACAGCACCCATGAAGAAGCTGCTCTAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcatcttcaatgtttcagccataaatacatttaatataagagtgttttgggtagatcaatcataaggatggtttgccatgcccatgcttattag...

Basic information

species Oryza sativa
transcript LOC_Os11g40510.2
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g40510.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM5G835213_T02 (Zea mays), 5'ss of exon 11
TGATAAAGGTTTTGGCTTTGTGCGTTACAGCACCCATGAAGAAGCTGCTCTAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcatcttcaatgtttcagccataaatacatttaatataagagtgttttggg---tagatcaatcataaggatggtttg-ccatgcccatgctt-attag
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TGATAAAGGCTTTGGCTTTGTGAGGTACAGCACCCATGAGGAGGCTGCATTGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAGgtatctttggttc--atgtttt---cacatttccttggtaacggagagtagattaggatttaataaaaccctgaaagttcctgggtcaattttacaatagaataa
















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|218488516|gb|FG953157.1|FG953157
EST:     TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|89172073|gb|CI721132.1|CI721132
EST:     GGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: GGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|29641559|gb|CB646566.1|CB646566
EST:     TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|218492528|gb|FG964892.1|FG964892
EST:     TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|88690783|gb|CI734862.1|CI734862
EST:     TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|88675589|gb|CI729702.1|CI729702
EST:     GGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: GGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|88594113|gb|CI713284.1|CI713284
EST:     GGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: GGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|218488001|gb|FG950016.1|FG950016
EST:     TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCACTA
genomic: TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|88689298|gb|CI732874.1|CI732874
EST:     TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|88211493|gb|CI211133.1|CI211133
EST:     TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|88665500|gb|CI715656.1|CI715656
EST:     GGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: GGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|88687915|gb|CI731491.1|CI731491
EST:     GGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: GGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|86259164|gb|CI010465.1|CI010465
EST:     TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|218500340|gb|FG948524.1|FG948524
EST:     TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCACTA
genomic: TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|88219588|gb|CI219148.1|CI219148
EST:     TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTC
genomic: TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|86543833|gb|CI184039.1|CI184039
EST:     TAGCTATTCAGACTGGTAATGGACAACTTATTGTCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|88675129|gb|CI729242.1|CI729242
EST:     GGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: GGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|29640531|gb|CB645540.1|CB645540
EST:     TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|55410007|gb|CV722383.1|CV722383
EST:     TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|88904553|gb|CI711852.1|CI711852
EST:     GGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: GGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|88666971|gb|CI719107.1|CI719107
EST:     GGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: GGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|87019113|gb|CI297314.1|CI297314
EST:     TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|218498744|gb|FG958423.1|FG958423
EST:     TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|88691922|gb|CI735497.1|CI735497
EST:     TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|88676390|gb|CI730503.1|CI730503
EST:     GGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: GGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|38480867|gb|CF964956.1|CF964956
EST:     TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|89173139|gb|CI720969.1|CI720969
EST:     GGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: GGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|86602523|gb|CI264851.1|CI264851
EST:     TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|58587445|gb|CF985753.1|CF985753
EST:     TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCACTA
genomic: TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|218482201|gb|FG960522.1|FG960522
EST:     TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|29642094|gb|CB647101.1|CB647101
EST:     TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: TAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|86254551|gb|CI059278.1|CI059278
EST:     TGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: TGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
EST: gi|89172269|gb|CI721328.1|CI721328
EST:     GGTAATGGACAACTTATTGGCGGTAGGCAGATCAAG                         TGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA
genomic: GGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcat ... ctacttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATAAAGGTTTTGGCTTTGTGCGTTACAGCACCCATGAAGAAGCTGCTCTAGCAATTCAGACTGGTAATGGACAACTTATTGGCGGTAGGCAGATCAAGgtacgttcatcttcaatgtttcagccataaatacatttaatataagagtgttttgggtagatcaatcataaggatggtttgccatgcccatgcttattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA