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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACGTCTGCATCGTGGGCGTCGCCCGCACGCCCATCGGCGCCCTGCTCGGCTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactccagtgctcctctcagttttcttctcctcttcctctctgaatccgatttggccatgcttccccacaaccag

Basic information

species Oryza sativa
transcript LOC_Os01g02020.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g02020.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM5G860137_T01 (Zea mays), 5'ss of exon 2
GACGTCTGCATCGTGGGCGTCGCCCGCACGCCCATCGGCGCCCTGCTCGGCTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgta---aactccagtgctcctc--tcagttttcttctcctcttcctctctgaatccgatttggccatgcttccccacaaccag----------------------
|| | ||||||||| |||||||||||||||||||||||||| || ||||| || || || ||||||||||||||||||||||||||| |||||||||||||||   | ||   | ||  |||  || | |      |  |   || |          |     | |    |  || ||||  |                      
GATGCCTGCATCGTCGGCGTCGCCCGCACGCCCATCGGCGCACTTCTCGGGTCGCTGTCGTCCCTCCCCGCCACCAAGCTCGGCTCCATCGCCATCCAGGgtacgtacctttcgcgccactcgctcggctccgacgtttttggccgcatcagcaataacccatcaacaaattgccgcaacacgtgtggtccctcccaaatcccag
















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|88343346|gb|CI627306.1|CI627306
EST:     CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGG                         CCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
genomic: CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactcca ... ccacaaccagCCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
EST: gi|88377671|gb|CI605506.1|CI605506
EST:     CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGG                         CCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
genomic: CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactcca ... ccacaaccagCCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
EST: gi|88736278|gb|CI759786.1|CI759786
EST:     CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGG                         CCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
genomic: CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactcca ... ccacaaccagCCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
EST: gi|117240405|gb|CT842781.1|CT842781
EST:     CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGG                         CCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
genomic: CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactcca ... ccacaaccagCCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
EST: gi|88736391|gb|CI759899.1|CI759899
EST:     TCCCTCTCCTCCCTCCCCGCCNAC-AAGCTCGGCTCCGTCGCCATCCAGG                         CCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
genomic: TCCCTCTCCTCCCTCCCCGCC-ACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactcca ... ccacaaccagCCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
EST: gi|88369645|gb|CI582840.1|CI582840
EST:     CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGG                         CCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
genomic: CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactcca ... ccacaaccagCCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
EST: gi|88314350|gb|CI604834.1|CI604834
EST:     CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGG                         CCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
genomic: CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactcca ... ccacaaccagCCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
EST: gi|29641199|gb|CB646206.1|CB646206
EST:     CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGG                         CCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
genomic: CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactcca ... ccacaaccagCCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
EST: gi|58588269|gb|CF986577.1|CF986577
EST:     TCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGGGCGCCATCCAGG                         CCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
genomic: TCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCC-GTCGCCATCCAGGgtaaactcca ... ccacaaccagCCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
EST: gi|88360863|gb|CI625169.1|CI625169
EST:     CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGG                         CCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
genomic: CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactcca ... ccacaaccagCCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
EST: gi|29675316|gb|CB671591.1|CB671591
EST:     CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGG                         CCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
genomic: CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactcca ... ccacaaccagCCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
EST: gi|88735500|gb|CI759008.1|CI759008
EST:     CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGC                         CCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
genomic: CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactcca ... ccacaaccagCCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
EST: gi|33804994|gb|CF328374.1|CF328374
EST:     CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGG                         CCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
genomic: CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactcca ... ccacaaccagCCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
EST: gi|58590983|gb|CF989291.1|CF989291
EST:     CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGG                         CCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
genomic: CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactcca ... ccacaaccagCCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
EST: gi|29634957|gb|CB639966.1|CB639966
EST:     CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGG                         CCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
genomic: CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactcca ... ccacaaccagCCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
EST: gi|88411332|gb|CI564453.1|CI564453
EST:     CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGG                         CCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
genomic: CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactcca ... ccacaaccagCCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
EST: gi|88420882|gb|CI620200.1|CI620200
EST:     CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGG                         CCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
genomic: CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactcca ... ccacaaccagCCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
EST: gi|88371085|gb|CI597562.1|CI597562
EST:     CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGG                         CCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
genomic: CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactcca ... ccacaaccagCCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
EST: gi|88340793|gb|CI636953.1|CI636953
EST:     CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGG                         CCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
genomic: CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactcca ... ccacaaccagCCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
EST: gi|29640750|gb|CB645757.1|CB645757
EST:     CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGG                         CCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
genomic: CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactcca ... ccacaaccagCCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
EST: gi|426273|gb|D22134.1|D22134
EST:     CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGG                         CCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
genomic: CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactcca ... ccacaaccagCCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
EST: gi|88389914|gb|CI626683.1|CI626683
EST:     CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGG                         CCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
genomic: CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactcca ... ccacaaccagCCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
EST: gi|58654730|gb|CK043410.1|CK043410
EST:     GTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGG                         CCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
genomic: CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactcca ... ccacaaccagCCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
EST: gi|88392592|gb|CI625414.1|CI625414
EST:     CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGG                         CCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
genomic: CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactcca ... ccacaaccagCCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
EST: gi|58608101|gb|CK036134.1|CK036134
EST:     CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTGCGGCGCCATCCAGG                         CCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA
genomic: CTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactcca ... ccacaaccagCCGCTCTCAGGAGAGCAAATGTGGAGCCGGCGCTCGTGCAGGAGGTCTTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACGTCTGCATCGTGGGCGTCGCCCGCACGCCCATCGGCGCCCTGCTCGGCTCCCTCTCCTCCCTCCCCGCCACCAAGCTCGGCTCCGTCGCCATCCAGGgtaaactccagtgctcctctcagttttcttctcctcttcctctctgaatccgatttggccatgcttccccacaaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT