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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTTTCATAAAAGAATGCCATCTGAAGCTGTAGATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCAgtaagtattaatgcatatatcaggaaatctcttgtaaatgtttctatgtactcattttacatcttcctttttttctcctcgcaccag

Basic information

species Oryza sativa
transcript LOC_Os01g19150.5
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g19150.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G075992_T01 (Zea mays), 5'ss of exon 6
----------------ATCTTTCATAAAAGAATGCCATCTGAAGCTGTAGATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCAgtaagtattaatgcatatatcaggaaatctcttgtaaatgtttctatgtactcattttacatcttcctttttttctcctcgcaccag
                ||||| || ||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||||  |||||| |||||||   | |  |||       |||||  ||   | |  || ||| |      || ||   ||| |||||     | |||
TCATATTTTTCACCAGATCTTCCACAAAAGAATGCCATCTGAAGCTGTAGATTTTGTGTCTCGGCTTCTGCAGTACTCACCAAACCTCCGGTGCACAGCAgtatgtattaa---acacttca-------tcttgggaaa--tccgttgcacttaacaataatatttagtttcttctctctctaacag
















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|29637278|gb|CB642287.1|CB642287
EST:     TCCGGTGCAGTGCA                         TTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
genomic: TCCGGTGCAGTGCAgtaagtatta ... ctcgcaccagTTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
EST: gi|86503762|gb|CI146395.1|CI146395
EST:     ACTCACCACACCTCCGGTGCAGTGCA                         TTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
genomic: ACTCACCACACCTCCGGTGCAGTGCAgtaagtatta ... ctcgcaccagTTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
EST: gi|29670122|gb|CB666397.1|CB666397
EST:     ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCA                         TTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
genomic: ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCAgtaagtatta ... ctcgcaccagTTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
EST: gi|29628248|gb|CB633259.1|CB633259
EST:     ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCA                         TTGGAGGTGTTAATTCATCCATTCTTCG
genomic: ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCAgtaagtatta ... ctcgcaccagTTGGAGGTGTTAATTCATCCATTCTTCG
EST: gi|29668964|gb|CB665239.1|CB665239
EST:     ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCA                         TTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
genomic: ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCAgtaagtatta ... ctcgcaccagTTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
EST: gi|29668828|gb|CB665103.1|CB665103
EST:     ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCA                         TTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCCAATGCT
genomic: ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCAgtaagtatta ... ctcgcaccagTTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
EST: gi|8856575|gb|AU093893.1|AU093893
EST:     ATCTTGTGTCTCGGCTTCTGCAGTACTCACCA-A-CTCCGGTGCAGTGCA                         TTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
genomic: ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCAgtaagtatta ... ctcgcaccagTTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
EST: gi|29666430|gb|CB662705.1|CB662705
EST:     ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCA                         TTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
genomic: ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCAgtaagtatta ... ctcgcaccagTTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
EST: gi|29619093|gb|CB624105.1|CB624105
EST:     AGTACTCACCACACGTCCGGTGCAGTGCA                         TTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
genomic: AGTACTCACCACACCTCCGGTGCAGTGCAgtaagtatta ... ctcgcaccagTTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
EST: gi|29614478|gb|CB619491.1|CB619491
EST:     ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCA                         TTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
genomic: ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCAgtaagtatta ... ctcgcaccagTTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
EST: gi|29675686|gb|CB671961.1|CB671961
EST:     ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCA                         TTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
genomic: ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCAgtaagtatta ... ctcgcaccagTTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
EST: gi|29624000|gb|CB629011.1|CB629011
EST:     GGTGCAGTGCA                         TTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
genomic: GGTGCAGTGCAgtaagtatta ... ctcgcaccagTTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
EST: gi|29645803|gb|CB650810.1|CB650810
EST:     ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCA                         TTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
genomic: ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCAgtaagtatta ... ctcgcaccagTTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
EST: gi|29676371|gb|CB672646.1|CB672646
EST:     ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCA                         TTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
genomic: ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCAgtaagtatta ... ctcgcaccagTTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
EST: gi|29666992|gb|CB663267.1|CB663267
EST:     ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCA                         TTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
genomic: ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCAgtaagtatta ... ctcgcaccagTTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
EST: gi|29666993|gb|CB663268.1|CB663268
EST:     ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCA                         TTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
genomic: ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCAgtaagtatta ... ctcgcaccagTTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
EST: gi|29666642|gb|CB662917.1|CB662917
EST:     ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCA                         TTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
genomic: ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCAgtaagtatta ... ctcgcaccagTTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
EST: gi|29674068|gb|CB670343.1|CB670343
EST:     ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCA                         TTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
genomic: ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCAgtaagtatta ... ctcgcaccagTTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
EST: gi|29628249|gb|CB633260.1|CB633260
EST:     ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCA                         TTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
genomic: ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCAgtaagtatta ... ctcgcaccagTTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
EST: gi|29623354|gb|CB628365.1|CB628365
EST:     ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCA                         TTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
genomic: ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCAgtaagtatta ... ctcgcaccagTTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
EST: gi|29668829|gb|CB665104.1|CB665104
EST:     ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCA                         TTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
genomic: ATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCAgtaagtatta ... ctcgcaccagTTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
EST: gi|33808952|gb|CF330361.1|CF330361
EST:     CACCTCCGGTGCAGTGCA                         TTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT
genomic: CACCTCCGGTGCAGTGCAgtaagtatta ... ctcgcaccagTTGGAGGTGTTAATTCATCCATTCTTCGATGAACTACGAGATCCAAATGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTTTCATAAAAGAATGCCATCTGAAGCTGTAGATCTTGTGTCTCGGCTTCTGCAGTACTCACCACACCTCCGGTGCAGTGCAgtaagtattaatgcatatatcaggaaatctcttgtaaatgtttctatgtactcattttacatcttcctttttttctcctcgcaccag

- - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG