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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAATACGCATTTGGTTCTACTGAGTCAAAGCAGGATCTCGCTGTAGTTCCACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAGgtgtgcttctctttatgctatatatttgtttgcatttcttttagttgctatgatgagtgcacaggaaaaccaattattattcatggtacacag

Basic information

species Oryza sativa
transcript LOC_Os08g41390.2
intron # 8
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 8
lower sequence: GRMZM2G096585_T05 (Zea mays), 5'ss of exon 8
TGAATACGCATTTGGTTCTACTGAGTCAAAGCAGGATCTCGCTGTAGTTCCACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAGgtgtgcttctctttatgctatatatttgtttgcatttcttttagttgctatgatgagtgcacaggaaaaccaattattattcatggtacacag-------------------------------------------------
|||||| ||||||||||| |||||||||||||||||||| ||||| |||||||| |||||||| || || ||||| ||||||||| | ||||| ||||||||| |    |   |    |   | | ||||   |  || || |  || | ||   | |||||| ||     | ||  | |   |  || |                                                    
TGAATATGCATTTGGTTCAACTGAGTCAAAGCAGGATCTTGCTGTTGTTCCACCTAACAGCACAGTAATATATGAAGTTGAGCTTATTTCATTTGTGAAGgtgcggacatgactgatattcgtgtctgttc-taaatcattgacctg-tgtg-caactgcacatgactgata-ttcgtgtctgttctaaatcattgacctgtgtgcaattgcaaaattgatcaatataatcttgtcacacag
















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|58673768|gb|CK062454.1|CK062454
EST:     CACCAAACAGCACTGTGATTTATGAGGTCGAGCTTGTATCATTCGTGAAG                         GATAAAGAATCATGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
genomic: CACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAGgtgtgcttct ... tggtacacagGATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
EST: gi|29615642|gb|CB620654.1|CB620654
EST:     CACCAAACAGCACTGTGATTTATGAGGTCGAGCTTGTATCATTCGTGAAG                         GATAAAGAATCATGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
genomic: CACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAGgtgtgcttct ... tggtacacagGATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
EST: gi|88691015|gb|CI735094.1|CI735094
EST:     CACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAG                         GATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
genomic: CACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAGgtgtgcttct ... tggtacacagGATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
EST: gi|2442986|gb|C74757.1|C74757
EST:     CACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAG                         GATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
genomic: CACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAGgtgtgcttct ... tggtacacagGATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
EST: gi|58695757|gb|CK084444.1|CK084444
EST:     CACCAAACAGCACTGTGATTTATGAGGTCGAGCTTGTATCATTCGTGAAG                         GATAAAGAATCATGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
genomic: CACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAGgtgtgcttct ... tggtacacagGATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
EST: gi|8956727|gb|BE230530.1|BE230530
EST:     CACCAAACAGCACTGTGATTTATGAGGTCGAGCTTGTATCATTCGTGAAG                         GATAAAGAATCATGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
genomic: CACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAGgtgtgcttct ... tggtacacagGATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
EST: gi|29628611|gb|CB633622.1|CB633622
EST:     CACCAAACAGCACTGTGATTTATGAGGTCGAGCTTGTATCATTCGTGAAG                         GATAAAGAATCATGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
genomic: CACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAGgtgtgcttct ... tggtacacagGATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
EST: gi|88688795|gb|CI732371.1|CI732371
EST:     CACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAG                         GATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
genomic: CACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAGgtgtgcttct ... tggtacacagGATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
EST: gi|58604776|gb|CK015304.1|CK015304
EST:     GTGATTTATGAGGTCGAGCTTGTATCATTCGTGAAG                         GATAAAGAATCATGGGACTTGAGCAATACCGAGAAGATTGAGACTGCTGGG
genomic: GTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAGgtgtgcttct ... tggtacacagGATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
EST: gi|58695816|gb|CK084503.1|CK084503
EST:     CACCAAACAGCACTGTGATTTATGAGGTCGAGCTTGTATCATTCGTGAAG                         GATAAAGAATCATGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
genomic: CACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAGgtgtgcttct ... tggtacacagGATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
EST: gi|58686617|gb|CK075304.1|CK075304
EST:     CACCAAACAGCACTGTGATTTATGAGGTCGAGCTTGTATCATTCGTGAAG                         GATAAAGAATCATGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
genomic: CACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAGgtgtgcttct ... tggtacacagGATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
EST: gi|88690866|gb|CI734945.1|CI734945
EST:     CACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAG                         GATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
genomic: CACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAGgtgtgcttct ... tggtacacagGATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
EST: gi|2427305|gb|C71768.1|C71768
EST:     ACCAAACAGCACTGTGATTTATGAGGGTTGAGCTTGTATCATTCGTGAAG                         GTTAAAGGAATCTT
genomic: ACCAAACAGCACTGTGATTTATGAGG-TTGAGCTTGTATCATTCGTGAAGgtgtgcttct ... tggtacacagGATAAAG-AATCTT
EST: gi|218497051|gb|FG946048.1|FG946048
EST:     CACCAAACAGCACTGTGATTTATGAGGTCGAGCTTGTATCATTCGTGAAG                         GATAAAGAATCATGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
genomic: CACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAGgtgtgcttct ... tggtacacagGATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
EST: gi|8956562|gb|BE230477.1|BE230477
EST:     CACCAAACAGCACTGTGATTTATGAGGTCGAGCTTGTATCATTCGTGAAG                         GATAAAGAATCATGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
genomic: CACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAGgtgtgcttct ... tggtacacagGATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
EST: gi|84117299|gb|CD151066.1|CD151066
EST:     CACCAAACAGCACTGTGATTTATGAGGTCGAGCTTGTATCATTCGTGAAG                         GATAAAGAATCATGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
genomic: CACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAGgtgtgcttct ... tggtacacagGATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
EST: gi|29666722|gb|CB662997.1|CB662997
EST:     ACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAG                         GATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
genomic: ACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAGgtgtgcttct ... tggtacacagGATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
EST: gi|88691275|gb|CI733859.1|CI733859
EST:     CACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAG                         GATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
genomic: CACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAGgtgtgcttct ... tggtacacagGATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
EST: gi|29624444|gb|CB629455.1|CB629455
EST:     CACCAAACAGCACTGTGATTTATGAGGTCGAGCTTGTATCATTCGTGAAG                         GATAAAGAATCATGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
genomic: CACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAGgtgtgcttct ... tggtacacagGATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
EST: gi|29675020|gb|CB671295.1|CB671295
EST:     CACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAG                         GATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG
genomic: CACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAGgtgtgcttct ... tggtacacagGATAAAGAATCTTGGGACTTGAACAATACCGAGAAGATTGAGACTGCTGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAATACGCATTTGGTTCTACTGAGTCAAAGCAGGATCTCGCTGTAGTTCCACCAAACAGCACTGTGATTTATGAGGTTGAGCTTGTATCATTCGTGAAGgtgtgcttctctttatgctatatatttgtttgcatttcttttagttgctatgatgagtgcacaggaaaaccaattattattcatggtacacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT