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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttcactcggaaccaagtaaatttcctacctccaacataatccactctcgccaccactaacatcagaaactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTGTTTTGCGCAAG

Basic information

species Oryza sativa
transcript LOC_Os08g08200.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g08200.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G042398_T02 (Zea mays), 3'ss of exon 10
gtaattttcactcgg-aaccaagtaaatttcctacctcc-aacataatccactctcgccaccactaacatcagaaactt---tgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTGTTTTGCGCAAG
||||| | | |  |  |||    || ||||  |||| |  ||      |  || |  ||  |   | ||  |     |    |||||||||||||||||| ||||| ||||||||  |||||||||| ||||| |||||  |||| |||
gtaatgtccccctgccaacttcatagattttgtacccctgaatgctgccggcttttccccacctcagcactaatgcgtgaaatgcagGTACACTGTCACAAGATGAGTGGGAGGTTTCCTATCTCTATCTCGCGTTTGTCCTGCGGAAG
















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|88514357|gb|CI441863.1|CI441863
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|88508690|gb|CI436196.1|CI436196
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTTTCACAGGATGAATGGGAGGTAGCCTATCTTTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|86413070|gb|CI067475.1|CI067475
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|88969123|gb|CI099074.1|CI099074
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|86426409|gb|CI071506.1|CI071506
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|88199436|gb|CI199286.1|CI199286
EST:     TGAGCTCATTCGGAGGCTGGGTGCCCTAGGTGGTGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|88542316|gb|CI471638.1|CI471638
EST:     GGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTN
genomic: GGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|86428518|gb|CI075199.1|CI075199
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|86541036|gb|CI181242.1|CI181242
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|88516881|gb|CI444461.1|CI444461
EST:     TCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|88518293|gb|CI445947.1|CI445947
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTTTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|88834373|gb|CI077656.1|CI077656
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
EST: gi|88971622|gb|CI388867.1|CI388867
EST:     TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAA                         GTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG
genomic: TGAGCTCATGCGGAGGCTGGGTGCCCTAGGTGATGGAAGGCAGGACCAAAgtaattttca ... aactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctacctccaacataatccactctcgccaccactaacatcagaaactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTGTTTTGCGCAAG
                                cactaac  putative branch site (score: 1)
           aacataat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattttcactcggaaccaagtaaatttcctacctccaacataatccactctcgccaccactaacatcagaaactttgcagGTACACTGTCACAGGATGAATGGGAGGTAGCCTATCTCTACCTCGCATTTGTTTTGCGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG