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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttgttctgctgataccaaaacctgtgctttgtttggtgttaatgttgaagcattcttcacactggtctgatgatctctgatcgacctgagaaatgcaaattatcctatttgtattctagccacttctattgctgtcctggacagttaattaatgacaccattgatttgtgaacattgtccccttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g16900.3
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16900.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G120857_T02 (Zea mays), 5'ss of exon 5
TGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttgttctgctgataccaaaacctgtgctttgtttggtgttaatgttgaagcattcttcacactggtctgatgatctctgatcgacctgagaaatgcaaattatcctatttgtattctagccacttctattgctgtcctggacagttaattaatgacaccattgatttgtgaacattgtccccttgcag
|| || ||||||||| |||| |||||||||||||||  ||||||||||||||||||||||||||| ||||||||||||||||      |||  |    ||  | | | ||  |  ||   | ||||||     |||| | | |  | |       | | |||  | |     || |    | |  | | || | |  | |  | |  |                                                            
TGTTGCCGTGAAGTGTCTGAAAAGTACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGCTGTATGACGgtatgtt------ctgtcagttgaaagtatccgtttctctgt-caattgttgataggctcttgatagttatttttcttaatattatcagcttttctgatac----tgttgtttatgaactgcatctgccttcag-----------------------------------------------------------

upper sequence: LOC_Os01g16900.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G404855_T01 (Zea mays), 5'ss of exon 5
TGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttgttctgctgataccaaaacctgtgctttgtttggtgttaat-gttgaagcattcttcacactggtctgatgatctctgatcgacctgagaaatgcaaattatcctatttgtattctagccacttctattgctgtcctggacagttaattaatgacaccattgatttgtgaacattgtccccttgcag
|| || |||||||||||||||| |||||||||||||  |||||||||||||||||||||||||||||||||||||||||||| |          |  |||   ||  |   |||  ||| ||| ||||  |   ||||     ||| |||       ||||   | |   | | ||| |||    | |||  | ||||  | | |   |  ||||| |||          |  |||    | | |||  |||||    |   | | |||
TGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttctctca-----gctgaaa---gtattcatttttctgtcaattgttgttgtgctcttagtgatggcctg------cctgaagcatc-aggcagtgctaata--tcaattatttttcttactattataa--gctgtgctga---------tgctgatgtaactcattc-tgaactgcatttgcctccag
















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|27920689|gb|CB096497.1|CB096497
EST:     GGAGGTCCTCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTCAT
genomic: GGAGGTCATCATTGACAATTGTTGTATGACGgtatgttgtt ... ccccttgcagCTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
EST: gi|55410982|gb|CV723358.1|CV723358
EST:     ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
genomic: ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttgtt ... ccccttgcagCTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
EST: gi|218503212|gb|FG950056.1|FG950056
EST:     ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
genomic: ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttgtt ... ccccttgcagCTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
EST: gi|27554418|gb|CA998318.1|CA998318
EST:     ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
genomic: ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttgtt ... ccccttgcagCTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
EST: gi|41883639|gb|BX928526.1|BX928526
EST:     ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
genomic: ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttgtt ... ccccttgcagCTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
EST: gi|29673427|gb|CB669702.1|CB669702
EST:     ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
genomic: ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttgtt ... ccccttgcagCTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
EST: gi|29616639|gb|CB621651.1|CB621651
EST:     AATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
genomic: AATTGTTGTATGACGgtatgttgtt ... ccccttgcagCTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
EST: gi|29639682|gb|CB644691.1|CB644691
EST:     ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
genomic: ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttgtt ... ccccttgcagCTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
EST: gi|58593071|gb|CF991379.1|CF991379
EST:     ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
genomic: ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttgtt ... ccccttgcagCTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
EST: gi|55410961|gb|CV723337.1|CV723337
EST:     ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
genomic: ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttgtt ... ccccttgcagCTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
EST: gi|29619531|gb|CB624543.1|CB624543
EST:     ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
genomic: ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttgtt ... ccccttgcagCTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
EST: gi|29664535|gb|CB660810.1|CB660810
EST:     ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
genomic: ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttgtt ... ccccttgcagCTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
EST: gi|58669476|gb|CK058162.1|CK058162
EST:     ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATC
genomic: ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttgtt ... ccccttgcagCTTGTGAAGAATC
EST: gi|27554444|gb|CA998344.1|CA998344
EST:     ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
genomic: ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttgtt ... ccccttgcagCTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
EST: gi|29616640|gb|CB621652.1|CB621652
EST:     ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
genomic: ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttgtt ... ccccttgcagCTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
EST: gi|4714232|gb|AU058199.1|AU058199
EST:     ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
genomic: ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttgtt ... ccccttgcagCTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
EST: gi|29671573|gb|CB667848.1|CB667848
EST:     ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
genomic: ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttgtt ... ccccttgcagCTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
EST: gi|86900281|gb|CI296324.1|CI296324
EST:     ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACG                         CTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT
genomic: ACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttgtt ... ccccttgcagCTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACGgtatgttgttctgctgataccaaaacctgtgctttgtttggtgttaatgttgaagcattcttcacactggtctgatgatctctgatcgacctgagaaatgcaaattatcctatttgtattctagccacttctattgctgtcctggacagttaattaatgacaccattgatttgtgaacattgtccccttgcag

- - - - - - - - - - - - - - - - - - - - - GAGGAG