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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATCTTGGGAATTTGAACTTATCTGGTCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCTgtaagcttttcttgcccatgtggtttgattctttgctagttcttctcaattattttgttttacttctaatatgacatagtttagtgattgaggtagataa...

Basic information

species Oryza sativa
transcript LOC_Os01g59440.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59440.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G121820_T01 (Zea mays), 5'ss of exon 2
GGATCTTGGGAATTTGAACTTATCTGGTCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCTgtaagcttttcttgcccatgtggtttgattctttgctagttcttctcaattattttgttttacttctaatatg---acatagtttagtgattgaggtagataa-
 |||||||| |||||||||||||||||||||||||||||||||||||| ||  |||| ||||| || |||||||||| | ||    ||||  |||||| ||   ||| ||||| ||  |||| |    ||   |  |  |||      |  |  ||| |  |    || |  ||| 
AGATCTTGGTAATTTGAACTTATCTGGTCATCTGGTGCCTGAGCTTGGGAAACTGGAGCATCTTCAGTATCTgtaagttcttac--cccaaatggttt-atgtcttggtagttgttagcaat-aggaagtcggaacttaaattcactcaactgctttgggcaacagggcatgtaat

upper sequence: LOC_Os01g59440.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G815009_T01 (Zea mays), 5'ss of exon 2
GGATCTTGGGAATTTGAACTTATCTGGTCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCTgtaagcttttcttgcccatgtggtttgattctttgctagttcttctcaattattttgttttacttctaatatgacatag-tttagtgattgaggtagataa---
 |||||||| |||||||||||||||||||||||||||||||||||||| || ||||| |||||||| || |||||||   ||||| ||||  |||||| ||   ||| ||||| ||  | | ||    ||   || |   |   |   |   |||  | | ||   |    |    
AGATCTTGGTAATTTGAACTTATCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCTgtaag---ttcttacccaaatggttt-atatcttggtagttgttagccaataggaagtcggaccttacactcgctgtttcttttttaactgctttgtgcatcag
















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|2317317|gb|C22371.1|C22371
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCT                         GGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCTgtaagctttt ... attggaacagGGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAA
EST: gi|29642936|gb|CB647943.1|CB647943
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCT                         GGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCTgtaagctttt ... attggaacagGGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAA
EST: gi|87018477|gb|CI252231.1|CI252231
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCT                         GGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCTgtaagctttt ... attggaacagGGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAA
EST: gi|58597997|gb|CK008525.1|CK008525
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCT                         GGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCTgtaagctttt ... attggaacagGGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAA
EST: gi|58678911|gb|CK067598.1|CK067598
EST:     TCTGGGCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCT                         GGAGCTATACAAGAATAATATTCCAGGAACGATCCCATCGGAACTTGGTAA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCTgtaagctttt ... attggaacagGGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAA
EST: gi|11442641|gb|BF430544.1|BF430544
EST:     CTGAGCTTGGAAAGTTGGATCATCTGCAATATCT                         GGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAA
genomic: CTGAGCTTGGAAAGTTGGATCATCTGCAATATCTgtaagctttt ... attggaacagGGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAA
EST: gi|3548933|gb|AF074734.1|AF074734
EST:     CATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCT                         GGAGCTATACAAGAATAATATTCAAGGNAACGATCCCATCGGAACTTGGTA
genomic: CATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCTgtaagctttt ... attggaacagGGAGCTATACAAGAATAATATTCAAGG-AACGATCCCATCGGAACTTGGTA
EST: gi|58602723|gb|CK013251.1|CK013251
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCT                         GTGGGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCTgtaagctttt ... attggaacagG-GAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTA
EST: gi|218479908|gb|FG956823.1|FG956823
EST:     TCTGGTCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCT                         GGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAA
genomic: TCTGGTCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCTgtaagctttt ... attggaacagGGAGCTATACAAGAATAATATTCAAGGAACGATCCCATCGGAACTTGGTAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATCTTGGGAATTTGAACTTATCTGGTCATCTGGTGCCTGAGCTTGGAAAGTTGGATCATCTGCAATATCTgtaagcttttcttgcccatgtggtttgattctttgctagttcttctcaattattttgttttacttctaatatgacatagtttagtgattgaggtagataa

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