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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTTTCACCGAATTGATCCAGGAGATGCAAGTAAAAGGTGTTCAGgttagcttccagggcctgtttctttcctaccatgaaaaattgttagaaacgaaatctatatcaagtgttcttgatatgtccttaggcttttaattattac...

Basic information

species Oryza sativa
transcript LOC_Os02g57630.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57630.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G108739_T01 (Zea mays), 5'ss of exon 3
GTGTTTTCACCGAATTGATCCAGGAGATGCAAGTAAAAGGTGTTCAGgttagcttccagggc-ctgtttctttcctaccatgaaaaa-ttgttagaaacgaaatctatatcaagtgttc--ttgatatgtccttaggcttttaattattac
|||| ||||| ||  |||| ||| | |||||||| |||||||| |||||||||||||||||| ||||| | |||||  | ||||    |||||    |  || | | | |    |  ||  ||||  | |  ||     |  |||      
GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttccagggctctgttgcgttccttgcctgaactgcttgttttgtagcaactgtttttttcctcatccattgaactattattgtatctgcaatgg----
















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|29668373|gb|CB664648.1|CB664648
EST:     GTGTTTTCACCGAATTGATCCAGGAGATGCAAGTAAAAGGTGTTCAG                         GTGGAAGAACTTTACTCTCTTGATGTGGACTCTATTAGTGAACTGCG
genomic: GTGTTTTCACCGAATTGATCCAGGAGATGCAAGTAAAAGGTGTTCAGgttagcttcc ... ctttaaacagGTGGAAGAACTTTACTCTCTTGATGTGGACTCTATTAGTGAACTGCG
EST: gi|58664755|gb|CK053441.1|CK053441
EST:     GTGTTTTCACCGAATTGATCCAGGAGATGCAAGTAAAAGGTGTTCAG                         GTGGAAGAACTTTACTCTCTTGATGTGGACTCTATTAGTGAACTGCG
genomic: GTGTTTTCACCGAATTGATCCAGGAGATGCAAGTAAAAGGTGTTCAGgttagcttcc ... ctttaaacagGTGGAAGAACTTTACTCTCTTGATGTGGACTCTATTAGTGAACTGCG
EST: gi|88363905|gb|CI607215.1|CI607215
EST:     GTGTTTT-ACCGAATTGATCCAGGAGATGCAAGTAAAAGGTGTCCAG                         GTGGAAGAACTTTACTCTCTTGATGTGGACTCTATTAGTGAACTGCG
genomic: GTGTTTTCACCGAATTGATCCAGGAGATGCAAGTAAAAGGTGTTCAGgttagcttcc ... ctttaaacagGTGGAAGAACTTTACTCTCTTGATGTGGACTCTATTAGTGAACTGCG
EST: gi|218484923|gb|FG943842.1|FG943842
EST:     AGATGCAAGTAAAAGGTG-TCAG                         GTGGAAGAACTTTACTCTCTTAGATGTGGACTCTATTAGTGAACTGCG
genomic: AGATGCAAGTAAAAGGTGTTCAGgttagcttcc ... ctttaaacagGTGGAAGAACTTTACTCTCTT-GATGTGGACTCTATTAGTGAACTGCG
EST: gi|29668412|gb|CB664687.1|CB664687
EST:     GTGTTCTCACCGAATTGATCCAGGAGATGCAAGTAAAAGGTGTTCAG                         GTGGAAGAACTTTACTCTCTTGATGTGGACTCTATTAGTGAACTGCG
genomic: GTGTTTTCACCGAATTGATCCAGGAGATGCAAGTAAAAGGTGTTCAGgttagcttcc ... ctttaaacagGTGGAAGAACTTTACTCTCTTGATGTGGACTCTATTAGTGAACTGCG
EST: gi|33797877|gb|CF324798.1|CF324798
EST:     GTGTTTTCACCGAATTGATCCATTATATGCAAGTAAAAGGTGTTCAG                         GTGGAAGAACTTTACTCTCTTGATGTGGACTCTATTAGTGAACTGCG
genomic: GTGTTTTCACCGAATTGATCCAGGAGATGCAAGTAAAAGGTGTTCAGgttagcttcc ... ctttaaacagGTGGAAGAACTTTACTCTCTTGATGTGGACTCTATTAGTGAACTGCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTTTTCACCGAATTGATCCAGGAGATGCAAGTAAAAGGTGTTCAGgttagcttccagggcctgtttctttcctaccatgaaaaattgttagaaacgaaatctatatcaagtgttcttgatatgtccttaggcttttaattattac

- - - - - - - - - -  AGGAGA
- - - - - - - - - - - GGAGAT
- - - - - - - - - - -  GAGATG