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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGGTGGCTTTTGAGAAACAATGTGGAGCTGTCCCTTTTGGCTGCTACAGTTAACTGCTTCATTTTTGTTATTGGgtactcttcctatgttaccagaacctgttgtttgattatatgatatatggcctgtttattgcattctaatctctttaaaaaatgttttttttcccatccacag

Basic information

species Oryza sativa
transcript LOC_Os01g25189.4
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g25189.6 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G473533_T06 (Zea mays), 5'ss of exon 10
GGATGGTGGCTTTTGAGAAACAATGTGGAGCTGTCCCTTTTGGCTGCTACAGTTAACTGCTTCATTTTTGTTATTGGgtactcttcctatgttaccagaacctgttg--tttgattatatgatatatggcctgtttattgcattctaatctc----tttaaaaaatgttttttttcccatccacag-----
|| |||||||||||||  ||||| || ||||||||||||||| ||| |  || |||||  | ||| ||| |||||||||||||||  | | |  ||||||  |      | |    || ||||||||  ||||||| ||||||| |||  |     | || |   | |    | |  |||           
GGGTGGTGGCTTTTGAAGAACAAAGTAGAGCTGTCCCTTTTGTCTGGTCTAGCTAACTTATGCATCTTTCTTATTGGgtactcttggtttttctccagaatatcaaagctatagcaatttgatatata-cctgtttcttgcattgtaactttgttgtctacatgctataccatgtggcatgtggtactcag
















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|33689268|gb|CF317507.1|CF317507
EST:     TGCTACAGTTAACTGCTTCATTTTTGTTATTGG                         CTATCTTGTGTTCAGAGGAGCCAATAAACAAAAACATGTCTTCAAGAAGAG
genomic: TGCTACAGTTAACTGCTTCATTTTTGTTATTGGgtactcttcc ... ccatccacagCTATCTTGTGTTCAGAGGAGCCAATAAACAAAAACATGTCTTCAAGAAGAG
EST: gi|58679610|gb|CK068297.1|CK068297
EST:     GAGCTGTCCCTTTTGGCTGCTACAGTTAACTGCTTCATTTTTGTTATTGG                         CTATCTTGTGTTCAGAGGAGCCAATAAACAAAAACATGTCTTCAAGAAGAG
genomic: GAGCTGTCCCTTTTGGCTGCTACAGTTAACTGCTTCATTTTTGTTATTGGgtactcttcc ... ccatccacagCTATCTTGTGTTCAGAGGAGCCAATAAACAAAAACATGTCTTCAAGAAGAG
EST: gi|88840388|gb|CI079842.1|CI079842
EST:     GAGCTGTCCCTTTTGGCTGCTACAGTTAACTGCTTCATTTTTGTTATNGG                         CTATCTTGTGTTCAGAGGAGCCAATAAACAAAAACATGTCTTCAAGAAGAG
genomic: GAGCTGTCCCTTTTGGCTGCTACAGTTAACTGCTTCATTTTTGTTATTGGgtactcttcc ... ccatccacagCTATCTTGTGTTCAGAGGAGCCAATAAACAAAAACATGTCTTCAAGAAGAG
EST: gi|87015902|gb|CI279654.1|CI279654
EST:     GAGCTGTCCCTTTTGGCTGCTACAGTTAACTGCTTCATTTTTGTTATTGG                         CTATCTTGTGTTCAGAGGAGCCAATAAACAAAAACATGTCTTCAAGAAGAG
genomic: GAGCTGTCCCTTTTGGCTGCTACAGTTAACTGCTTCATTTTTGTTATTGGgtactcttcc ... ccatccacagCTATCTTGTGTTCAGAGGAGCCAATAAACAAAAACATGTCTTCAAGAAGAG
EST: gi|88227443|gb|CI226923.1|CI226923
EST:     AACTGCTTCATTTTTGTTATTGG                         CTATCTTGTGTTCAGAGGAGCCAATAAACAAATACATGTCTTCAAGAAGAG
genomic: AACTGCTTCATTTTTGTTATTGGgtactcttcc ... ccatccacagCTATCTTGTGTTCAGAGGAGCCAATAAACAAAAACATGTCTTCAAGAAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGGTGGCTTTTGAGAAACAATGTGGAGCTGTCCCTTTTGGCTGCTACAGTTAACTGCTTCATTTTTGTTATTGGgtactcttcctatgttaccagaacctgttgtttgattatatgatatatggcctgtttattgcattctaatctctttaaaaaatgttttttttcccatccacag

- - - - - - - - - - - - - - - - - - - - - GCTGCT