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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGAGTAAAACAGCCGATGGCATAAAAGTTGTCACTGACAAAGGAGAGGAGATCATTGCAGATGTTGTTCTGTTTGCTACAGgtatttaggatagttcaatgctgaaagttatgttctctgtcactttaataatttctttgaatacatctctcttgatgactgttctgtgctggatgaaaaa...

Basic information

species Oryza sativa
transcript LOC_Os02g56850.4
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g56850.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM5G806449_T01 (Zea mays), 5'ss of exon 9
TTGAGTAAAACAGCCGATGGCATAAAAGTTGTCACTGACAAAGGAGAGGAGATCATTGCAGATGTTGTTCTGTTTGCTACAGgtatttaggatagttcaat-gctgaaagttatgttctctgtcactttaata-atttctttgaatacatctctcttgatgactgt--tctgtgctggatgaaaaa
||||||||||| || || || ||||||||||| ||||| |||||||| ||| |||||||||||||||| || ||||| |||||||||| |||||  ||  | | ||||  ||||   || |||  | | |||| | ||  ||  |        | | ||     ||  ||  ||     |    | 
TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttgggatatctcggtagttgaattttat---ctttgttgcataaatacagttgcttagacgtccagttttggactgtagtcttccttggcaatttggta-
















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|58692171|gb|CK080858.1|CK080858
EST:     CACTGACAAAGGAGAGGAGATCATTGCAGATGTTGTTCTGTTTGCTACAG                         GTCGCACACCAAACTCCCAGAGGTTGAACTTGGAAGCTGCTGGTGTTGAAG
genomic: CACTGACAAAGGAGAGGAGATCATTGCAGATGTTGTTCTGTTTGCTACAGgtatttagga ... ttgcgtgcagGTCGCACACCAAACTCCCAGAGGTTGAACTTGGAAGCTGCTGGTGTTGAAG
EST: gi|218503186|gb|FG945930.1|FG945930
EST:     TGCAGATGTTGTTCTGTTTGCTACAG                         GTCGCACACCAAACTCCCAGAGGTTGAACTTGGAAGCTGCTGGTGTTGAAG
genomic: TGCAGATGTTGTTCTGTTTGCTACAGgtatttagga ... ttgcgtgcagGTCGCACACCAAACTCCCAGAGGTTGAACTTGGAAGCTGCTGGTGTTGAAG
EST: gi|27578226|gb|CB000921.1|CB000921
EST:     CACTGACAAAGGAGAGGAGATCATTGCAGATGTTGTTCTGTTTGCTACAG                         GTCGCACACCAAACTCCCAGAGGTTGAACTTGGAAGCTGCTGGTGTTGAAG
genomic: CACTGACAAAGGAGAGGAGATCATTGCAGATGTTGTTCTGTTTGCTACAGgtatttagga ... ttgcgtgcagGTCGCACACCAAACTCCCAGAGGTTGAACTTGGAAGCTGCTGGTGTTGAAG
EST: gi|58601900|gb|CK012428.1|CK012428
EST:     CACTGACAAAGGAGAGGAGATCATTGCAGATGTCGTGCTGTTTGCTACAG                         GTCGCACACCAAACTCCCAGAGGTTGAACTTGGAAGCTGCTGGTGTTGAAG
genomic: CACTGACAAAGGAGAGGAGATCATTGCAGATGTTGTTCTGTTTGCTACAGgtatttagga ... ttgcgtgcagGTCGCACACCAAACTCCCAGAGGTTGAACTTGGAAGCTGCTGGTGTTGAAG
EST: gi|319908658|gb|HS977786.1|HS977786
EST:     CACTGACAAAGGAGAGGAGATCATTGCAGATGTTGTTCTGTTTGCTACAG                         GTCGCACACCAAACTCCCAGAGGTT
genomic: CACTGACAAAGGAGAGGAGATCATTGCAGATGTTGTTCTGTTTGCTACAGgtatttagga ... ttgcgtgcagGTCGCACACCAAACTCCCAGAGGTT
EST: gi|4714976|gb|AU056093.1|AU056093
EST:     ACTGACAAAGGGAGAGGAGATCATTGCAGATGTTGTTCTGTTTGCTACAG                         GTCGCACACCAAACTCCCAGAGGTTGAACTTGGAAGCTGCTGGTGTTGAAG
genomic: ACTGACAAAGG-AGAGGAGATCATTGCAGATGTTGTTCTGTTTGCTACAGgtatttagga ... ttgcgtgcagGTCGCACACCAAACTCCCAGAGGTTGAACTTGGAAGCTGCTGGTGTTGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGAGTAAAACAGCCGATGGCATAAAAGTTGTCACTGACAAAGGAGAGGAGATCATTGCAGATGTTGTTCTGTTTGCTACAGgtatttaggatagttcaatgctgaaagttatgttctctgtcactttaataatttctttgaatacatctctcttgatgactgttctgtgctggatgaaaaa

- - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG