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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttttttatattcttttgtctactttttacctagaactgtcattaccatctgagattatttgacaaccttagttacatctcgcttttcttttttttagCATTGCTTGAAGCTGCCAGGAAAGCTAACTTCCGAGATGTATTAAGTAGAATTTCAGCCGGGTTTGCATCCAACAG

Basic information

species Oryza sativa
transcript LOC_Os04g55180.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g55180.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G117531_T04 (Zea mays), 3'ss of exon 8
-tttttttttatattcttt-tgtctactttttacctagaactgtcattaccatctgagattatttgacaaccttagttacatctcgcttttcttttt--tttagCATTGCTTGAAGCTGCCAGGAAAGCTAACTTCCGAGATGTATTAAGTAGAATTTCAGCCGGGTTTGCATCCAACAG
 |  |  | ||| | |  | | |||| ||||| |      |||| |  |   |||   ||| | |  |||  | | ||    || |  | || ||||  |||||| ||||||||||||||||||||    || |||| ||||||| ||||||||||||| ||||| ||| | |||||| |
atagtaatctatttgcagtgtttctagtttttgc--gattctgtaa--aatttctacaattgtcttgcaatttgacttggtacttgtatgtccttttcttttagCTTTGCTTGAAGCTGCCAGGAAGATCAATTTCCAAGATGTACTAAGTAGAATTTCCGCCGGATTTTCGTCCAACGG
















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|29613342|gb|CB618355.1|CB618355
EST:     GGCTGATGTATACAGATTACCATATCTATCAAGTGGTGCACCTGGATTTG                         CATTGCTTGAAGCTGCCAGGAAAGCTAACTTCCGAGATGTATTAAGTAGAA
genomic: GGCTGATGTATACAGATTACCATATCTATCAAGTGGTGCACCTGGATTTGgttagtctgt ... ttttttttagCATTGCTTGAAGCTGCCAGGAAAGCTAACTTCCGAGATGTATTAAGTAGAA
EST: gi|89188617|gb|CI115866.1|CI115866
EST:     TATCTATCAAGTGGTGCACCTGGATTTG                         CATTGCTTGAAGCTGCCAGGAAAGCTAACTTCCGAGATGTATTAAGTAGAA
genomic: TATCTATCAAGTGGTGCACCTGGATTTGgttagtctgt ... ttttttttagCATTGCTTGAAGCTGCCAGGAAAGCTAACTTCCGAGATGTATTAAGTAGAA
EST: gi|87029188|gb|CI276456.1|CI276456
EST:     GGCTGATGTATACAGATTACCATATCTATCAAGTGGTGCACCTGGATTTG                         CATTGCTTGAAGCTGCCAGGAAAGCTAACTTCCGAGATGTATTAAGTAGAA
genomic: GGCTGATGTATACAGATTACCATATCTATCAAGTGGTGCACCTGGATTTGgttagtctgt ... ttttttttagCATTGCTTGAAGCTGCCAGGAAAGCTAACTTCCGAGATGTATTAAGTAGAA
EST: gi|29678504|gb|CB674779.1|CB674779
EST:     GGCTGATGTATACAGATTACCATATCTATCAAGTGGTGCACCTGGATTTG                         CATTGCTTGAAGCTGCCAGGAAAGCTAACTTCCGAGATGTATTAAGTAGAA
genomic: GGCTGATGTATACAGATTACCATATCTATCAAGTGGTGCACCTGGATTTGgttagtctgt ... ttttttttagCATTGCTTGAAGCTGCCAGGAAAGCTAACTTCCGAGATGTATTAAGTAGAA
EST: gi|29641867|gb|CB646874.1|CB646874
EST:     GGCTGATGTATACAGATTACCATATCTATCAAGTGGTGCACCTGGATTTG                         CATTGCTTGAAGCTGCCAGGAAAGCTAACTTCCGAGATGTATTAAGTAGAA
genomic: GGCTGATGTATACAGATTACCATATCTATCAAGTGGTGCACCTGGATTTGgttagtctgt ... ttttttttagCATTGCTTGAAGCTGCCAGGAAAGCTAACTTCCGAGATGTATTAAGTAGAA
EST: gi|29613236|gb|CB618249.1|CB618249
EST:     GGCTGATGTATACAGATTACCATATCTATCAAGTGGTGCACCTGGATTTG                         CATTGCTTGAAGCTGCCAGGAAAGCTAACTTCCGAGATGTATTAAGTAGAA
genomic: GGCTGATGTATACAGATTACCATATCTATCAAGTGGTGCACCTGGATTTGgttagtctgt ... ttttttttagCATTGCTTGAAGCTGCCAGGAAAGCTAACTTCCGAGATGTATTAAGTAGAA
EST: gi|29614084|gb|CB619097.1|CB619097
EST:     GGCTGATGTATACAGATTACCATATCTATCAAGTGGTGCACCTGGATTTG                         CATTGCTTGAAGCTGCCAGGAAAGCTAACTTCCGAGATGTATTAAGTAGAA
genomic: GGCTGATGTATACAGATTACCATATCTATCAAGTGGTGCACCTGGATTTGgttagtctgt ... ttttttttagCATTGCTTGAAGCTGCCAGGAAAGCTAACTTCCGAGATGTATTAAGTAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccatctgagattatttgacaaccttagttacatctcgcttttcttttttttagCATTGCTTGAAGCTGCCAGGAAAGCTAACTTCCGAGATGTATTAAGTAGAATTTCAGCCGGGTTTGCATCCAACAG
              atttgac  putative branch site (score: 4)
                             ttacatctcgcttttc  putative PPT
                                        ttttctttttttta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttttttatattcttttgtctactttttacctagaactgtcattaccatctgagattatttgacaaccttagttacatctcgcttttcttttttttagCATTGCTTGAAGCTGCCAGGAAAGCTAACTTCCGAGATGTATTAAGTAGAATTTCAGCCGGGTTTGCATCCAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG