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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgactacagtgactcataatccccttgtaaattgggtgtgttcaaatttctttgtttctgtgtaaccagcaactttactttaatctttaattgcagAAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTC

Basic information

species Oryza sativa
transcript LOC_Os02g56850.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g56850.4 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G806449_T03 (Zea mays), 3'ss of exon 12
gtaagtgactacagtgactcataatccccttgtaaattgggtgtgttcaaatttctttgtttctgtgtaaccagcaact--ttactttaatc-----tttaattgcagAAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTC
                               |||| | |     ||  | ||  ||||  |||| ||||||  | |  |  ||||  |  ||     || || ||||||||||||||||||||||||||| |  ||| |||||| |||||||||| |||||||||||||||||
-------------------------------gtaagtggttgcagtagagatcgctttagttctttgtaactggtagttccttacccttttcacactttcaactgcagAAAACTGTGTTTGGTGGCCAGCAAGTTAAGCCTGATCACAGAGATGTTCCTTGTGCTGTTTTCTC

upper sequence: LOC_Os02g56850.4 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv05s0051g00870.t01 (Vitis vinifera), 3'ss of exon 13
---------------------------------gtaagtgactacagtgactcataatccccttgtaaattgggtgtgttcaaatttctttgtttctgtgtaaccagcaactttactttaatctttaattgcagAAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTC
                                  | | |||  |  ||     ||  |       |||| |  |   |     |||  ||  | | ||| |||        |||  ||   |       ||||||||||||| |||||||| || || |  |||||||| ||||  ||| ||||||||||||| |||| 
gtaagtgtttcatctggaccatcactaaaaatcatcattgatgatggtt-tcaattgtttttccctaaaatatggaggaaatgattgattcatgt-tgtttaaagcattcatttgtttgggttccc---tgcagAAAACTGTCTTTGGTGGGCAACCTAGCAAACCTGACTACAAGGATATACCTTGTGCTGTGTTCTG
















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:     ACCGGATAAATTTAACACCTGTTGCACTGATGGAGGCTACCTGCTTTTCT                         AAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCT
genomic: ACCGGATAAATTTAACACCTGTTGCACTGATGGAGGCTACCTGCTTTTCTgtaagtgact ... ttaattgcagAAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCT
EST: gi|218503186|gb|FG945930.1|FG945930
EST:     ACCGGATAAATTTAACACCTGTTGCACTGATGGAGGCTACCTGCTTTTCT                         AAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCT
genomic: ACCGGATAAATTTAACACCTGTTGCACTGATGGAGGCTACCTGCTTTTCTgtaagtgact ... ttaattgcagAAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCT
EST: gi|9886227|gb|AU102120.1|AU102120
EST:     CGGATAAATTTAACACCCTGTTGCACTGATGGAGGCNCCCTGCTTTTTCT                         -AAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACCAGAGATGTAC
genomic: CGGATAAATTTAACA-CCTGTTGCACTGATGGAGGCTACCTGC-TTTTCTgtaagtgact ... ttaattgcagAAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTA-CAGAGATGTAC
EST: gi|27578226|gb|CB000921.1|CB000921
EST:     ACCGGATAAATTTAACACCTGTTGCACTGATGGAGGCTACCTGCTTTTCT                         AAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCT
genomic: ACCGGATAAATTTAACACCTGTTGCACTGATGGAGGCTACCTGCTTTTCTgtaagtgact ... ttaattgcagAAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCT
EST: gi|29675049|gb|CB671324.1|CB671324
EST:     ACCGGATAAATTTAACCCCTGTTGCACTGATGGAGGCTACCTGCTTTTCT                         AAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCT
genomic: ACCGGATAAATTTAACACCTGTTGCACTGATGGAGGCTACCTGCTTTTCTgtaagtgact ... ttaattgcagAAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCT
EST: gi|87015137|gb|CI273535.1|CI273535
EST:     ACCGGATAAATTTAACACCTGTTGCACTGATGGAGGCTACCTGCTTTTCT                         AAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCT
genomic: ACCGGATAAATTTAACACCTGTTGCACTGATGGAGGCTACCTGCTTTTCTgtaagtgact ... ttaattgcagAAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCT
EST: gi|33675534|gb|CF303773.1|CF303773
EST:     ACCGGATAAATTTAACACCTGTTGCACTGATGGAGGCTACCTGCTTTTCT                         AAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCT
genomic: ACCGGATAAATTTAACACCTGTTGCACTGATGGAGGCTACCTGCTTTTCTgtaagtgact ... ttaattgcagAAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCT
EST: gi|29625188|gb|CB630199.1|CB630199
EST:     ACCGGATAAATTTAACACCTGTTGCACTGATGGAGGCTACCTGCTTTTCT                         AAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCT
genomic: ACCGGATAAATTTAACACCTGTTGCACTGATGGAGGCTACCTGCTTTTCTgtaagtgact ... ttaattgcagAAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCT
EST: gi|4714976|gb|AU056093.1|AU056093
EST:     CGGATAAATTTTAACACCTGTTTGCACTGATGGAGGCTACCTGCNTTTCT                         AAAACTGTGTTTGGTGGCCAGCCAACTAAACCNGATTACAGANATGTACCT
genomic: CGGATAAATTT-AACACCTGTT-GCACTGATGGAGGCTACCTGCTTTTCTgtaagtgact ... ttaattgcagAAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCT
EST: gi|86594937|gb|CI258191.1|CI258191
EST:     CGGATAAATTTAACACCTGTTGCACTGATGGAGGCTACCTGCTTTTCT                         AAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTATCT
genomic: CGGATAAATTTAACACCTGTTGCACTGATGGAGGCTACCTGCTTTTCTgtaagtgact ... ttaattgcagAAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCT
EST: gi|218481326|gb|FG969724.1|FG969724
EST:     ACCGGATAAATTTAACACCTGTTGCACTGATGGAGGCTACCTGCTTTTCT                         AAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCT
genomic: ACCGGATAAATTTAACACCTGTTGCACTGATGGAGGCTACCTGCTTTTCTgtaagtgact ... ttaattgcagAAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaatttctttgtttctgtgtaaccagcaactttactttaatctttaattgcagAAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTC
                                          tcttt  CT-rich tract
                             aactttactttaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgactacagtgactcataatccccttgtaaattgggtgtgttcaaatttctttgtttctgtgtaaccagcaactttactttaatctttaattgcagAAAACTGTGTTTGGTGGCCAGCCAACTAAACCTGATTACAGAGATGTACCTTGTGCTGTTTTCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT