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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttcacaatcaatattacctgtttataactgtgaaaaaaatatatcctatttgcaatttagatgcacctttcaattctttggtttgtaattttcataactgtcctattttatttcagCTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTG

Basic information

species Oryza sativa
transcript LOC_Os02g15550.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g15550.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G120578_T02 (Zea mays), 3'ss of exon 6
------------------gtacgttcacaatcaatattacctgtttataactgtgaa-----aaaaatatatcctatttgcaatttagatgcacctttcaattctttggtttgtaattt------tcataactgtcctatttta--tttcagCTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTG
                  |  |  | |  |  | | |||  |||| ||| |||   |      |   |   |  | |||   || | | |   ||||||| || | ||   | |||||       | | || |||  |  ||    ||||||||||||||||||| || ||||||||||||||||||||||||||||| ||||| |||||||| ||||| || |
gtatgttgataatcccatgagccatgatgacta-tgttatttgttgatatctgccgattgctgaggtttcctgttgttttagatattggtaatcctttcagtt-tgtgagctctaattccatatgtaacaattgtttttcttccactttcagCTGTGGAGTTCTTGAGAAATGCTCCTGAAGGGACATATGATGCTATCATTGTTGATTCATCTGACCCAATAG

upper sequence: LOC_Os02g15550.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G060896_T02 (Zea mays), 3'ss of exon 7
----------------gtacgttcacaatca--atattacctgtttataactgtgaaaaaaatatatcctatttgcaatttag-atgcacctttcaattctttggtttgtaattttc--ataactgtcct--attttatttcagCTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTG
                 |  |   |  || |  | ||||  |  | |||  ||    |      | |    |||  |  || | |   |  |    | |  |||   ||||||||    | || |||  |  || |  ||||||||||||||||||| || ||||||||||||||||||||||||||||| ||||| ||||| ||||| || || |
gtatgtagataattccatgaggctatgatgactacattattttctgatatatgctgtagcttcttgtttcttttagatattggtaaataaatactcagttcttgaactgtaatttcacaagaattgttttttatctactttcagCTGTGGAGTTCTTGAGAAATGCTCCTGAAGGGACATATGATGCTATCATTGTTGATTCGTCAGATCCAATAG

upper sequence: LOC_Os02g15550.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 7
gtacgttcacaatcaatattacct-----gtttataactgtgaaaaaaatatatcctatttgcaatttagatgcacctttc-aattctttggtttgtaattttcataactgtcctattttattt-cagCTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTG
||| |||||   |||| || |  |        | | ||| |     |  ||  |   ||    | || || |||   |||| |||   ||| | |    | || ||  |  |   ||  | ||  ||||||| || ||  | ||  |||  ||||||||||  |||||||| |||||||| ||||||||||| ||  | |
gtatgttcattctcaaaataatttcaaagagatcttactttatcctatgtaactagaataatgacttcagctgcttttttccaatatcttgctgtaccttcttgatttcattttcatgattttggcagCTGTTGAATTTCTTAGACATGTACCTGAAGGGAAGTATGATGCAATTATTGTTGATTCATCAGATCCTGTGG

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|218497061|gb|FG955846.1|FG955846
EST:     TTTATCTGTTGGATTCAAAGATCCTCGTGTTCGGCTTCATGTTGGTGATG                         CTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATT
genomic: TTTATCTGTTGGATTCAAAGATCCTCGTGTTCGGCTTCATGTTGGTGATGgtacgttcac ... tttatttcagCTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATT
EST: gi|58602035|gb|CK012563.1|CK012563
EST:     TTTATCTGTTGGATTCAAAGATCCTCGTGTTCGGCTTCATGTTGGTGATG                         CTGTGGAGTTCTTAAGGAATGCTCCT
genomic: TTTATCTGTTGGATTCAAAGATCCTCGTGTTCGGCTTCATGTTGGTGATGgtacgttcac ... tttatttcagCTGTGGAGTTCTTAAGGAATGCTCCT
EST: gi|58695758|gb|CK084445.1|CK084445
EST:     TTTATCTGTTGGATTCAAAGATCCTCGTGTTCGGCTTCATGTTGGTGATG                         CTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATTG
genomic: TTTATCTGTTGGATTCAAAGATCCTCGTGTTCGGCTTCATGTTGGTGATGgtacgttcac ... tttatttcagCTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATTG
EST: gi|218497953|gb|FG959345.1|FG959345
EST:     TTTATCTGTTGGATTCAAAGATCCTCGTGTTCGGCTTCATGTTGGTGATG                         CTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATTG
genomic: TTTATCTGTTGGATTCAAAGATCCTCGTGTTCGGCTTCATGTTGGTGATGgtacgttcac ... tttatttcagCTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATTG
EST: gi|58695993|gb|CK084680.1|CK084680
EST:     TTTATCTGTTGGATTCAAAGATCCTCGTGTTCGGCTTCATGTTGGTGATG                         CTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATTG
genomic: TTTATCTGTTGGATTCAAAGATCCTCGTGTTCGGCTTCATGTTGGTGATGgtacgttcac ... tttatttcagCTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATTG
EST: gi|33793719|gb|CF322742.1|CF322742
EST:     TTTATCTGTTGGATTCAAAGATCCTCGTGTTCGGCTTCATGTTGGTGATG                         CTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATTG
genomic: TTTATCTGTTGGATTCAAAGATCCTCGTGTTCGGCTTCATGTTGGTGATGgtacgttcac ... tttatttcagCTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATTG
EST: gi|29664250|gb|CB660525.1|CB660525
EST:     TTTATCTGTTGGATTCAAAGATCCTCGTGTTCGGCTTCATGTTGGTGATG                         CTGTGGAGTTCTTAAAGAATGCTCCTGAAGGGACATATGA
genomic: TTTATCTGTTGGATTCAAAGATCCTCGTGTTCGGCTTCATGTTGGTGATGgtacgttcac ... tttatttcagCTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGA
EST: gi|33794317|gb|CF323046.1|CF323046
EST:     TTTATCTGTTGGATTCAAAGATCCTCGTGTTCGGCTTCATGTTGGTGATG                         CTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATTG
genomic: TTTATCTGTTGGATTCAAAGATCCTCGTGTTCGGCTTCATGTTGGTGATGgtacgttcac ... tttatttcagCTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATTG
EST: gi|84117386|gb|CD151153.1|CD151153
EST:     TTTATCTGTTGGATTCAAAGATCCTCGTGTTCGGCTTCATGTTGGTGATG                         CTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATTG
genomic: TTTATCTGTTGGATTCAAAGATCCTCGTGTTCGGCTTCATGTTGGTGATGgtacgttcac ... tttatttcagCTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 73 (downstream exon)
Score: 48

GTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGTGTTCGGCTTCATGTTGGTGATGgtacgttcac ... tttatttcagCTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcacctttcaattctttggtttgtaattttcataactgtcctattttatttcagCTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTG
                              tcataac  putative branch site (score: 48)
                                       tcctattttatttc  putative PPT
                    tttgtaattttcataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttcacaatcaatattacctgtttataactgtgaaaaaaatatatcctatttgcaatttagatgcacctttcaattctttggtttgtaattttcataactgtcctattttatttcagCTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTG

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