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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaaaataattctaggattgtttttttcccctcagctgctggagctaaaatattttattgtaacagaagattttccagtgcttctgtgcttgtgcttgaactaattcagctttatactgatcatcagGTCAGGAAAGTGAAGCCTCATGTGCTTTTAGGACTTTCTGGAGTTGGGGGCATATTTAATGAGGAG

Basic information

species Oryza sativa
transcript LOC_Os10g35960.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g35960.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G085747_T01 (Zea mays), 3'ss of exon 11
gtataaaaataa---ttctaggattgtttttttcccctcagctgctggagctaaaatattttattgtaacagaagattttccagtgcttctgtgcttgtgcttgaactaattcagctttatactgatcatcagGTCAGGAAAGTGAAGCCTCATGTGCTTTTAGGACTTTCTGGAGTTGGGGGCATATTTAATGAGGAG
|||| | ||||    |||||  ||||  |||    |    || ||     |   | |||| |||  ||  | |  |||| ||| |||||||||||||| ||      |||||||| || ||||| ||  |||||||| |||||| ||||| ||||||||||||||||| ||||||||||||||||||||||||||||||
gtatgataatatgatttctacaattgcatttacagctgttgcagcatagacagtactattatataatactatagtattt-ccaatgcttctgtgcttgggc------taattcagtttgatactaattgtcagGTCAAGAAAGTTAAGCCCCATGTGCTTTTAGGACTATCTGGAGTTGGGGGCATATTTAATGAGGAG

upper sequence: LOC_Os10g35960.2 (Oryza sativa), 3'ss of exon 11
lower sequence: PP1S332_33V6.1 (Physcomitrella patens), 3'ss of exon 12
--------------------------------------------------gtataaaaataattctaggattgtttt--------tttcccctcagctgctggagctaaaatattttattgtaacagaagatttt-----ccagt----gcttctgtgcttgtgcttgaactaattca---gctttatactgatcatcagGTCAGGAAAGTGAAGCCTCATGTGCTTTTAGGACTTTCTGGAGTTGGGGGCATATTTAATGAGGAG
                                                   | |   ||||||  |   |||| |||        |||            |  ||| | |  |  |  |  |  ||  |  ||||     ||| |    |  | | |     | |      ||| ||    || ||||        | ||||    |||||||| ||| |||| ||||| ||||||||||||||||| ||| | || |   || ||
gtgagtcaccactacattcactggtcattttttttagtctcttgctgtttttctgctaataatcatgacattggtttgagaagagtttgtgtggcatatataaagccagacaaactagtaatgccaacatttttttgcctccaatttttgtctttatttcaattcccaggataactcttgtgccttatgtc--ctgttagGTTCAAAAAGTGAAACCTGATGTACTTTTGGGACTTTCTGGAGTTGGAGGCCTTTTCACCCAGCAG
















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|58596497|gb|CK007025.1|CK007025
EST:     GTCCTGAAGAGGTGCAAGATCTCCATGAGGGGGCTAGTCTTGTTGAAGTG                         GTCAGGAAAGTGAAGCCTCATGTGCTTTTAGGACTTTCTGGAGTTGGGGGC
genomic: GTCCTGAAGAGGTGCAAGATCTCCATGAGGGGGCTAGTCTTGTTGAAGTGgtataaaaat ... tgatcatcagGTCAGGAAAGTGAAGCCTCATGTGCTTTTAGGACTTTCTGGAGTTGGGGGC
EST: gi|58673493|gb|CK062179.1|CK062179
EST:     GTCCTGAAGAGGTGCAAGATCTCCATGAGGGGGCTAGTCTTGTTGAAGTG                         GTCAGGAAAGTGAAGCCTCATGTGCTTTTAGGACTTTCTGGAGTTGGGGGC
genomic: GTCCTGAAGAGGTGCAAGATCTCCATGAGGGGGCTAGTCTTGTTGAAGTGgtataaaaat ... tgatcatcagGTCAGGAAAGTGAAGCCTCATGTGCTTTTAGGACTTTCTGGAGTTGGGGGC
EST: gi|58601869|gb|CK012397.1|CK012397
EST:     GTCCTGAAGAGGTGCAAGATCTCCATGAGGGGGCTAGTCTTGTTGAAGTG                         GTCAGGAAAGTGAAGCCTCATGTGCTTGTAGGACTTTCTGGAGTTGGGGGC
genomic: GTCCTGAAGAGGTGCAAGATCTCCATGAGGGGGCTAGTCTTGTTGAAGTGgtataaaaat ... tgatcatcagGTCAGGAAAGTGAAGCCTCATGTGCTTTTAGGACTTTCTGGAGTTGGGGGC
EST: gi|29662805|gb|CB659080.1|CB659080
EST:     GTCCTGAAGAGGTGCAAGATCTCCATGAGGGGGCTAGTCTTGTTGAAGTG                         GTCAGGAAAGTGAAGCCTCATGTGCTTTTAGGACTTTCTGGAGTTGGGGGC
genomic: GTCCTGAAGAGGTGCAAGATCTCCATGAGGGGGCTAGTCTTGTTGAAGTGgtataaaaat ... tgatcatcagGTCAGGAAAGTGAAGCCTCATGTGCTTTTAGGACTTTCTGGAGTTGGGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccagtgcttctgtgcttgtgcttgaactaattcagctttatactgatcatcagGTCAGGAAAGTGAAGCCTCATGTGCTTTTAGGACTTTCTGGAGTTGGGGGCATATTTAATGAGGAG
                                          tactgat  putative branch site (score: 2)
                          aactaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataaaaataattctaggattgtttttttcccctcagctgctggagctaaaatattttattgtaacagaagattttccagtgcttctgtgcttgtgcttgaactaattcagctttatactgatcatcagGTCAGGAAAGTGAAGCCTCATGTGCTTTTAGGACTTTCTGGAGTTGGGGGCATATTTAATGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG