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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGTTGTTAAGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcctcgtgtactacttgtgtttagtgtttattactagactttacacttggctgtttgagaaaacaatattattagatttattgactcattaacaaagtttggtttgttctgcattgaagtaagctaactggcatgtattttacag

Basic information

species Oryza sativa
transcript LOC_Os12g42884.3
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g42884.3 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G149751_T02 (Zea mays), 5'ss of exon 9
TGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGTTGTTAAGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcctcg----tgtactacttgtgtttagtgtttattactagactttacacttggctgtttgagaaaaca-atattattagatttattgactcat-taacaaagtttggtttgttctgcattgaagtaagctaactggcatgtattttacag
|||||| || ||||||| |||||||||||||||||||| |||||| |||||| | || |||||||||||||||||||||||||| || ||||||||||||||||||   || |      | || || || |||  ||| ||  |  |||     | |    |  |  | | |  |  || | |||   ||||||| |  || |   | ||                                                
TGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGTCGTTAAGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAGCCTGAGgtcagtgctcttgaatccattctgctggtttttgatgtcta--agaagataaacccccataccatgagtgtagtcgcatttaattgactttattggcctatgttctacag------------------------------------------------
















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|300215517|gb|HO088143.1|HO088143
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGA
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGA
EST: gi|218492493|gb|FG951515.1|FG951515
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|300216253|gb|HO088038.1|HO088038
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|11863315|gb|AU065792.2|AU065792
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTTGTGAGCAG-TTTCTNGTTT-GCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|29637650|gb|CB642659.1|CB642659
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|218478602|gb|FG965538.1|FG965538
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|571921|gb|D41432.1|D41432
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|218483058|gb|FG951439.1|FG951439
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|163927825|gb|EG709417.1|EG709417
EST:     TTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: TTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|88724067|gb|CI749077.1|CI749077
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|571693|gb|D41204.1|D41204
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|88718273|gb|CI741362.1|CI741362
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|570079|gb|D40928.1|D40928
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|88729113|gb|CI752623.1|CI752623
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|41884047|gb|BX928878.1|BX928878
EST:     AGAT-CAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|58688902|gb|CK077589.1|CK077589
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|58678399|gb|CK067086.1|CK067086
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCAGGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|428589|gb|D24741.1|D24741
EST:     CTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: CTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|33800724|gb|CF326232.1|CF326232
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|58661898|gb|CK050578.1|CK050578
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGTTGTTAAGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcctcgtgtactacttgtgtttagtgtttattactagactttacacttggctgtttgagaaaacaatattattagatttattgactcattaacaaagtttggtttgttctgcattgaagtaagctaactggcatgtattttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT