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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcttatttttttaggacgttggcattttgtctatttttctgtggttgtgtagatcatgactaatgccttccattattgttgctgttgttctatgaccagTTGGCAGCACGGAGGGAACCAACTTCGGATCCTACTAAATATACTGCTGCTGATGTTCGAATT

Basic information

species Oryza sativa
transcript LOC_Os03g62640.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g62640.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G069916_T04 (Zea mays), 3'ss of exon 7
-------------------------------------------------------------------------------------------ctcttatttttttaggacgttggcattttgtctatttttctgtggttgtgtagatcatgactaatgccttccattattgttgctgttgttctatgaccagTTGGCAGCACGGAGGGAACCAACTTCGGATCCTACTAAATATACTGCTGCTGATGTTCGAATT
                                                                                           |    |    |||| ||| |||||| | |   | ||||| | | |||   |  | | ||||| |||      || |||  || | |||  |||| |  || ||||  ||||    || ||| |||| || ||| | |||||||||||||||||||||||||||
gtagtcaattagccataatttcgtattttgatgttcattttaccagtttaggtagtttttttacttctttttaccttgctgtgagctgtctcagacaagggtttatgacattggcagtat---tctttttatcttgtttaatgaaccttgactgatgg-----ataatt--tggttttga-ctattattagCTGGCGCCACGTTCAGAGCCACCTTCAGACCCTTCGAAATATACTGCTGCTGATGTTCGAATT
















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|29665629|gb|CB661904.1|CB661904
EST:     TGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGGCTTTGAAAAAG                         TTGGCAGCACGGAGGGAACCAACTTCGGATCCTACTAAATATACTGCTGCT
genomic: TGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGGCTTTGAAAAAGgtagatatcg ... ctatgaccagTTGGCAGCACGGAGGGAACCAACTTCGGATCCTACTAAATATACTGCTGCT
EST: gi|29623911|gb|CB628922.1|CB628922
EST:     TGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGGCTTTGAAAAAG                         TTGGCAGCACGGAGGGGACCAACTTCGGATCCTACTAAATATACTGCTG
genomic: TGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGGCTTTGAAAAAGgtagatatcg ... ctatgaccagTTGGCAGCACGGAGGGAACCAACTTCGGATCCTACTAAATATACTGCTG
EST: gi|29630312|gb|CB635321.1|CB635321
EST:     TGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGGCTTTGAAAAAG                         TTGGCAGCACGGAGGGAACCNACTTCGGATCCTACTAAATATACTGCTGCT
genomic: TGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGGCTTTGAAAAAGgtagatatcg ... ctatgaccagTTGGCAGCACGGAGGGAACCAACTTCGGATCCTACTAAATATACTGCTGCT
EST: gi|84117476|gb|CD151243.1|CD151243
EST:     TGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGGCTTTGAAAAAG                         TTGGCAGCACGGAGGGAACCAACTTCGGATCCTACTAAATATACTGCTGCT
genomic: TGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGGCTTTGAAAAAGgtagatatcg ... ctatgaccagTTGGCAGCACGGAGGGAACCAACTTCGGATCCTACTAAATATACTGCTGCT
EST: gi|454535|gb|D28304.1|D28304
EST:     TGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGGCTTTGAAAAAG                         TTGGCAGCACGGAGGGAACCAACTTCGGATCCTACTAAATATACTGCTGCT
genomic: TGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGGCTTTGAAAAAGgtagatatcg ... ctatgaccagTTGGCAGCACGGAGGGAACCAACTTCGGATCCTACTAAATATACTGCTGCT
EST: gi|29664073|gb|CB660348.1|CB660348
EST:     TGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGGCTTTGAAAAAG                         TTGGCAGCACGGAGGGAACCAACTTCGGATCCTACTAAATATACTGCTGCT
genomic: TGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGGCTTTGAAAAAGgtagatatcg ... ctatgaccagTTGGCAGCACGGAGGGAACCAACTTCGGATCCTACTAAATATACTGCTGCT
EST: gi|29661288|gb|CB657563.1|CB657563
EST:     TGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGGCTTTGAAAAAG                         TTGGCAGCACGGAGGGAACCAACTTCGGATCCTACTAAATATACTGCTGCT
genomic: TGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGGCTTTGAAAAAGgtagatatcg ... ctatgaccagTTGGCAGCACGGAGGGAACCAACTTCGGATCCTACTAAATATACTGCTGCT
EST: gi|29674744|gb|CB671019.1|CB671019
EST:     TGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGGCTTTGAAAAAG                         TTGGCAGCACGGAGGGAACCAACTTCGGATCCTACTAAATATACTGCTGCT
genomic: TGGTAGATGAAGCACAGAAAGTTATGGAAGAAGCAGAGGCTTTGAAAAAGgtagatatcg ... ctatgaccagTTGGCAGCACGGAGGGAACCAACTTCGGATCCTACTAAATATACTGCTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgtagatcatgactaatgccttccattattgttgctgttgttctatgaccagTTGGCAGCACGGAGGGAACCAACTTCGGATCCTACTAAATATACTGCTGCTGATGTTCGAATT
             gactaat  putative branch site (score: 2)
                                        ttgttct  putative PPT
                           attattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcttatttttttaggacgttggcattttgtctatttttctgtggttgtgtagatcatgactaatgccttccattattgttgctgttgttctatgaccagTTGGCAGCACGGAGGGAACCAACTTCGGATCCTACTAAATATACTGCTGCTGATGTTCGAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT