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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctattatcgtactgagattacctttttttgttctgttatttgtgtttttgccaactctctgatttatgtggtgtgttctggttacttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG

Basic information

species Oryza sativa
transcript LOC_Os03g01850.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01850.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G143213_T02 (Zea mays), 3'ss of exon 6
gttctattatcgtactgagattacctttttttgttctgttatttgtgtttttgccaactctctgatttatgtggtgtgttctggttacttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG
|||||||  | || |||   |||  ||| ||   |||  ||||||    |||      | |||||||    | || |  | |||| ||| ||||||||| ||||| || || ||||||||| ||||||| ||||| || |  || ||||||| |||| |||||||||||| |||||| || |||
gttctatgtttgtgctggcgttagatttctta--tcttgtatttgcacattttaggtttatctgattctgtttgtat-ctatggtcactgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG

upper sequence: LOC_Os03g01850.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 5
gttctattatcgtactgagattacctttttttgttctgttatttgtgtttttgccaactctctgatttatgtggtgtgttctggttacttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG
||||||| || || |||  ||||  ||| ||  |||||| ||||| || |||   | || ||||| || |||  |||||  | |  |||  |||||| ||||||| || || ||||| || |||||||||||||| || |  || ||||||| |||| | |||||||||| |||||| || |||
gttctatgattgtgctggcattaaatttctt-attctgt-atttgcgtattttagacctgtctgactt-tgtt-tgtgtcattgccactgctgaagGATACTAGGTACACCGAATGAGCAGAGTTGGCCAGGAGTCAGTTGTTTGCCTGACTTCAAGACAGCTTTCCCCAGGTGGCAAGCTCAG
















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|33803869|gb|CF327809.1|CF327809
EST:     GGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: GGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|29662032|gb|CB658307.1|CB658307
EST:     CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|88253212|gb|CI351838.1|CI351838
EST:     CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAAATGAACAAAAGTTGGCCAGGAGTTAGCTCATTA
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCC-AAATGAAC-AAAGTTGGCCAGGAGTTAGCTCATTA
EST: gi|88978284|gb|CI384727.1|CI384727
EST:     ATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: ATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|86885548|gb|CI318699.1|CI318699
EST:     CCACTGTTCCCTGGTGATTCTGACATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|88509819|gb|CI437325.1|CI437325
EST:     AGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: AGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|38482398|gb|CF966438.1|CF966438
EST:     CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|88522726|gb|CI450366.1|CI450366
EST:     GATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: GATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtgtttttgccaactctctgatttatgtggtgtgttctggttacttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG
                  ctctgat  putative branch site (score: 4)
                                           ttactttt  putative PPT
                     tgatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctattatcgtactgagattacctttttttgttctgttatttgtgtttttgccaactctctgatttatgtggtgtgttctggttacttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA