Skip to another splice site:
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctattattgtactgagattacctttttttgttctgttaattgtgtttttgccaactctatgatttatgtgttgtgttctggttacttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAAGCACAG

Basic information

species Oryza sativa
transcript LOC_Os03g02680.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g02680.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G143213_T02 (Zea mays), 3'ss of exon 6
gttctattattgtactgagattacctttttttgttctgttaattgtgtttttgccaactctatgatttatgtgttgtgttc-tggttacttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAAGCACAG
|||||||  |||| |||   |||  ||| ||   |||  || |||    |||      | | |||||  ||| |||| |   |||| ||| ||||||||| ||||| || || ||||||||| ||||||| ||||| || |  || ||||||| |||| |||||||||||| ||||||||| |||
gttctatgtttgtgctggcgttagatttctta--tcttgtatttgcacattttaggtttatctgattc-tgt-ttgtatctatggtcactgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG

upper sequence: LOC_Os03g02680.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 5
gttctattattgtactgagattacctttttttgttctgttaattgtgtttttgccaactctatgatttatgtgttgtgttctggttacttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAAGCACAG
||||||| ||||| |||  ||||  ||| ||  |||||| | ||| || |||   | || | ||| || ||| ||||||  | |  |||  |||||| ||||||| || || ||||| || |||||||||||||| || |  || ||||||| |||| | |||||||||| ||||||||| |||
gttctatgattgtgctggcattaaatttctt-attctgt-atttgcgtattttagacctgtctgactt-tgt-ttgtgtcattgccactgctgaagGATACTAGGTACACCGAATGAGCAGAGTTGGCCAGGAGTCAGTTGTTTGCCTGACTTCAAGACAGCTTTCCCCAGGTGGCAAGCTCAG
















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|88490176|gb|CI427448.1|CI427448
EST:     TGATGAATTATTTAAGATATTCGG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGGCCAGGAGTTAGCTCATTAC
genomic: TGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTT-GGCCAGGAGTTAGCTCATTAC
EST: gi|86870748|gb|CI323624.1|CI323624
EST:     CCACTCTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|29658305|gb|CB654580.1|CB654580
EST:     CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|86499530|gb|CI142163.1|CI142163
EST:     CACTGTT-CCTCGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CACTGTTCCCT-GGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|86418763|gb|CI053564.1|CI053564
EST:     CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|88906182|gb|CI375254.1|CI375254
EST:     CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCA-                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|88524547|gb|CI450545.1|CI450545
EST:     ATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: ATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|86540731|gb|CI180937.1|CI180937
EST:     CCACTGTTCTCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACTAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|87029121|gb|CI276389.1|CI276389
EST:     CCCTGTTCCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CACTGTT-CCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|89183309|gb|CI045874.1|CI045874
EST:     CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|88220434|gb|CI219994.1|CI219994
EST:     CCACTGTTCTCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|218491447|gb|FG947046.1|FG947046
EST:     CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|88263363|gb|CI367137.1|CI367137
EST:     TGAGATTGATGAATTATTTAAGATATTCA-                         GGTAGTA-GAACTCCAAATGAACAAAGTT-GCCAGGAGTTAGCTCATTACC
genomic: TGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|29688121|gb|CB684396.1|CB684396
EST:     CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|88975335|gb|CI023586.1|CI023586
EST:     CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|86537872|gb|CI178078.1|CI178078
EST:     CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|88218941|gb|CI220353.1|CI220353
EST:     TTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: TTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|88536105|gb|CI465829.1|CI465829
EST:     TAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACCAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: TAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|58664154|gb|CK052840.1|CK052840
EST:     CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|87021528|gb|CI274135.1|CI274135
EST:     CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|86539207|gb|CI179413.1|CI179413
EST:     CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|86501713|gb|CI144346.1|CI144346
EST:     CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|86541116|gb|CI181322.1|CI181322
EST:     GATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: GATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|86429915|gb|CI082338.1|CI082338
EST:     CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|89181446|gb|CI112952.1|CI112952
EST:     CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|88239570|gb|CI240047.1|CI240047
EST:     CCACTGTTCGCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|58604550|gb|CK015078.1|CK015078
EST:     GTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCGAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: GTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|88220311|gb|CI219871.1|CI219871
EST:     GATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: GATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|88834148|gb|CI000512.1|CI000512
EST:     CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAGAATGAACAAAGTTGGCCAGGAGTTAGCTCATTAC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCA-AATGAACAAAGTTGGCCAGGAGTTAGCTCATTAC
EST: gi|88531994|gb|CI461448.1|CI461448
EST:     ATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: ATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
EST: gi|8860073|gb|AU097391.1|AU097391
EST:     CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAG                         GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC
genomic: CCACTGTTCCCTGGTGATTCTGAGATTGATGAATTATTTAAGATATTCAGgttctattat ... acttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtgtttttgccaactctatgatttatgtgttgtgttctggttacttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAAGCACAG
 tgttaat  putative branch site (score: 3)
                                           ttactttt  putative PPT
                   tatgatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctattattgtactgagattacctttttttgttctgttaattgtgtttttgccaactctatgatttatgtgttgtgttctggttacttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAAGCACAG

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