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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACCACAATGTGAACATCAATGTTGCTGTACAAACTGAGGATGGCTTGTTTGTTCCCGTAATAAGGgtatgccatttatttccatggtttttttaaaaaaattattcagcatctttaacttgtattgtttttacag

Basic information

species Oryza sativa
transcript LOC_Os06g01630.6
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g01630.5 (Oryza sativa), 5'ss of exon 16
lower sequence: AT3G13930.1 (Arabidopsis thaliana), 5'ss of exon 16
ATACCACAATGTGAACATCAATGTTGCTGTACAAACTGAGGATGGCTTGTTTGTTCCCGTAATAAGGgtatgccatttatttccatggtt------tttttaaaaaaattattcagcatctttaacttgtattgtttttacag--------------
||   | ||||||||||||||||| ||||||||||| ||  ||||  | |  ||||| ||  | | |||  |  |  | ||   |  |||       ||       |   | |    || | | |        |||  |  |               
ATTTAAAAATGTGAACATCAATGTCGCTGTACAAACAGAAAATGGGCTCTACGTTCCTGTGGTCAAGgttagggagctcttgatacagttattaaccttcctctgcagaaacttgagatttctgaaaaactcagttcatctaattgcttgatttcag

upper sequence: LOC_Os06g01630.5 (Oryza sativa), 5'ss of exon 16
lower sequence: Vv09s0002g01800.t01 (Vitis vinifera), 5'ss of exon 16
ATACCACAATGTGAACATCAATGTTGCTGTACAAACTGAGGATGGCTTGTTTGTTCCCGTAATAAGGgtatgccatttatttccatggtttt--tttaaaaaaattattcagc-atctttaacttgtattgtttttacag------------------------
 |||||||||||||| |||||||||||||| || || ||  ||||  | ||||| ||||| || | |||  |  |||| |     || || |  || ||| |  |||| |    |  |  ||      ||  ||| |||                         
GTACCACAATGTGAATATCAATGTTGCTGTGCAGACGGATAATGGACTCTTTGTCCCCGTCATCAAGgtgggttatttctcagtttgtttataattgaaacagtttatgcttttagttccaataaaagtttatttaacacaaaatcataccatgaaatttgcag

upper sequence: LOC_Os06g01630.5 (Oryza sativa), 5'ss of exon 16
lower sequence: Vv11s0016g01870.t01 (Vitis vinifera), 5'ss of exon 15
ATACCACAATGTGAACATCAATGTTGCTGTACAAACTGAGGATGGCTTGTTTGTTCCCGTAATAAGGgtatgccatttatttccatggtttttttaaa---------aaaattattcagcatcttt---aacttgtattgttt--ttacag
 ||||||||||||||||| ||||||||||| || || ||  ||||  | | ||| || ||  | |||||  |   |   ||||  |  || ||||| |         ||   ||| || ||   ||   ||   ||| |||||  || |||
GTACCACAATGTGAACATAAATGTTGCTGTTCAGACCGACAATGGGCTTTATGTCCCAGTTGTCAGGgtgggttttagttttctttctttgttttagatccatttgtaagtgtatgcaacaagcttgagaaacagtactgtttctttgcag

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|25803971|gb|CA759932.1|CA759932
EST:     GGCTTGTTTGTCCCCGTAATAAGG                         GATGCTGCCAAGAAAGGGCCTAGCCCCTATCGCTGGTGAGGTGAAGCAACT
genomic: GGCTTGTTTGTTCCCGTAATAAGGgtatgccatt ... gtttttacagGATGCTGACAAG-AAGGGCCTAGCCACTATCGCTGATGAGGTGAAGCAACT
EST: gi|38477221|gb|CF961354.1|CF961354
EST:     TCAATGTTGCTGTACAAACTGAGGATGGCTTGTGTGTTCCCGTAATAAGG                         GATGCTGACAAGAAGGGCCTAGCCACTATCGCTGATGAGGTGAAGCAACTG
genomic: TCAATGTTGCTGTACAAACTGAGGATGGCTTGTTTGTTCCCGTAATAAGGgtatgccatt ... gtttttacagGATGCTGACAAGAAGGGCCTAGCCACTATCGCTGATGAGGTGAAGCAACTG
EST: gi|58585940|gb|CF984248.1|CF984248
EST:     TCAATGTTGCTGTACAAACTGAGGATGGCTTGTTTGTGGCCGTAATAAGG                         GATGCTGACAAGAAGGGCCTAGCCACTATCGCTGATGAGGTGAAGCAACTG
genomic: TCAATGTTGCTGTACAAACTGAGGATGGCTTGTTTGTTCCCGTAATAAGGgtatgccatt ... gtttttacagGATGCTGACAAGAAGGGCCTAGCCACTATCGCTGATGAGGTGAAGCAACTG
EST: gi|24468761|gb|CA305710.1|CA305710
EST:     GTACAAACTGAGGATGGCTTGTTTGTTCCCGTAATAAGG                         GATGCTGACAAGAAGGGCCTAGCCACTATCGCTGATGAGGTGAAGCAACTT
genomic: GTACAAACTGAGGATGGCTTGTTTGTTCCCGTAATAAGGgtatgccatt ... gtttttacagGATGCTGACAAGAAGGGCCTAGCCACTATCGCTGATGAGGTGAAGCAAC-T
EST: gi|2442983|gb|C74754.1|C74754
EST:     TCAATGTTGCTGTACAA-CTGAGGATGGCTTGTTTGTNCC-GTAATAAGG                         GATGCTGNCA-GAAGGGCN-AGCCACTATCGCTGAT
genomic: TCAATGTTGCTGTACAAACTGAGGATGGCTTGTTTGTTCCCGTAATAAGGgtatgccatt ... gtttttacagGATGCTGACAAGAAGGGCCTAGCCACTATCGCTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATACCACAATGTGAACATCAATGTTGCTGTACAAACTGAGGATGGCTTGTTTGTTCCCGTAATAAGGgtatgccatttatttccatggtttttttaaaaaaattattcagcatctttaacttgtattgtttttacag

- - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - AGGATG