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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacgccctcccctcccctcccctgccctgcatatttattttattttctcaacatactactaattactctcttccatttcttgctgctgattcattccgatccatctttctctctacag

Basic information

species Oryza sativa
transcript LOC_Os08g44340.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44340.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G134708_T01 (Zea mays), 5'ss of exon 3
GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacgccctcccctcccctcccctgccctgcatatttattttattttctcaacatactactaattactctcttccatttcttgctgctgattcattccgatccatctttctctctacag
||||| || || ||||| ||||| |||||||||||||||||||| |||||||||| | |  |    |   | | |  |  ||   |   |    |   |  | ||  |  || || |     || | |    || ||||  | ||||| |   ||||| | |  | || || ||||
GTGGCCCCTTATGAGCGCCCTGCACTCAGCAAGGGATACCTCTTCCCTCAGAgtaagccctgaatgcagatgcacagcggtgtgtttttt-cacacgctgctgtccgatgatcctgc-----acgcacg---atctctt--tactgatac---ccgatgc-ttgtcctgtcaacag
















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|88344389|gb|CI677431.1|CI677431
EST:     GCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATNAC-TCTTTCCTCAGA                         ATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGAT-ACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|88721114|gb|CI744413.1|CI744413
EST:     GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|58591551|gb|CF989859.1|CF989859
EST:     GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGGCTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|58670757|gb|CK059443.1|CK059443
EST:     GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGGCTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|33653794|gb|CF276408.1|CF276408
EST:     GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|88354143|gb|CI637709.1|CI637709
EST:     GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|58672555|gb|CK061241.1|CK061241
EST:     GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGGCTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|38568445|gb|CD670660.1|CD670660
EST:     GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|88717903|gb|CI739415.1|CI739415
EST:     GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|58689760|gb|CK078447.1|CK078447
EST:     GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGGCTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|88722467|gb|CI745977.1|CI745977
EST:     GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|88408710|gb|CI686220.1|CI686220
EST:     GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|88363053|gb|CI616210.1|CI616210
EST:     GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|58665042|gb|CK053728.1|CK053728
EST:     GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGGCTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|58594766|gb|CF993074.1|CF993074
EST:     GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGGCTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|88575546|gb|CI669691.1|CI669691
EST:     GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|88408685|gb|CI686192.1|CI686192
EST:     GGCTCCCTACGAGCGTNCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|58599157|gb|CK009685.1|CK009685
EST:     GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGGCTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|88330972|gb|CI638380.1|CI638380
EST:     GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|88586453|gb|CI704154.1|CI704154
EST:     GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|29636698|gb|CB641707.1|CB641707
EST:     GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|58591384|gb|CF989692.1|CF989692
EST:     GGCTCCCTACGAGCGTGCGGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGGCTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|88693460|gb|CI737035.1|CI737035
EST:     GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|117233824|gb|CT847763.1|CT847763
EST:     GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGGCTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|58586261|gb|CF984569.1|CF984569
EST:     GGCTCCCTACGAGGGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGGCTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|88353573|gb|CI632964.1|CI632964
EST:     GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|25797720|gb|CA753681.1|CA753681
EST:     GGCTCCCTACGGGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|66912833|gb|CX099681.1|CX099681
EST:     GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGGCTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA
EST: gi|88744711|gb|CI768071.1|CI768071
EST:     GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA                         ATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGNGGAGAGA
genomic: GGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 52 (upstream exon), 53 (downstream exon)
Score: 101

GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacg ... ctctctacagATGCAGCCAGACTTCCGGGATTCCACACCTGCGTCGGGAGCGGCGGAGAGAGGCTCTTGCCTGAATGGTATTCCGAGAAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGAgtacgtcacgccctcccctcccctcccctgccctgcatatttattttattttctcaacatactactaattactctcttccatttcttgctgctgattcattccgatccatctttctctctacag

- - - - - - - - - - - - -  AGCAAG