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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAATTTTGTCACTGTTCCTTTGAGAGATGAATTCCTTGAAAATGCTCGTCTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgtttctgtcaatatactaattttttttttgctgacatgaaaaaaagttcactaagacgaatggtagaaattgtagttatacattatcatttcaa...

Basic information

species Oryza sativa
transcript LOC_Os07g12110.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g12110.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA02G33770.1 (Glycine max), 5'ss of exon 6
GGAATTTTGTCACTGTTCCTTTGAGAGATGAATTCCTTGAAAATGCTCGTCTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgtttctgtcaatatactaattttttttttgctgacatgaaaaaaagttcactaagacgaatggtagaaattgt-agttatacattatcatttcaa-
| || |||   ||||| ||  | || ||||| ||||||||||||||| | || |||||||||||||| |||||  | || || |   | ||||| || ||||| |    | |   ||||||   || || |   |  || | | | ||    |    || |    |   | | |  ||| |   | ||| | |    ||   
GCAACTTTTCAACTGTACCACTAAGGGATGAGTTCCTTGAAAATGCTAGGCTATTTATCTTTGAAACATACTGTAGAATACACCAACGGATTGACATGGGgtatgcaccttt-ctaatataa-gatgttgtagctcttggctttataatttttctgatatgctacaattttgcacctgtgaaaaacacaatgtagcctctgt
















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|88842384|gb|CI081640.1|CI081640
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTTATCGGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|89179941|gb|CI044220.1|CI044220
EST:     TATTCATCGGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: TATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|3763416|gb|AU030168.1|AU030168
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|218502388|gb|FG960205.1|FG960205
EST:     TGTTTTATTTTTGGAACTTACTGCCGTATTCATCAGTGCATTGATATTGG                         CATCGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAA
genomic: TGTTT-ATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCAT-GCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAA
EST: gi|86858778|gb|CI275039.1|CI275039
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|89193464|gb|CI050762.1|CI050762
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|2311303|gb|C27458.1|C27458
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|88964659|gb|CI070005.1|CI070005
EST:     GGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: GGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|58602782|gb|CK013310.1|CK013310
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCAGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|86258563|gb|CI064916.1|CI064916
EST:     GGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: GGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|86434782|gb|CI106015.1|CI106015
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|33653757|gb|CF276371.1|CF276371
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCAGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|29630665|gb|CB635674.1|CB635674
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGG                         CATGCTTTCGCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|89183444|gb|CI046009.1|CI046009
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|88955951|gb|CI092239.1|CI092239
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTTATCGGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|89193445|gb|CI050743.1|CI050743
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|29688864|gb|CB685139.1|CB685139
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|86413625|gb|CI019210.1|CI019210
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|29682306|gb|CB678581.1|CB678581
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|58676370|gb|CK065057.1|CK065057
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCAGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|88903377|gb|CI088915.1|CI088915
EST:     GGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACTTGAGCTACGATGAGGCAGAATTGTGGAT
genomic: GGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|88989818|gb|CI018696.1|CI018696
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|88829372|gb|CI074242.1|CI074242
EST:     GGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: GGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|89178973|gb|CI043478.1|CI043478
EST:     TTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: TTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|29617590|gb|CB622602.1|CB622602
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGG                         CATGCTTTCGCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|89194973|gb|CI051086.1|CI051086
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|29628321|gb|CB633332.1|CB633332
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGG                         CATGCTTTCGCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|33693926|gb|CF322165.1|CF322165
EST:     TATTCATCAGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: TATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|33794202|gb|CF322991.1|CF322991
EST:     CTGTTTATCTTTGAAACTTACTGCCGTATTCATCAGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: CTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
EST: gi|86870378|gb|CI319484.1|CI319484
EST:     TGAAACTTACTGCCGTATTGATCGGTGCATTGATATTGG                         CATGGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGA
genomic: TGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCAT-GCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGA
EST: gi|88955382|gb|CI091474.1|CI091474
EST:     GGTGCATTGATATTGG                         CATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT
genomic: GGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGAT

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: 75 (upstream exon), 75 (downstream exon)
Score: 36

GGAATTTTGTCACTGTTCCTTTGAGAGATGAATTCCTTGAAAATGCTCGTCTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgttt ... caatgaacagCATGCTTTCTCAGAAGCTGAACATGAGCTACGATGAGGCAGAATTGTGGATTATGAACTTAGTTAGGAATTCAAAGCTCGACGCCAAGATTGATTCAGTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAATTTTGTCACTGTTCCTTTGAGAGATGAATTCCTTGAAAATGCTCGTCTGTTTATCTTTGAAACTTACTGCCGTATTCATCGGTGCATTGATATTGGgtaggtgtttctgtcaatatactaattttttttttgctgacatgaaaaaaagttcactaagacgaatggtagaaattgtagttatacattatcatttcaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa