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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgctagccttttgtgttcagtatgtgctcctatcttttgtgtctgtgactgcaatgctttaaattctgggctttgtttgtattaacctgttgga...

Basic information

species Oryza sativa
transcript LOC_Os01g44040.3
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g44040.3 (Oryza sativa), 5'ss of exon 10
lower sequence: AT2G34410.3 (Arabidopsis thaliana), 5'ss of exon 13
GTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgctagccttttgtgttc-----agtatgtgctcct-atcttttgtgtctgtgactgcaatgctttaaattctgggctttgtttgtattaacctgttgga
|||||| ||||||||||||||||| |||||||| |||||| | ||||| ||| | ||||  |     | |  |||   |||     | |||||   |   |     | ||||||      | | |  | ||||| |         || | |    |||  |  
GTGGCTCGGCAAGATTACTCTGGAAACCTATATTTCTCAGTTTCACATCTGGTTAAGgtcagcgagaaactgtttcctttctcccaattatgtaggcaagagaccatttgtctgaaggatctaggaatgaaattttaactgcaaattatgt-gttctgcag--

upper sequence: LOC_Os01g44040.3 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv10s0003g02830.t01 (Vitis vinifera), 5'ss of exon 8
GTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgctagccttttgtgttcagtatgtgctcctatcttttgtgtctgtgactgcaatgctttaaattctgggctttgtttgtattaacctgttgga-
 |||||||||||||| ||| ||||||| ||||| |||||  ||||||| ||| | |||||||  |       ||||| ||  || | |  | |  | ||       |   | |  |||  ||  | |  |    |   | ||   |||    |   | 
TTGGCTTGGCAAGATCACTTTGGAGACTTATATTTCTCAATTCCACATCTGGTTGAGgtatgcagacttaaatttgt-ttttgtctctctttcactgttaaacagattgcatttgaattgttgtactggtatattcattatgacataaaaactgaaat
















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|86885457|gb|CI318608.1|CI318608
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCACCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|88995453|gb|CI022776.1|CI022776
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|88513138|gb|CI440644.1|CI440644
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|88502372|gb|CI429878.1|CI429878
EST:     TACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: TACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|88477010|gb|CI414281.1|CI414281
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGGCTTCTCTCTTTCATTCCGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAAT-GGCTTCTCTCTTTCATTCCGG
EST: gi|88560911|gb|CI491614.1|CI491614
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|29659100|gb|CB655375.1|CB655375
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|88322184|gb|CI537767.1|CI537767
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|88846659|gb|CI373427.1|CI373427
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|88515591|gb|CI443245.1|CI443245
EST:     GGCAAGATTACTGTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|86498852|gb|CI141485.1|CI141485
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|89177189|gb|CI043692.1|CI043692
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|88517436|gb|CI445090.1|CI445090
EST:     GGCAAGATTAGTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|86502826|gb|CI145459.1|CI145459
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|88956170|gb|CI092458.1|CI092458
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
EST: gi|88507120|gb|CI434626.1|CI434626
EST:     GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG                         GTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG
genomic: GGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGG

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: 47 (upstream exon), 60 (downstream exon)
Score: 18

GTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgct ... atgcatacagGTCTAACATGCCTAACGGGCAGCCAAAATGGCTTCTCTCTTTCATTCCGGGTTACCCACTGCTCAACTTTATGCTTGCTACAGCAATATATCTTCTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGgtatgatgctagccttttgtgttcagtatgtgctcctatcttttgtgtctgtgactgcaatgctttaaattctgggctttgtttgtattaacctgttgga

- - - - GCAAGA
- - - - - - - - - - TGGAGA