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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGGTTGTCATGGTGTAGGAATGAGGAATATAATGCGACAGATAGGACTAGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaacagttgctccaatttttatgctatatcttgctgcaaaattgtgatttcttaggagcctgctttatgtttgtaatgttctatacttgatcag

Basic information

species Oryza sativa
transcript LOC_Os04g46390.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g46390.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA03G27030.1 (Glycine max), 5'ss of exon 5
TATGGTTGTCATGGTGTAGGAATGAGGAATATAATGCGACAGATAGGACTAGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaacagttgctccaatttttatgctatatcttgctgcaaaattgtgatttcttaggagcctgctttatgtttgtaatgttctatacttgatcag
| ||| ||  | ||    || ||||  | || ||   | ||||| |||||||||||||||||||| |||||   |||||||||||| ||||||||||| ||||    |  |   ||  | |||  ||  | | | | | |||   ||  || || ||   |  |    || ||   || |                   
TTTGGATGCAAAGGCACTGGTATGAAAATTACAAGAAGGCAGATTGGACTAGGCATGATTCAACAAATGCAACATGTCTGTCCTGACTGCAGAGGATCTGgta----atggaaactttattttccatattttgtttggttgctttatgatgtttcctccagctcacctttcattgatgcag------------------

upper sequence: LOC_Os04g46390.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA07G14540.2 (Glycine max), 5'ss of exon 5
TATGGTTGTCATGGTGTAGGAATGAGGAATATAATGCGACAGATAGGACTAGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaacagttgctccaatttttatgctatatcttgctgcaaaattgtgatttcttaggagcctgctttatgtttgtaatgttctatacttgatcag
| ||| || || ||    || ||||  | || ||   | ||||| |||||||||||||||||||| |||||   |||||||||||| ||||||||||| ||||    |  |  |||  | |||  ||  | | | | | |||   ||  || || ||   |  |    || ||   || |                   
TTTGGATGCCAAGGCACTGGTATGAAAATTACAAGAAGGCAGATTGGACTAGGCATGATTCAACAAATGCAACATGTCTGTCCTGACTGCAGAGGATCTGgta----atggaagctttattttccatattttgtttggttgctttatgatgtttcctccagctcacctttcattgatgcag------------------

upper sequence: LOC_Os04g46390.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv15s0021g02090.t01 (Vitis vinifera), 5'ss of exon 5
TATGGTTGTCATGGTGTAGGAATGAGGAATATAATGCGACAGATAGGACTAGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaacagttgctccaatttttatgctatatcttgctgca-aaattgtgatttcttagg------agcctgctttatgtttgtaatgttctatacttgat-cag
||||| || || |||  |||||||| || || ||  |||||||| | || ||||||||||||||| |||||   |||||||| |||||||||||| |||||||   ||| |   |     ||| | |  | | | ||| |    ||||| |  || ||||        |   |  ||||||  |||| | || | |  ||||| |||
TATGGCTGCCAAGGTTCAGGAATGAAGATTACAACCCGACAGATTGCACCAGGCATGATTCAACAAATGCAACATGTCTGTCATGAATGCAGAGGGTCAGgtaattaactgaaacctatttttgtttcatgttttttgtttttcaaattttttttccttaattttttcaaaattttttatgcctgta-tcttatttggttgattcag

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|29637040|gb|CB642049.1|CB642049
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         GTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... acttgatcagGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
EST: gi|29683515|gb|CB679790.1|CB679790
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         GTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... acttgatcagGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
EST: gi|29645124|gb|CB650131.1|CB650131
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         -TGA---CA---G-G---G--ATAAATGCACAAACTGCAGAGCTAGCAAAG
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... acttgatcagGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
EST: gi|14714017|gb|AU197958.1|AU197958
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGA-TGCAGAGGATCAG                         GTGAGATCATAAGTGACAGGGATAAATGCACAA-CTGCAGAGCTAGCAAAG
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... acttgatcagGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
EST: gi|29643291|gb|CB648298.1|CB648298
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         GTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... acttgatcagGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
EST: gi|29614042|gb|CB619055.1|CB619055
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         GTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... acttgatcagGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
EST: gi|29643236|gb|CB648243.1|CB648243
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         GTGAGATCATAAGTGACAGGGATAGATGCACAAACTGCAGAGCTAGCAAAG
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... acttgatcagGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
EST: gi|29643292|gb|CB648299.1|CB648299
EST:     TGCAGAGGATCAG                         GGGAGATCATAAGTGACAGGGATAAATGCACAAACTGCGGAGCTAGCAAAG
genomic: TGCAGAGGATCAGgtatgcaaca ... acttgatcagGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
EST: gi|29678572|gb|CB674847.1|CB674847
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         GTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... acttgatcagGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
EST: gi|29670817|gb|CB667092.1|CB667092
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         GTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... acttgatcagGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
EST: gi|186893157|gb|FG124842.1|FG124842
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         GTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... acttgatcagGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
EST: gi|218494336|gb|FG947221.1|FG947221
EST:     CCTGAAATGCAGAGGATCAG                         GTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
genomic: CCTG-AATGCAGAGGATCAGgtatgcaaca ... acttgatcagGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
EST: gi|29685950|gb|CB682225.1|CB682225
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         GTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... acttgatcagGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
EST: gi|88734728|gb|CI758236.1|CI758236
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         GTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... acttgatcagGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
EST: gi|218503695|gb|FG958495.1|FG958495
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         GTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... acttgatcagGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
EST: gi|33657059|gb|CF279673.1|CF279673
EST:     GGCATGATTCAACATATGCAGAACTGTCTGTCCTGAATGCAGAGGATCAG                         GGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAA
genomic: GGCATGATTCAACATATGCAGA-CTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... acttgatcagG-TGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAA
EST: gi|29678521|gb|CB674796.1|CB674796
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         GTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... acttgatcagGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
EST: gi|29680639|gb|CB676914.1|CB676914
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         GTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... acttgatcagGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
EST: gi|29663531|gb|CB659806.1|CB659806
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         GTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... acttgatcagGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
EST: gi|29639999|gb|CB645008.1|CB645008
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         GTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... acttgatcagGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
EST: gi|38476212|gb|CF960345.1|CF960345
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         GTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAGG
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... acttgatcagGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAA-A
EST: gi|29644137|gb|CB649144.1|CB649144
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         GTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... acttgatcagGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
EST: gi|88762189|gb|CI771745.1|CI771745
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         GTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... acttgatcagGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
EST: gi|29668764|gb|CB665039.1|CB665039
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         GTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... acttgatcagGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
EST: gi|25798325|gb|CA754286.1|CA754286
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         GTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... acttgatcagGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAG

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), 74 (downstream exon)
Score: 287

TATGGTTGTCATGGTGTAGGAATGAGGAATATAATGCGACAGATAGGACTAGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... acttgatcagGTGAGATCATAAGTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAGTTATTCAGGAGAAAAAGGTGCTTGAGGTTCATATTGAGAAGGGAATGCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATGGTTGTCATGGTGTAGGAATGAGGAATATAATGCGACAGATAGGACTAGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaacagttgctccaatttttatgctatatcttgctgcaaaattgtgatttcttaggagcctgctttatgtttgtaatgttctatacttgatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT