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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTGATCAGGATGACTGGGTTCACTATGCTAAGATGACCGAAGAAATTGGAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttacttgctaatcatatgacttatatactgcttttttcagtttccttgttggcttcaatattcaaaccaatttgacttgcag

Basic information

species Oryza sativa
transcript LOC_Os03g14450.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14450.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA09G28100.1 (Glycine max), 5'ss of exon 12
ATTTGATCAGGATGACTGGGTTCACTATGCTAAGATGACCGAAGAAATTGGAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttacttgctaatcatatgacttatatactgcttttttcagtttccttgttggcttcaatattcaaaccaatttgacttgcag
||||||||||||||||||||  |||||||| ||  | || |  ||| ||||  | || |||||||||||||| |||||||||||||||||||||||||  ||||| ||  |  ||| | ||  |  | |   ||   || | ||  |   |  |      |||| |||   | | | | |  |  ||
ATTTGATCAGGATGACTGGGAGCACTATGCAAAATTAACAGCTGAAGTTGGCCAGCAGGTGCAGATTGTTGGTGATGATCTCCTTGTCACCAACCCAAAGgtatgcta--tattaa-cttaaaatctgtgacctatgttctgcaaatatgt-atcattgacaatgttctgtctattattaactctag

upper sequence: LOC_Os03g14450.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA16G32960.1 (Glycine max), 5'ss of exon 12
ATTTGATCAGGATGACTGGGTTCACTATGCTAAGATGACCGAAGAAATTGGAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttacttgctaatcatatgacttatatactgcttttttcagtttccttgttggcttcaatattcaaaccaat-ttgact-tgcag
||||||||||||||||||||  |||||||| ||  | || |  ||| ||||  | ||||||||||||||||| ||||||||||| ||||||||||| |  ||||| ||  |  |||   ||   || | ||| || | |    |  |   |  |||    |||| |||   | | | || ||| || ||
ATTTGATCAGGATGACTGGGAGCACTATGCGAAATTAACAGCTGAAGTTGGCCAGCAAGTGCAGATTGTTGGTGATGATCTCCTCGTCACCAACCCGAAGgtatgcta--tattaactttaaatctgagata-tgttctgcaaatatgtatcattga---caatgttctgtctattattaactctgtag

upper sequence: LOC_Os03g14450.2 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv16s0022g01770.t01 (Vitis vinifera), 5'ss of exon 12
ATTTGATCAGGATGACTGGGTTCACTATGCTAAGATGACCGAAGAAATTGGAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttacttgcta--atcatatgacttatatactgcttttttcagtttccttgttggcttcaatattcaaaccaatttgacttgcag--------------------------------
||||||||||||||| ||||  |||||||| ||||||||    |||||||| ||  |||| ||||||||||| |||||||||||||| || || || |  | | | | ||| |||  | || | |    | ||      |       |  ||    |    |||| ||  ||   |       ||                                    
ATTTGATCAGGATGATTGGGAGCACTATGCAAAGATGACATCTGAAATTGGCGAGAAAGTTCAGATTGTTGGTGATGATCTCCTTGTTACAAATCCTAAGgcaagct-cttactaccaccaaaagctaaaaatctaagatgagcttatgaccaccataagctcaaaatgtaagatatgcgtgtttatgacgtcaaatccctttttattgtggctgctacag

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|8527321|gb|AU092136.1|AU092136
EST:     GATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: GATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|287175|gb|D15980.1|D15980
EST:     AGATGATCTCCTTGTCACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: AGATGATCTCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|86525380|gb|CI165586.1|CI165586
EST:     GTTGGAGATGATCTCCTTGTCACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: GTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|88219213|gb|CI220486.1|CI220486
EST:     TTGTCACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: TTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|89184182|gb|CI046747.1|CI046747
EST:     GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|27576854|gb|CA999548.1|CA999548
EST:     GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|86854613|gb|CI258906.1|CI258906
EST:     AGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: AGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|5900716|gb|AU078371.1|AU078371
EST:     GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|25799533|gb|CA755494.1|CA755494
EST:     GAGATCAAGTGCAGATTGTGGGAGATGATCTCCTTGTCACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|29678594|gb|CB674869.1|CB674869
EST:     GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|9864951|gb|AU100701.1|AU100701
EST:     GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|8528267|gb|AU093082.1|AU093082
EST:     GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|88974238|gb|CI019911.1|CI019911
EST:     GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|86535052|gb|CI175258.1|CI175258
EST:     TTGGAGATGATCTCCTTGTCACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: TTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|86430895|gb|CI083318.1|CI083318
EST:     ACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: ACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|87024296|gb|CI257037.1|CI257037
EST:     GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|88841649|gb|CI080905.1|CI080905
EST:     CCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: CCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|89184770|gb|CI048326.1|CI048326
EST:     GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|86251762|gb|CI018954.1|CI018954
EST:     GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCGACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|33810063|gb|CF330919.1|CF330919
EST:     GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|86435388|gb|CI106621.1|CI106621
EST:     TCCTGGTCACCAACCCAACT                         AGGGTAGCCAAGGCAGTTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: TCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|86415101|gb|CI069504.1|CI069504
EST:     ACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: ACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|89197240|gb|CI051970.1|CI051970
EST:     GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|89175061|gb|CI041139.1|CI041139
EST:     GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|218503770|gb|FG954179.1|FG954179
EST:     GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|568037|gb|D38872.1|D38872
EST:     AGATGATCTCCTTGTCACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: AGATGATCTCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|86436429|gb|CI118151.1|CI118151
EST:     CCTTGTCACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: CCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|86594831|gb|CI258085.1|CI258085
EST:     GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACGCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|325493849|gb|JG458373.1|JG458373
EST:     GAGATCACGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACT                         AGGGTAGCCAATGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
EST: gi|2797284|gb|AA750578.1|AA750578
EST:     GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGG
genomic: GAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGG
EST: gi|8528193|gb|AU093008.1|AU093008
EST:     GTTGGAGATGATCTCCTTGTCACCAACCCAACT                         AGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG
genomic: GTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttact ... tgacttgcagAGGGTAGCCAAGGCAATTAAGGACAAGGCCTGCAATGCTCTTCTCCTTAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTGATCAGGATGACTGGGTTCACTATGCTAAGATGACCGAAGAAATTGGAGATCAAGTGCAGATTGTTGGAGATGATCTCCTTGTCACCAACCCAACTgtatgttacttgctaatcatatgacttatatactgcttttttcagtttccttgttggcttcaatattcaaaccaatttgacttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG