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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAATTGGTGATGCATTGAGAGCAAAGCTCCATCACCTGGGCAGGCTTGTGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataattgccgccagttcttccactcagagcttcattgttttttgcactcaggataggaaatgaccactatattgtgtttcttcagaatattcag...

Basic information

species Oryza sativa
transcript LOC_Os09g26880.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g26880.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G130440_T01 (Zea mays), 5'ss of exon 3
GCAAATTGGTGATGCATTGAGAGCAAAGCTCCATCACCTGGGCAGGCTTGTGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataattgccgccagttcttccactcagagcttcattgttttttgcactcaggataggaaatgaccactatattgtgtttcttcagaatattcag--
|||||| ||||||||| |||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| || |||||||||||||| ||   |       | |      ||   || | |||||| |        || |  | | | ||  | | |      || || |||     ||||   
GCAAATCGGTGATGCACTGAGAGCAAAGCTCCATCACCTTGGCAGGCTTGTGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATCGGTGAGGTTCAGgtaggaatggatcatagttgcttgattgcttctag-tgcattgtctacaaactgcaagtcatgtattgtgctc-accaaaagtatcatcattgagttcacgc

upper sequence: LOC_Os09g26880.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA09G08150.2 (Glycine max), 5'ss of exon 2
GCAAATTGGTGATGCATTGAGAGCAAAGCTCCATCACCTGGGCAGGCTTGTGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataattgccgccagttcttccactcagagcttcattgttttttgcactcaggataggaaatgaccactatattgtgtttcttcagaatattcag------
 || |||||||| |||||||| || ||  |  |||   |||| ||||| ||||| ||||||||||| |||||||| || ||||| ||||| || |||||||||     ||||  |    ||||| |||      | | |||   |  |  |||  | || |  | |        ||  ||| |      | |||| |         
ACAGATTGGTGAAGCATTGAGGGCCAAATTGGATCCTTTGGGTAGGCTGGTGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtat-cgcaattctcttt-gttctgccatattatgttacat--gtcctgacaccaaagaaatcaga--gtttagattgtgtataaggctataatacttctttgatg

upper sequence: LOC_Os09g26880.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA15G19670.1 (Glycine max), 5'ss of exon 3
GCAAATTGGTGATGCATTGAGAGCAAAGCTCCATCACCTGGGCAGGCTTGTGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataattgccgccagttcttccactcagagcttcattgttttttgcact-caggataggaaatgaccactatattgtgtttctt--cagaatattcag
 || |||||||| |||||||| || ||| |  |||   |||| || || ||||| ||||||||||| |||||||| || ||||| ||||| || |||||||||   | ||||    |  ||||| | |||        |||  | |   |     ||| |||| ||        || ||||||| |  |   | || | |   
ACAGATTGGTGAAGCATTGAGGGCCAAGTTGGATCCTTTGGGTAGACTGGTGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtat-cacaattataact-gttctgcaactttttttgacatattatcaggtttgacagcatagaaatcagagtttagattgtgtataatactataacacttc-

upper sequence: LOC_Os09g26880.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv11s0016g00900.t01 (Vitis vinifera), 5'ss of exon 3
GCAAATTGGTGATGCATTGAGAGCAAAGCTCCATCACCTGGGCAGGCTTGTGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataattgccgccagttcttccactcagagcttcattgttttttgcactcaggataggaaatgaccactatattgtgtttcttcagaatattcag---
||| ||||| || ||  | ||||| ||  |       || ||  |||||||||| || |||||||||||||| ||  ||||||| || |||||||||||||||       |      |       | |   |||| || || |||    |   ||   ||  |  ||   |  | | |  ||  |    | ||   ||||   
GCAGATTGGGGAAGCGCTTAGAGCGAAATTGGGGAGTCTTGGTCGGCTTGTGTCGCTGGAGATGGGGAAAATACTGGCTGAAGGAATCGGAGAGGTTCAGgtataacctttcttttactcacaagcgagctagagattgat-gttgagagtgttcc--atgaggcattgtccttttgtgctgcattaagacaagcctcaggtg

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|29661446|gb|CB657721.1|CB657721
EST:     TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataa ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29639262|gb|CB644271.1|CB644271
EST:     TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataa ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|59930146|gb|AB178688.1|AB178688
EST:     TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataa ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29668613|gb|CB664888.1|CB664888
EST:     TGAGATGGGGAAAATTCTTCNTGAAGGGATTGGAGACCTTCAG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: TGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataa ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|59930127|gb|AB178669.1|AB178669
EST:     TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataa ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29674834|gb|CB671109.1|CB671109
EST:     TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataa ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29677488|gb|CB673763.1|CB673763
EST:     TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataa ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|88730430|gb|CI754043.1|CI754043
EST:     TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAG                         GAAATCATTGA
genomic: TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataa ... tgttttgtagGAAATCATTGA
EST: gi|58689444|gb|CK078131.1|CK078131
EST:     TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataa ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29638871|gb|CB643880.1|CB643880
EST:     TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataa ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29628521|gb|CB633532.1|CB633532
EST:     TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataa ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29656045|gb|CB652320.1|CB652320
EST:     TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataa ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29673252|gb|CB669527.1|CB669527
EST:     TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataa ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29655872|gb|CB652147.1|CB652147
EST:     TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataa ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|33681819|gb|CF310058.1|CF310058
EST:     TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataa ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|33675985|gb|CF304224.1|CF304224
EST:     TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataa ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29668655|gb|CB664930.1|CB664930
EST:     TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataa ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29617477|gb|CB622489.1|CB622489
EST:     TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataa ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|33797257|gb|CF324491.1|CF324491
EST:     TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataa ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29672295|gb|CB668570.1|CB668570
EST:     TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataa ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29656047|gb|CB652322.1|CB652322
EST:     TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataa ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|33683878|gb|CF312117.1|CF312117
EST:     GTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGGAGAGGTTCAG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: GTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATT-GGAGAGGTTCAGgtaggtataa ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|33676797|gb|CF305036.1|CF305036
EST:     TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataa ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|59930152|gb|AB178694.1|AB178694
EST:     TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: TGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataa ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAATTGGTGATGCATTGAGAGCAAAGCTCCATCACCTGGGCAGGCTTGTGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGgtaggtataattgccgccagttcttccactcagagcttcattgttttttgcactcaggataggaaatgaccactatattgtgtttcttcagaatattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgccgcc