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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTACATCCACTGTTCAGgtagttaactttttactaaaaaaactttgggtaggatcattataagcagtgagcctcatatggaatcattctttttcaagagatttgaaacagaacgatg...

Basic information

species Oryza sativa
transcript LOC_Os01g56670.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56670.3 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G173868_T04 (Zea mays), 5'ss of exon 12
TGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTACATCCACTGTTCAGgtagttaactttttactaaaaaaactttgggtaggatcattataagcagtgagcctcatatggaatcattctttttcaagagatttgaaacagaacgatg---
|||||||||||| ||||| || ||||||||||||||||| || |||||||| ||||| || ||||| ||||| ||||||||||||||||||||||| |||||| | ||  | |||  |  | ||   |    || || |  |||| |    |  || |  |       ||   | |||  |    | | | | ||| ||    
TGTTGATCCTGCTATTCGCACACATGCTGCCTTCTTCAGCGTCTGGAAAAAGTATGGTTTTACCCCTGAAGGTTTTAATCTTGCTACATCCACTGTACAGgtaatgaaactgttaa-actataatagtcaagagtattagcataatctccta-tctaaggtttgccatttgcctctcattatccctaaca-aaaacaattttt

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G173868_T02 (Zea mays), 5'ss of exon 11
-------------------------------------------------TGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTACATCCACTGTTCAGgtagttaacttttta--ctaaaaaaactttgggtaggatcattataagcagtgagcctcatatggaatcattctttttcaagagatttgaaacagaacgatg
                                                 |||||||||||| ||||| || ||||||||||||||||| || |||||||| ||||| || ||||| ||||| ||||||||||||||||||||||| |||||| | ||  | |||  ||| || |     | |||  | ||| ||   |                                                     
ATTCTAGATGATTGCTTATGCTGCTTAGATTTAAGGTTTTAGCTGGAGATGTTGATCCTGCTATTCGCACACATGCTGCCTTCTTCAGCGTCTGGAAAAAgtatggttttacccctgaaggttttaatcttgctacatccactgtacaggtaatgaaactgttaaactataatagtcaagagtattagcataatctccta---------------------------------------------------

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA20G35290.1 (Glycine max), 5'ss of exon 7
TGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTACATCCACTGTTCAGgtagttaactttttactaaaaaaactttgggt--aggatcattataagcagtgagcctcat-atggaatcattctttt-----tcaagag-atttgaaacagaacgatg
| |  ||||||| ||||| ||||||||||||||||| ||||| |||| || |||||| || ||||| ||  | |||||||||||||    || ||||||||||  |||    ||| |   || || | |||   |  ||   | | |  |    || | || || |  |||  ||| |     | ||| | ||||     || |     
TATCAATCCTGCAATTCGCACTCATGCTGCCTTCTTGAGTGTCTGGAGAAGATATGGTTTTACCCCTGAGAGCTTTAATCTTGCTAGTCTCAGTGTTCAGgta--taa----ttagtcctaatacctggggcccaatatagctgttaaaacaatgcttaattatagcttcagccttctatctattaagtgcatttagggtagcata---

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA10G32320.1 (Glycine max), 5'ss of exon 11
TGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTACATCCACTGTTCAGgtagttaactttttactaaaaaaactttggg--taggatcattataagcagtgagcctcat-atggaatcattctttttcaagagatttgaaacagaacgatg---
| |  |||| || ||||| || |||||||||||||| ||||| |||| || |||||| || || || || || |||||||||||||    || ||||||||||  |||    ||| |   ||||| | |||   |  ||   | | |  |    || | || ||    |||  ||| ||      | ||| |    |  |  |   
TATCAATCCCGCAATTCGCACCCATGCTGCCTTCTTGAGTGTCTGGAGAAGATATGGTTTTACTCCTGAGGGCTTTAATCTTGCTAGTCTCAGTGTTCAGgta--taa----ttagtcctaaaacctgggggccaatatagctgttaaaacgatgcttaattataccttcagccttctttctattagttgcattttagggtagggt

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 5'ss of exon 12
lower sequence: AT5G43710.1 (Arabidopsis thaliana), 5'ss of exon 12
TGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTACATCCACTGTTCAGgtagttaactttttactaaaaaaactttgggtaggatcat----tataagcagtgagcctcatatggaatcattctttttcaagagatttgaaacagaacgatg-
 |||||||| || ||  |||||||  |||||||||| || || ||||||  |||||| |||||||| || || |||||||||||||||   | ||| |||||| |  |  ||    | ||    || || |     |  |    ||| |    |||      ||||   | |    ||   |     | |  |        |   
CGTTGATCCAGCAATAAGAACTCACACTGCCTTCTTTAGCGTCTGGAAACGATATGGTTTCACCCCTGAGGGTTTTAATCTTGCTACACTTAGTGTCCAGgtactctatcttaattttaagtgtctctgtgatcacttgtcacttattacgtctgatggcactatgatgttacagcttcatatctattcttcattttccttacag

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv05s0020g04650.t01 (Vitis vinifera), 5'ss of exon 13
TGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTACATCCACTGTTCAGgtagttaactttttactaaaaaaactttgg-gtaggatcattataagcagtgagcctcatatggaatcattcttttt-caagagatttgaaacagaacgatg
  |||| ||||| |||||||| ||| ||||||| || ||||| ||||||| |||||||||||||||||| || ||||||||||| ||||  | ||||||||||  | |  |   | ||    ||   ||  | |  |   || |      | |      | |    |     ||  | |||||    |  || |        
CATTGACCCTGCTATTCGAACGCATACTGCCTTTTTTAGTGTTTGGAAAAGATATGGCTTCACCCCAGAGGGTTTTAATCTTGCCACATTAAGTGTTCAGgtatctgaactgccattatctgaaaactgatgcaatactgttgttgattcttattaatttttacctttgggtttcatgcaagaagcatataatattcaag--

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 5'ss of exon 12
lower sequence: EFJ28925 (Selaginella moellendorffii), 5'ss of exon 12
TGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTACATCCACTGTTCAGgtagttaactttttactaaaaaaactttgggtaggatcattataagcagtgagcctcatatggaatcattctttttcaagagatttgaaacagaacgatg
||| || || || | || ||||||  | || || |||  ||| ||||| || | |||||||||||||||||| ||||||||||| |     |   | |||||  ||   || ||  |       | |    |||  |||  | ||  | ||      |  |||| || | |                             
TGTAGAACCCGCTACTCAAACTCACACAGCATTTTTCTCTGTGTGGAAGAAGTTTGGCTTCACCCCAGAAGGATTTAATCTTGCAAGCATGAGCATACAGgt--ttggtttattgtt-------cctcatttagtttcaacagaaa-aatgctttctaactggattcttgcag---------------------------

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|33796226|gb|CF323979.1|CF323979
EST:     AATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTACATCCACTGTTCAG                         AATGGACAAAGGAGCTACCCGCTGCGGCCTGAATTGATTGAAAGCACATAN
genomic: AATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTACATCCACTGTTCAGgtagttaact ... tatttcacagAATGGACAAAGGAGCTACCCGCTGCGGCCTGAATTGATTGAAAGCACATA-
EST: gi|58601755|gb|CK012283.1|CK012283
EST:     AATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTACATCCACTGTTCAG                         AATGGACAAAGGAGCTACCCGCTGCGGCCTGAATTGATTGAAAGCACATAT
genomic: AATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTACATCCACTGTTCAGgtagttaact ... tatttcacagAATGGACAAAGGAGCTACCCGCTGCGGCCTGAATTGATTGAAAGCACATAT