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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTGTCGGAGCGGGAGGAGTGGGCGGGGCTCCAGCCCGGCCGCAAGTACTTCTTCACGCGCAACCACTCCACCATCGTCGCCTTCGCCATCGGCGCCAAgtgagcctctgctagatccacttttaccttgtcctcacactccttggattgctcgaggctataggattatttaatttgtcatactttttctatttttttt...

Basic information

species Oryza sativa
transcript LOC_Os12g13390.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g13390.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G057942_T02 (Zea mays), 5'ss of exon 3
AGCTGTCGGAGCGGGAGGAGTGGGCGGGGCTCCAGCCCGGCCGCAAGTACTTCTTCACGCGCAACCACTCCACCATCGTCGCCTTCGCCATCGGCGCCAAgtgagcctctgctagatccactt-----ttaccttgtcctcacactccttggattgctcgaggctataggattatttaa-------tttgt-catactttttctatttttttt-----------------------------
|||||||||||||||||||||||||||| ||| ||||||| ||||||||||||||||| |||||||||||||| || ||||| || ||||||||||| |||||||  |  ||||||||| |||        |||| | |||||   ||||  ||| |||    ||| || | | || ||         ||| |||| |  | | | || |||                              
AGCTGTCGGAGCGGGAGGAGTGGGCGGGTCTCGAGCCCGGGCGCAAGTACTTCTTCACACGCAACCACTCCACTATTGTCGCTTTTGCCATCGGCGCAAAgtgag--tgagctagatccgcttgccgtcctccttattctcaccagccttaaattcctcttctctacagcagttttaaaaaaatatcctgtgcatattcctccgagttctttgctatgtggaattgtggattaattggctag

upper sequence: LOC_Os12g13390.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G057942_T01 (Zea mays), 5'ss of exon 3
AGCTGTCGGAGCGGGAGGAGTGGGCGGGGCTCCAGCCCGGCCGCAAGTACTTCTTCACGCGCAACCACTCCACCATCGTCGCCTTCGCCATCGGCGCCAAgtgagcctctgctagatccactt-----ttaccttgtcctcacactccttggattgctcgaggctataggattatttaa-------tttgt-catactttttctatttttttt---------------------------------------------------
|||||||||||||||||||||||||||| ||| ||||||| ||||||||||||||||| |||||||||||||| || ||||| || ||||||||||| |||||||  |  ||||||||| |||        |||| | |||||   ||||  ||| |||    ||| || | | || ||         ||| |||| |  | | | || |||                                                    
AGCTGTCGGAGCGGGAGGAGTGGGCGGGTCTCGAGCCCGGGCGCAAGTACTTCTTCACACGCAACCACTCCACTATTGTCGCTTTTGCCATCGGCGCAAAgtgag--tgagctagatccgcttgccgtcctccttattctcaccagccttaaattcctcttctctacagcagttttaaaaaaatatcctgtgcatattcctccgagttctttgctatgtggaattgtggattaattggctagcttatgtgttaatgtttcacag

upper sequence: LOC_Os12g13390.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA04G36940.1 (Glycine max), 5'ss of exon 2
---AGCTGTCGGAGCGGGAGGAGTGGGCGGGGCTCCAGCCCGGCCGCAAGTACTTCTTCACGCGCAACCACTCCACCATCGTCGCCTTCGCCATCGGCGCCAAgtgagcctctgctagatccacttttaccttgtcctcacactc-cttggattgctcgaggctataggattatttaatttgtcatactttttctatttttttt
   | || |||||| ||||   |||   |   || || || |||  |||||||||||||||  | |||||||||||||||||||||||||||||||||   ||||  || ||   |  || |   | ||  ||     || ||   |  |||    |        ||| |||  | |   ||||    |||||| | || |   
ACCAACTCTCGGAGAGGGAACCGTG---GAAACTTCAACCGGGCAACAAGTACTTCTTCACCAGAAACCACTCCACCATCGTCGCCTTCGCCATCGGCAAAAAgttcgc-tccattctattcctctctatttttcaaccaaacaaacacggaacaattatat---tagtattgataataatgtctctttttttcaacttgtcag

upper sequence: LOC_Os12g13390.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA06G18040.1 (Glycine max), 5'ss of exon 2
---AGCTGTCGGAGCGGGAGGAGTGGGCGGGGCTCCAGCCCGGCCGCAAGTACTTCTTCACGCGCAACCACTCCACCATCGTCGCCTTCGCCATCGGCGCCAAgtgagcctctgctagatccacttttaccttgtcctcacactccttggattgctcgaggctatag-gattatttaatttgtcatactttttctatttttttt
   | || || ||| |||| | |||   ||  || || || |||  |||||||||||||||  | || ||||||||||||||||||||||||||||||   ||||  ||  |        ||||| ||   || |   |||  |  || |     | |        | |  |    |  |   |  |     |    || ||| 
ACCAACTCTCTGAGAGGGAAGTGTG---GGAACTGCAACCGGGCAACAAGTACTTCTTCACCAGAAATCACTCCACCATCGTCGCCTTCGCCATCGGCAAAAAgttcgctccattctatcccactctttttttttagccaccgtaattagggcctttggtttcccggtggatcccgagctatccccagaagcttcggttcttt-

upper sequence: LOC_Os12g13390.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EDP05857 (Chlamydomonas reinhardtii), 5'ss of exon 3
AGCTGTCGGAGCGGGAGGAGTGGGCGGGGCTCCAGCCCGGCCGCAAGTACTTCTTCACGCGCAACCACTCCACCATCGTCGCCTTCGCCATCGGC-----------GCCAAgtgagcctc-----tgctagatccacttttaccttgtcctcacactccttggattgctcgaggctataggattatttaatttgtcatactttttctatttttttt
                         |    | ||||||||| ||   ||||||||||| |||||||  ||||||||||| ||||||||| | |||           |||  ||||||  |      | | | |  |||  |     |   |   |       |      | |  | | | |   |   ||   |   | |           |    
-------------------------GTCTGTTCAGCCCGGCGGCCGCTACTTCTTCACACGCAACCTGTCCACCATCGTGGCCTTCGCCGTGGGCCAGCAGTTCAAGCCGGgtgagcagcggaggcgttgggtggactggtttgggggggttgtaaataccagcccaaactaaacca-aagccaacgaaaacgggagtgcaggcagaggcgt----

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|88364719|gb|CI612534.1|CI612534
EST:     TTCTTCACGCGCAACCACTCCACCATCGTCGCCTTCGCCATCGGCGCCAA                         GTATGCTGCCGGCAATGGGTTTCACATAATCGGTGCGCATACTGACAGTCC
genomic: TTCTTCACGCGCAACCACTCCACCATCGTCGCCTTCGCCATCGGCGCCAAgtgagcctct ... tgtgttgtagGTATGCTGCCGGCAATGGGTTTCACATAATCGGTGCGCATACTGACAGTCC
EST: gi|218488179|gb|FG957837.1|FG957837
EST:     CGCGCAACCACTCCACCATCGTCGCCTTCGCCATCGGCGCCAAA                         GTATGCTGCCGGCAATGGGTTTCACATAATCGGTGCGCATACTGACAGTC
genomic: CGCGCAACCACTCCACCATCGTCGCCTTCGCCATCGGCGCC-AAgtgagcctct ... tgtgttgtagGTATGCTGCCGGCAATGGGTTTCACATAATCGGTGCGCATACTGACAGTC
EST: gi|58600748|gb|CK011276.1|CK011276
EST:     TCTTCAGCGCGCAACCACTCCACCATCGTCGCCTTCGCCATCGGGGCCAA                         GTATGCTGCCGGCAATGGGTTTCACATAATCGGTGCGCATACTGGACAGTC
genomic: TCTTCA-CGCGCAACCACTCCACCATCGTCGCCTTCGCCATCGGCGCCAAgtgagcctct ... tgtgttgtagGTATGCTGCCGGCAATGGGTTTCACATAATCGGTGCGCATACTG-ACAGTC
EST: gi|58677773|gb|CK066460.1|CK066460
EST:     TTCTTCACGCGCAACCACTCCACCATCGTCGCCTTCGCCATCGGCGCCAA                         GTATGCTGCCGGCAATGGGTTTCACATAATCGGTGCGCATACTGACAGTCC
genomic: TTCTTCACGCGCAACCACTCCACCATCGTCGCCTTCGCCATCGGCGCCAAgtgagcctct ... tgtgttgtagGTATGCTGCCGGCAATGGGTTTCACATAATCGGTGCGCATACTGACAGTCC