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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAGgttactgctgttctcctggagcttaatagttagcttttaaatttatttcttttggggttttagatacaagtagatgctttgcatgtcctgcag

Basic information

species Oryza sativa
transcript LOC_Os01g60040.2
intron # 46
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 46
lower sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 29
GTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAGgttactgctgttctcctggagcttaatagttagcttttaaatttatttcttttggggttttagatacaagtagatgctttgcatgtcctgcag
||| | || ||||||||||||||||||||||||||||| |||||||| ||||| ||||||||||| |||||||| || |||||||| || ||||||||||  ||||   || | ||||          ||||| || ||    ||||||    || ||| | |  || |||||    || ||   ||| ||
GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgt--ctgcc--tcccttgga----------tagctctttaacaattttctt----ggattttggtttaaatagatatcctgtataatctgtag

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 46
lower sequence: GRMZM2G068755_T01 (Zea mays), 5'ss of exon 47
GTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAGgttactgctgttctcctggagcttaatagttagcttttaaatttatttcttttggggttttagata-caagtagatgctttgcatgtcctgcag
||| | || ||||||||||||||||||||||||||||| |||||||| ||||| ||||||||||| |||||||| ||||||||||| || ||||||||||     |||    ||| ||          ||||| || || |  ||| | |||   ||||  |   | |  |  |    |   | | ||| ||
GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAGgt-----ctgcctcccttga----------tagctcttcaact--tttttcttgtttttttgaacgtccatcatgtatcatctgtattctgtag

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 46
lower sequence: GLYMA10G35140.1 (Glycine max), 5'ss of exon 49
GTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAGgt-tactgctgttctcctggagcttaatagttagcttttaaatttatttcttttggggttttagatacaagtagatgctttgcatgtcctgcag
||| | || || || || ||||| ||||||||||||||||| ||||||||||| ||| | ||  |||||||  | || ||||| || ||| ||||||||| ||   || |  |        ||| |  ||   ||||   |||  || |          ||||  ||  |      ||   ||||  |  ||
GTTCTTCAGAGCACTATCTATGATGTTGACCTTGATCGCATACTTCAAAGCATCCATTTGTACCTGCAAGACTTGGGAATGGAGGAAATTAGGAGAAGgtatataactttgttggatagagttactgcttcttttttttttttccttataaaataaaactagaaccactttttattttctaatgttgtatag

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 46
lower sequence: GLYMA20G32430.1 (Glycine max), 5'ss of exon 48
GTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAGgttactgctgttctcctggagcttaatagttagcttttaaatttatttcttttggggttttagatacaagtagatgct-ttgcatgtcctgcag--
||| | || || || || ||||| ||||||||||||||||| ||||||||||| ||| | ||  |||||||  | || ||||| || ||| |||||||||   |     | |  ||||    | |   || || |    ||| |              | ||  ||  ||  | || |||  |    || |   
GTTCTTCAGAGCACTATCTATGATGTTGACCTTGATCGCATACTTCAAAGCATCCATTTGTACCTGCAAGACTTGGGAATGGAGGAAATTAGGAGAAGgtatatataactttgttgga-tagagttacta-ctctcctttttttaaaaaaaaaaaaactcgaatcacttattttctattgttttatttgtatag

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 46
lower sequence: PP1S66_170V6.1 (Physcomitrella patens), 5'ss of exon 47
GTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGA-----AGgttactgctgttctcctggagcttaatagttagcttttaa-atttatttcttttggggttttagatacaagtagatgctttgcatgtcctgcag-------------------------------------------------------------------------------
||| |       ||  |   |||||| ||||||||||| |||||||||||||||||    |||||  |||| || || |||| ||| || |||| |     || | | | | |  ||| |  | |  ||   ||    | ||| ||   ||| |  | |  | ||| | |  |||   ||| | ||  |  |||                                                                                  
GTTCTTGGTTCAACTTTGCTTGAAGTAGACCTTGATCGAATTCTTCAAAGCATTCACGAGTATTTTGAAGAGCTGGGAATGGCAGAAATACGGAAACGgtaagatgatttccgagctcgttcaccacaacgtttgcaatataatatccgtttttactagattgttaaaaa--agttcttgcgtcgctggctctgagattttagttgactgctattccgttcacggccgtttggttattaacttgatatgtaatgcatgggaatgtctctggatcag

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|58612256|gb|CK039968.1|CK039968
EST:     AGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAG                         GGCAGGAGCCGATGACAAGCCACTTAGAATGGTCAAAACTGTGTTGCATGA
genomic: AGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAGgttactgctg ... tgtcctgcagGGCAGGAGCCGATGACAAGCCACTTAGAATGGTCAAAACTGTGTTGCATGA
EST: gi|58600986|gb|CK011514.1|CK011514
EST:     AGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAG                         GGCAGGAGCCGATGACAAGCCACTTAGAATGGTCAAAACTGTGTTGCATGA
genomic: AGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAGgttactgctg ... tgtcctgcagGGCAGGAGCCGATGACAAGCCACTTAGAATGGTCAAAACTGTGTTGCATGA
EST: gi|58597274|gb|CK007802.1|CK007802
EST:     AGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAG                         GGCAGGAGCCGATGACAAGCCACTTAGAATGGTCAAAACTGTGTTGCATGA
genomic: AGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAGgttactgctg ... tgtcctgcagGGCAGGAGCCGATGACAAGCCACTTAGAATGGTCAAAACTGTGTTGCATGA
EST: gi|88571710|gb|CI663083.1|CI663083
EST:     AGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAG                         GGCAGGAGCCGATGACAAGCCACTTAGAATGGTCAAAACTGTGTTGCATGA
genomic: AGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAGgttactgctg ... tgtcctgcagGGCAGGAGCCGATGACAAGCCACTTAGAATGGTCAAAACTGTGTTGCATGA
EST: gi|163921634|gb|EG714160.1|EG714160
EST:     AGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAG                         GGCAGGAGCCGATGACAAGCCACTTAGAATGGTCAAAACTGTGTTGCATGA
genomic: AGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAGgttactgctg ... tgtcctgcagGGCAGGAGCCGATGACAAGCCACTTAGAATGGTCAAAACTGTGTTGCATGA
EST: gi|29680245|gb|CB676520.1|CB676520
EST:     AGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAG                         GGCAGGAGCCGATGACAAGCCACTTAGAATGGTCAAAACTGTGTTGCATGA
genomic: AGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAGgttactgctg ... tgtcctgcagGGCAGGAGCCGATGACAAGCCACTTAGAATGGTCAAAACTGTGTTGCATGA
EST: gi|58667817|gb|CK056503.1|CK056503
EST:     AGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAG                         GGCAGGAGCCGATGACAAGCCACTTAGAATGGTCAAAACTGTGTTGCATGA
genomic: AGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAGgttactgctg ... tgtcctgcagGGCAGGAGCCGATGACAAGCCACTTAGAATGGTCAAAACTGTGTTGCATGA
EST: gi|58673773|gb|CK062459.1|CK062459
EST:     AGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAG                         GGCAGGAGCCGATGACAAGCCACTTAGAATGGTCAAAACTGTGTTGCATGA
genomic: AGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAGgttactgctg ... tgtcctgcagGGCAGGAGCCGATGACAAGCCACTTAGAATGGTCAAAACTGTGTTGCATGA
EST: gi|58690696|gb|CK079383.1|CK079383
EST:     GAGATTCGGAGAAG                         GGCAGGAGCCGATGACAAGCCACTTAGAATGGTCAAAACTGTGTTGCATGA
genomic: GAGATTCGGAGAAGgttactgctg ... tgtcctgcagGGCAGGAGCCGATGACAAGCCACTTAGAATGGTCAAAACTGTGTTGCATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAGgttactgctgttctcctggagcttaatagttagcttttaaatttatttcttttggggttttagatacaagtagatgctttgcatgtcctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA