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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagttctaatctgagatattttcttaatactttattatttttatttaatattgtggttaatttgtgctgcttcgcactggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG

Basic information

species Oryza sativa
transcript LOC_Os04g41470.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G006428_T01 (Zea mays), 3'ss of exon 9
---------gtacagttctaatctgagatattttcttaatactttattatttttatttaatattgtggtt----aatttgtgc-tgcttcgcactggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG
          |    ||| ||||||| || |||| |     ||  |  ||||   |    || |    ||    ||||| |   || || |   ||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||||
gtagcaattctgagcttccaatctgatatcttttgtccggcctgcaaaatttgggtcatgtactagattttctgaatttatttatgttttgttgtggctacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCG

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G876621_T02 (Zea mays), 3'ss of exon 9
---------gtacagttctaatctgagatattttcttaatactttattattt---ttatttaata-----ttgtggttaatttgtgct--gcttcgcactggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG
          | |  ||| ||||| | || |||| |     ||  |   |||   | || || ||     |     || |||| || |  | || |   ||  |||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||| ||||||||||| ||||||||||||||||||
gtaggagttcttcgcttccaatctaatatcttttgtctgacctgcaaagtttgggtcatgtactagatcttctcaatttatttatgttttggtttgttgtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 9
gtac-agttcta-atctgagatattttcttaa-tact--ttattatttttatttaatattgtggttaatttgtgctgcttcgcactggtt----acagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG
|||  ||||||  |  |    ||| ||| | | ||     || ||| | ||||||   |||    || ||| ||    |||  | |  ||     |||||||||||  ||||||   |  |||| |||||||||||||| |||||||||||||| ||||| |||||  | |||||| ||||||| |||
gtatgagttctgtacattgtttatgttcctgactaacaactaatatgtctatttatctttgaacatattttttgtc-tttcataatctttctgtgcagTATGATGAGACTGAAAAACGCCGAGAGATGGCAAAGAACTCTCTTGAGAGATATACCCACTACTATGAGAGATGGGCAACCAATCAATCG

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S114_2V6.1 (Physcomitrella patens), 3'ss of exon 9
-----------gtacagttctaatctgagatattt-tcttaatactttattatttttatt-taatattgtggttaatttgtgctgcttcgcactggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG
                  |  || |   || |||| ||||     | | || |  |  ||  |||   | |  | |  | | ||   |   | |  || |||||||||||| | ||  ||||||| |||||||| ||||||||||||||  | |||||||| || |||||||| |||||  | ||  | || 
tagaggctggcacttgaattcaagcgacgagatttatcttttgggtctgttttcctagttacaatccagagagtgacgtttacttagtttgagt--ttgcagTATGATGAAGCAGAGCGGAGAAGGGAAATGGCTAAGAACTCGCTTGAACGCTATACACATTACTATGAACGTTGGGCTACAAACGAATCT

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S9_199V6.1 (Physcomitrella patens), 3'ss of exon 10
gtacagttctaatctgagatattttcttaatactttattatt-------tttatttaatattgtggttaatttgtgctgcttcgcactggtta------cagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG
     ||  || | ||  | |  | ||    |  || |   |       ||  || ||  |  |  | |||||| |||   |   || | | |      |||||||||||| | ||  ||||||| |||||||| |||||||| |||||  | || |||||||||||||| || |||||  | ||  | || 
agctggtcatactttgcaacaggtcctagccatattctaggtgacagaattctttcaaagtcct--tgaatttgagctaactgctacagttcattcttccagTATGATGAAGCAGAGCGGAGAAGGGAAATGGCGAAGAACTCCCTTGAACGTTACACACACTATTATGAGCGTTGGGCTACAAACGAATCT

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ08409 (Selaginella moellendorffii), 3'ss of exon 9
gtacagttctaatctgagatattttcttaatactttattatttttatttaatattgtggttaatttgtgctgcttcgcactggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG
                           ||  | || || ||||   |||    |   ||   | |  | ||| ||       || |||||| |||||| |||| ||||| || |||||||| ||||||||| | |||||||||||||| || || || || |||||  | ||  | || 
--------------------------gtaccaattgat-atttacgtttcccttcacgg---actcatcctgtttgt-----gtaacagTACGATGAAGCTGAGAGGAGGAGGGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCA

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ15174 (Selaginella moellendorffii), 3'ss of exon 9
gtacagttctaatctgagatattttcttaatactttattatttttatttaatattgtggttaatttgtgctgcttcgcactggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG
                           ||  | || || ||||   |||    |   ||   | |  | ||| ||       || |||||| |||||| |||| ||||| ||||||||||| ||||||||| | |||||||||||||| || || || || |||||  | ||  | || 
--------------------------gtaccaattgat-atttacgtttcccttcacgg---actcatcctgtttgt-----gtaacagTACGATGAAGCTGAGAGGAGGAGAGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCA

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ16231 (Selaginella moellendorffii), 3'ss of exon 9
gtacagttctaatctgagatattttcttaatactttattatttttatttaatattgtggttaatttgtgctgcttcgcactggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG----------
                              ||| |   ||    || ||   | ||     |||||       |||       ||||||||||||||| |||||||| | ||||| ||||| ||||||  ||||||  | ||||||||||| || ||| | |||||  | ||  ||||           
-----------------------------gtacgtatctagg--tagttctcactgcctcaaatttacaagttttc-------ttacagTATGATGAAGCTGAAAGGCGTAGAGAGATGGCTAAGAACATGCTTGAACGTTATACACACTACTACGAAAGATGGGCCACAAACGAGTCATCCAGGCAAA

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ17699 (Selaginella moellendorffii), 3'ss of exon 9
gtacagttctaatctgagatattttcttaatactttattatttttatttaatattgtggttaatttgtgctgcttcgcactggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG----------
                              ||| |   ||    || ||   | ||     | |||       |||       ||||||||||||||| |||||||| | ||||| ||||| ||||||  ||||||  | ||||||||||| || ||| | |||||  | ||  ||||           
-----------------------------gtacgtatctagg--tacttctcactgcctcaactttacaaattttc-------ttacagTATGATGAAGCTGAAAGGCGTAGAGAGATGGCTAAGAACATGCTTGAACGTTATACACACTACTACGAAAGATGGGCCACAAACGAGTCATCCAGGCAAA

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|29681156|gb|CB677431.1|CB677431
EST:     GTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCG                         TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGA
genomic: GTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCGgtacagttct ... ctggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattatttttatttaatattgtggttaatttgtgctgcttcgcactggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG
                       ggttaat  putative branch site (score: 4)
     atttttatttaatatt  TA-rich tract