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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtttgaattctccttgatttcccccttattatactatatgtggcgccgctaaagtgctaatgcaatctattctgcacatttccacatcagTTATGATAGGCCCCTCCAATGTGAATAAAAAGCTGTGGCCTCTGTAGAGAAGGCTCGGCGAGGGTGGTGTTTCTCTGCCATCTCAATAAAGCATTCATAG

Basic information

species Oryza sativa
transcript LOC_Os01g15460.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15460.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G036837_T03 (Zea mays), 3'ss of exon 7
gttggtttgaattctccttgatttcccccttattatactatatgtggcgccgctaaagtgctaatgcaatctattctgcacatttccacatcagTTATGATAGGCCCCTCCAATGTGAATAAAAAGCTGTGGCCTCTGTAGAGAAGGCTCGGCGAGGGTGGTGTTTCTCTGCCATCTCAATAA---AGCATTCATAG----------
                     |          ||  | | ||| |  |  |   | | ||||   |  |   ||| |     | | |  || |||| ||||||||| ||||||||||||||   |||||||| |||||||||||||   |||||||||||| |||||| | |||||  |||||   |||||| ||||          
--------------------gtactttgagccttcaattttatttttcatcaacatactgctgccgacaatgattat-tttttattcgtattagttctgatagGCCTCTCCAATGTGAATA---AGCTGTGGTCTCTGTAGAGAAGCTGCGGCGAGGGTGG-GTTTCTTTACCATCAGAATAAGAGAGCATTGATAGGTCACACGCA

upper sequence: LOC_Os01g15460.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G086994_T01 (Zea mays), 3'ss of exon 7
gttggtttgaattctccttgatttcccccttattatactata-tgtggcgccgctaaagtgctaatgcaatctattctgcacatttccacatcagTTATGATAGGCCCCTCCAATGTGAATAAAAAGCTGTGGCCTCTGTAGAGAAGGCTCGGCGAGGGTGGTGTTTCTCTGCCATCTCAATAA---AGCATTCATAG
||   |||    ||   |||  ||   | | ||     || |   |   || ||  |    | ||||     |||  |||   | |  | ||||||| |||||||||  | |||||||||||| ||||||||||||||||||||||| |  |||||||||||| ||||||| |||||  |||||   |||||| ||  
gtacctttagcctccgattgtatttttcatcatctcgttaaaacatactgctgccga----caaatgattattatcttgctt-tattgatatcagTTCTGATAGGCCTTTACAATGTGAATAAGAAGCTGTGGCCTCTGTAGAGAAGCCGTGGCGAGGGTGGT-TTTCTCTACCATCAGAATAAGAGAGCATTGAT--

upper sequence: LOC_Os01g15460.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G036837_T02 (Zea mays), 3'ss of exon 7
gttggtttgaattctccttgatttcccccttattatactatatgtggcgccgctaaagtgctaatgcaatctattctgcacatttccacatcagTTATGATAGGCCCCTCCAATGTGAATAAAAAGCTGTGGCCTCTGTAGAGAAGGCTCGGCGAGGGTGGTGTTTCTCTGCCATCTCAATAA---AGCATTCATAG---------------------------------------------
                     |          ||  | | ||| |  |  |   | | ||||   |  |   ||| |     | | |  || |||| ||||||||| ||||||||||||||   |||||||| |||||||||||||   |||||||||||| |||||| | |||||  |||||   |||||| ||||                                             
--------------------gtactttgagccttcaattttatttttcatcaacatactgctgccgacaatgattat-tttttattcgtattagttctgataggcctctccaatgtgaata---agctgtggtctctgtagAGAAGCTGCGGCGAGGGTGG-GTTTCTTTACCATCAGAATAAGAGAGCATTGATAGGTCACACGCAAGCTCGATTCACTAGCAATTTTGGGTTCTTCCGTT

upper sequence: LOC_Os01g15460.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G086994_T03 (Zea mays), 3'ss of exon 8
gttggtttgaattctccttgatttcccccttattatactata-tgtggcgccgctaaagtgctaatgcaatctattctgcacatttccacatcagTTATGATAGGCCCCTCCAATGTGAATAAAAAGCTGTGGCCTCTGTAGAGAAGGCTCGGCGAGGGTGGTGTTTCTCTGCCATCTCAATAA---AGCATTCATAG-------
||   |||    ||   |||  ||   | | ||     || |   |   || ||  |    | ||||     |||  |||   | |  | ||||||| |||||||||  | |||||||||||| ||||||||||||||||||||||| |  |||||||||||| ||||||| |||||  |||||   |||||| || |       
gtacctttagcctccgattgtatttttcatcatctcgttaaaacatactgctgccga----caaatgattattatcttgctt-tattgatatcagttctgatagGCCTTTACAATGTGAATAAGAAGCTGTGGCCTCTGTAGAGAAGCCGTGGCGAGGGTGGT-TTTCTCTACCATCAGAATAAGAGAGCATTGATCGGTTACAA

upper sequence: LOC_Os01g15460.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G036837_T01 (Zea mays), 3'ss of exon 7
gttggtttgaattctccttgatttcccccttattatactatatgtggcgccgctaaagtgctaatgcaatctattctgcacatttccacatcagTTATGATAGGCCCCTCCAATGTGAATAAAAAGCTGTGGCCTCTGTAGAGAAGGCTCGGCGAGGGTGGTGTTTCTCTGCCATCTCAATAA---AGCATTCATAG-
                     |          ||  | | ||| |  |  |   | | ||||   |  |   ||| |     | | |  || |||| ||||||||| ||||||||||||||   |||||||| |||||||||||||   |||||||||||| |||||| | |||||  |||||   |||||| |||| 
--------------------gtactttgagccttcaattttatttttcatcaacatactgctgccgacaatgattat-tttttattcgtattagTTCTGATAGGCCTCTCCAATGTGAATA---AGCTGTGGTCTCTGTAGAGAAGCTGCGGCGAGGGTGG-GTTTCTTTACCATCAGAATAAGAGAGCATTGATAGG

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|116875554|gb|EC366062.1|EC366062
EST:     TTTTTCTGAGCTGAGAGATCTCAGCACAATTTTTCAATCACTTGACACAG                         TTATGATAGGCCCCTCCAATGTGAATAAAAAGCTGTGGCCTCTGTAGAGAA
genomic: TTTTTCTGAGCTGAGAGATCTCAGCACAATTTTTCAATCACTTGACACAGgttggtttga ... tccacatcagTTATGATAGGCCCCTCCAATGTGAATAAAAAGCTGTGGCCTCTGTAGAGAA
EST: gi|116874997|gb|EC365505.1|EC365505
EST:     TTTTTCTGAGCTGAGAGATCTCAGCACAATTTTTCAATCACTTGACACAG                         TTATGATAGGCCCCTCCAATGTGAATAAAAAGCTGTGGCCTCTGTAGAGAA
genomic: TTTTTCTGAGCTGAGAGATCTCAGCACAATTTTTCAATCACTTGACACAGgttggtttga ... tccacatcagTTATGATAGGCCCCTCCAATGTGAATAAAAAGCTGTGGCCTCTGTAGAGAA
EST: gi|33680921|gb|CF309160.1|CF309160
EST:     TTTTTCTGAGCTGAGAGATCTCAGCACAATTTTTCAATCACTTGACACAG                         TTATGATAGGCCCCTCCAATGTGAATAAAAAGCTGTGGCCTCTGT
genomic: TTTTTCTGAGCTGAGAGATCTCAGCACAATTTTTCAATCACTTGACACAGgttggtttga ... tccacatcagTTATGATAGGCCCCTCCAATGTGAATAAAAAGCTGTGGCCTCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgtggcgccgctaaagtgctaatgcaatctattctgcacatttccacatcagTTATGATAGGCCCCTCCAATGTGAATAAAAAGCTGTGGCCTCTGTAGAGAAGGCTCGGCGAGGGTGGTGTTTCTCTGCCATCTCAATAAAGCATTCATAG
                   tgctaat  putative branch site (score: 2)
                                         catttcc  putative PPT
                            aatctatt  TA-rich tract