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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactagatttgtattgtattgtactgctgtttgcagtgacttgttttgatgcccagcagaatttaattatattttccccacgcagAACAAATGCAATGTTGGCTACGCGTTCATTAACATGATATCACCTGTGCACATTGTATCGTTCTACCAG

Basic information

species Oryza sativa
transcript LOC_Os02g48790.4
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g48790.4 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G004455_T01 (Zea mays), 3'ss of exon 10
gtactagatttgta-----ttgtattgtactgctgtttgcagtgact-tgttttgatgccca-----gcagaatttaattat-----attttccccacgcagAACAAATGCAATGTTGGCTACGCGTTCATTAACATGATATCACCTGTGCACATTGTATCGTTCTACCAG
||||||||||         |||| | |  ||  |||||     | || |  |||   | |||     |   |||||| ||||     ||| | |  | ||||||||||||||||||||| || ||||||||||||||| ||||||| ||||||||| |||| |||||||||
gtactagattaactccaatttgtgtggctcttttgtttttgaggcctgtactttataggccacacctgtttaatttacttatgtattattgtgcttatgcagAACAAATGCAATGTTGGATATGCGTTCATTAACATGGTATCACCGGTGCACATTATATCCTTCTACCAG

upper sequence: LOC_Os02g48790.4 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G154229_T01 (Zea mays), 3'ss of exon 10
gtactagattt-gtattgtattgtactgctgtt--tgcagtgacttgt-tttgatgcccagcag------aatttaattat--------attttccccacgcagAACAAATGCAATGTTGGCTACGCGTTCATTAACATGATATCACCTGTGCACATTGTATCGTTCTACCAG
||||||||||| | |     |||| || || ||  |   | | | ||| ||| ||   |  ||       |||||| ||||        ||| | |  | ||||||||||||||||||||| ||||||||| ||||||||||||| || ||||| ||| |||| |||||||||
gtactagatttagcaccaatttgtgctactcttgtttttgaggcctgtattttataggccacacctattcaatttacttatgttgtattattgtgcttatgcagAACAAATGCAATGTTGGATACGCGTTCGTTAACATGATATCGCCGGTGCATATTATATCCTTCTACCAG

upper sequence: LOC_Os02g48790.4 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G154229_T02 (Zea mays), 3'ss of exon 10
gtactagattt-gtattgtattgtactgctgtt--tgcagtgacttgt-tttgatgcccagcag------aatttaattat--------attttccccacgcagAACAAATGCAATGTTGGCTACGCGTTCATTAACATGATATCACCTGTGCACATTGTATCGTTCTACCAG-------------------------------
||||||||||| | |     |||| || || ||  |   | | | ||| ||| ||   |  ||       |||||| ||||        ||| | |  | ||||||||||||||||||||| ||||||||| ||||||||||||| || ||||| ||| |||| |||||||||                               
gtactagatttagcaccaatttgtgctactcttgtttttgaggcctgtattttataggccacacctattcaatttacttatgttgtattattgtgcttatgcagAACAAATGCAATGTTGGATACGCGTTCGTTAACATGATATCGCCGGTGCATATTATATCCTTCTACCAGGTGCTTTCCTTTCTTGGCCTTTGTCCTGTGT

upper sequence: LOC_Os02g48790.4 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S271_57V6.2 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------------------------------------------------------------------------gtactagatttgtattgtat-tgtactgctgtttgcagtgac--ttgttttgatgcccagcagaatttaattatattttccccacgcagAACAAATGCAATGTTGGCTACGCGTTCATTAACATGATATCACCTGTGCACATTGTATCGTTCTACCAG-------------------------------
                                                                                                                 |   | || | |  |  | |||  ||  ||  |||| ||   | |    | ||    | |             |  | |   |||||||||| ||||| ||||| |||||||||||||| ||||  || || | ||  || ||  |||||||| |                                
gtacggtgtgcagcagttgcatggagtggggcggggcggggcatggtggtgtgttgcatggggtgggggtgggcgaagtgggtgtggagtggggaagtgtggggtgtgcggagagatggttgggagggcgtgtgttttggagtgagcagagagggtgggaggggtggttgggaatgggctgacgggtgatgcgtgcgcagAACAAGTGCAACGTTGGGTACGCGTTCATTAATATGACGTCGCCAGCGCGGATCGTGCCGTTCTACAAAGCGTTCAACGGGAAGAAGTGGGAGAAGTTCA

upper sequence: LOC_Os02g48790.4 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S78_22V6.1 (Physcomitrella patens), 3'ss of exon 12
----------------------------------------------------------------------------------------gtactagatttgtattgtattgt--actgctgtttgcagtgacttgt-tttgatgcccagcagaatt--taattatattttcccca-------cgcagAACAAATGCAATGTTGGCTACGCGTTCATTAACATGATATCACCTGTGCACATTGTATCGTTCTACCAG-------------------------------
                                                                                        | || |||       ||   |||  |  |  |   |    |  |||| |||| |||  ||  |  |   |||  |  |    |          |||||||||| ||||||||||| || |||||||| |||||||| || ||   || ||| ||  |||| ||| ||                               
gtacgttgaccggcactgtgatgggttgagtatttggtagtggtcgggtggagcataggtgtgcattccaagtaggtttggggggacagaacgagacagtgggtgaggtgtggaggggggcacgtgtggggttgtgtttggtgcgaaggcgtgtgggtaacgaggtggcgcgtgatgggtgcgcagAACAAGTGCAATGTTGGGTATGCGTTCATCAACATGATGTCGCCGTCGCGCATAGTTCCGTTTTACAAGGCGTTCAACGGGAAGAAGTGGGAGAAGTTCA

upper sequence: LOC_Os02g48790.4 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ28200 (Selaginella moellendorffii), 3'ss of exon 9
gtactagatttgtattgtattgtactgctgtttgcagtgacttgttttgatgcccagcagaatttaattatattttccccacgcagAACAAATGCAATGTTGGCTACGCGTTCATTAACATGATATCACCTGTGCACATTGTATCGTTCTACCAG
                          |   |||   | ||       || | ||| |      || ||    |||| ||   ||||||||||||||| |||||||| || ||||| |||||||     || |  ||||| ||  | || ||| ||
--------------------------gtgattttaggcgagcaaaagtgtttccctg---gtattgatcggcttttgcctgtgcagAACAAATGCAACGTTGGCTATGCATTCATCAACATGACCGAGCCAGCTCACATCGTCCCCTTTTACAAG

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|29672191|gb|CB668466.1|CB668466
EST:     AGTTTCATAAAGGAACCTATGACTTTTTCTACCTGCCAATTGATTTCAAG                         AACAAATGCAATGTTGGCTACGCGTTCATTAACATGATATCACCTGTGCAC
genomic: AGTTTCATAAAGGAACCTATGACTTTTTCTACCTGCCAATTGATTTCAAGgtactagatt ... ccccacgcagAACAAATGCAATGTTGGCTACGCGTTCATTAACATGATATCACCTGTGCAC
EST: gi|29677798|gb|CB674073.1|CB674073
EST:     AGTTTCATAAAGGAACCTATGACTTTTTCTACCTGCCAATTGATTTCAAG                         AACAAATGCAATGTTGGCTACGCGTTCATTAACATGATATCACCTGTGCAC
genomic: AGTTTCATAAAGGAACCTATGACTTTTTCTACCTGCCAATTGATTTCAAGgtactagatt ... ccccacgcagAACAAATGCAATGTTGGCTACGCGTTCATTAACATGATATCACCTGTGCAC
EST: gi|29629250|gb|CB634261.1|CB634261
EST:     AGTTTCATAAAGGAACCTATGACTTTTTCTACCTGCCAATTGATTTCAAG                         AACAAATGCAATGTTGGCTACGCGTTCATTAACATGATATCACCTGTGCAC
genomic: AGTTTCATAAAGGAACCTATGACTTTTTCTACCTGCCAATTGATTTCAAGgtactagatt ... ccccacgcagAACAAATGCAATGTTGGCTACGCGTTCATTAACATGATATCACCTGTGCAC
EST: gi|42414391|gb|CK665031.1|CK665031
EST:     AGTTTCATAAAGGAACCTATGACTTTTTCTACCTGCCAATTGATTTCAAG                         AACAAATGCAATGGTGGCTACGCGTTCATTAACATGATATCACCTGTGCAC
genomic: AGTTTCATAAAGGAACCTATGACTTTTTCTACCTGCCAATTGATTTCAAGgtactagatt ... ccccacgcagAACAAATGCAATGTTGGCTACGCGTTCATTAACATGATATCACCTGTGCAC
EST: gi|29622964|gb|CB627975.1|CB627975
EST:     AGTTTCATAAAGGAACCTATGACTTTTTCTACCTGCCAATTGATTTCAAG                         AACAAATGCAATGTTGGCTACGCGTTCATTAACATGATATCACCTGTGCAC
genomic: AGTTTCATAAAGGAACCTATGACTTTTTCTACCTGCCAATTGATTTCAAGgtactagatt ... ccccacgcagAACAAATGCAATGTTGGCTACGCGTTCATTAACATGATATCACCTGTGCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcagtgacttgttttgatgcccagcagaatttaattatattttccccacgcagAACAAATGCAATGTTGGCTACGCGTTCATTAACATGATATCACCTGTGCACATTGTATCGTTCTACCAG
                              atttaat  putative branch site (score: 4)
                                       tattttcccc  putative PPT
                        agcagaatttaattat  TA-rich tract