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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggatacaacttgtattgtaatactctagtactgttatcactgaaattttcagttaatcttttttgacttgtggattggtgttcttttttcgtgctacagAGGATGGAAGAAGTGGCACATTTATGATTGGAAATGAAAGCTTTCCAGCATCTCTCTTAGATCTCCCAACTGTTATGGAGTCATACAAGACATACAATGA

Basic information

species Oryza sativa
transcript LOC_Os01g46020.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g46020.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G147614_T05 (Zea mays), 3'ss of exon 2
--tggatacaacttgtattgtaatactctagtactgttatcactgaaattttcagttaatcttttttgacttgtggattggtgttcttttttcgtgctacagAGGATGGAAGAAGTGGCACATTTATGATTGGAAATGAAAGCTTTCCAGCATCTCTCTTAGATCTCCCAACTGTTATGGAGTCATACAAGACATACAATGA
   | ||| |||||| | | ||   ||  | ||    | |   | | | ||  | ||      | ||  ||||||  ||| ||   | |||   |  ||||||||||||||||| ||||||||||||||| || ||||| |||||||| ||||||||||| ||||| ||  ||||  ||||||||||||| |||||  ||||
tgagcatataacttgaactcta-cgctagactagatatgtatttaagaattgaaattttgaactgttcccttgtgcgttgatgagatatttgt-tcttacagAGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCATCTCTCTTGGATCTACCTGCTGTGGTGGAGTCATACAAAACATATGATGA

upper sequence: LOC_Os01g46020.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G029038_T01 (Zea mays), 3'ss of exon 1
tggatacaacttgtattgtaa--tactctagtactgttatca---ctgaaattttcagttaatcttttttgacttgtggattggtgttcttttttcgtgctacagAGGATGGAAGAAGTGGCACATTTATGATTGGAAATGAAAGCTTTCCAGCATCTCTCTTAGATCTCCCAACTGTTATGGAGTCATACAAGACATACAATGA
 | ||| |||||| | | ||   ||  ||||   |||  | |     |||||||| |  |  ||  ||    ||||||  ||| ||   | |||   | ||||||||||||||| || ||||||||||||||| || ||||| |||||||| ||||||||||| ||||| ||  ||||  ||||||||||||| |||||  ||||
agcatataacttgaactctacgctagactagatatgtattaagaatcgaaattttgaactgttccctt----cttgtgcgttgatgagatatttgt-tcctacagAGGATGGAACAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCATCTCTCTTGGATCTACCTGCTGTGGTGGAGTCATACAAAACATATGATGA

upper sequence: LOC_Os01g46020.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G454830_T01 (Zea mays), 3'ss of exon 2
tggatacaacttgtattgtaa--tactctagtactgttatca---ctgaaattttcagttaatcttttttgacttgtggattggtgttcttttttcgtgctacagAGGATGGAAGAAGTGGCACATTTATGATTGGAAATGAAAGCTTTCCAGCATCTCTCTTAGATCTCCCAACTGTTATGGAGTCATACAAGACATACAATGA
 | ||| |||||| | | ||   ||  ||||   |||  | |     |||||||| |  |  ||  ||     |||||  ||| ||   | |||   | |||||||||||||||||| ||||||||||||||| || ||||| ||||||||  |||||||||| ||||| ||  ||||  ||||||||||||| |||||  ||||
agcatataacttgaactctacgctagactagatatgtattaagaatcgaaattttgaactgttccctta----ttgtgcgttgatgcgatatttgt-tcctacagAGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTTCATCTCTCTTGGATCTACCTGCTGTGGTGGAGTCATACAAAACATATGATGA

upper sequence: LOC_Os01g46020.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G143935_T01 (Zea mays), 3'ss of exon 1
tggatacaacttgtattgtaa--tactctagtactgttatca---ctgaaattttcagttaatcttttttgacttgtggattggtgttcttttttcgtgctacagAGGATGGAAGAAGTGGCACATTTATGATTGGAAATGAAAGCTTTCCAGCATCTCTCTTAGATCTCCCAACTGTTATGGAGTCATACAAGACATACAATGA
 | ||| |||||| | | ||   ||  ||||   |||  | |     |||||||| |  |  ||  ||    ||||||  ||| ||   | |||   | |||||||||||||||||| || |||||||||||| || ||||| |||||||| ||||||||||| ||||| ||  ||||  ||||||||||||| | |||  ||| 
agcatataacttgaactctacgctagactagatatgtattaagaatcgaaattttgaactgttccctt----cttgtgcgttgatgagatatttgt-tcctacagAGGATGGAAGAAATGACACATTTATGATCGGTAATGAGAGCTTTCCTGCATCTCTCTTGGATCTACCTGCTGTGGTGGAGTCATACAAAATATATGATGC

upper sequence: LOC_Os01g46020.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA17G29810.1 (Glycine max), 3'ss of exon 2
tggatacaacttgtattgtaatactctagtactgttatcactgaaattttcagttaatcttttttgacttgtggattggt-gttcttttttcgtgctacagAGGATGGAAGAAGTGGCACATTTATGATTGGAAATGAAAGCTTTCCAGCATCTCTCTTAGATCTCCCAACTGTTATGGAGTCATACAAGACATACAATGA
                                              | |  |   |||  || || |   |  ||   ||   |   |||      ||  ||||||||||||||||| |||||||||||||| ||||||  ||| ||||| ||||| || ||||| ||    ||| | || || ||               
---------------------------------------------gtatgaaaacaatgcttcttcatcagaagacaagtcactagATTTGTCATTTAGTGAGGATGGAAGAAGTGGTACATTTATGATTGGGAATGAACACTTCCCAGCTTCTCTATTGGATCTTCCTTGCGTTGTTGAATCCTA---------------

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|163929559|gb|EG713490.1|EG713490
EST:     CGCGTCATCCTCCAACCCCGACGACGCCTCCCTCGATCTCTCCTTCTCAG                         AGGATGGAAGAAGTGGCACATTTATGATTGGAAATGAAAGCTTTCCAGCAT
genomic: CGCGTCATCCTCCAACCCCGACGACGCCTCCCTCGATCTCTCCTTCTCAGgtgattcttt ... cgtgctacagAGGATGGAAGAAGTGGCACATTTATGATTGGAAATGAAAGCTTTCCAGCAT
EST: gi|88355167|gb|CI651870.1|CI651870
EST:     CGCGTCATCCTCCAACCCCGACGACGCCTCCCTCGATCTCTCCTTCTCAG                         AGGATGGAAGAAGTGGCACATTTATGATTGGAAATGAAAGCTTTCCAGCAT
genomic: CGCGTCATCCTCCAACCCCGACGACGCCTCCCTCGATCTCTCCTTCTCAGgtgattcttt ... cgtgctacagAGGATGGAAGAAGTGGCACATTTATGATTGGAAATGAAAGCTTTCCAGCAT
EST: gi|218499703|gb|FG961375.1|FG961375
EST:     CGCGTCATCCTCCAACCCCGACGACGCCTCCCTCGATCTCTCCTTCTCAG                         AGGATGGAAGAAGTGGCCCATTTAGGATTGGAAATGAAAGCTTTCCAGCAT
genomic: CGCGTCATCCTCCAACCCCGACGACGCCTCCCTCGATCTCTCCTTCTCAGgtgattcttt ... cgtgctacagAGGATGGAAGAAGTGGCACATTTATGATTGGAAATGAAAGCTTTCCAGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttcagttaatcttttttgacttgtggattggtgttcttttttcgtgctacagAGGATGGAAGAAGTGGCACATTTATGATTGGAAATGAAAGCTTTCCAGCATCTCTCTTAGATCTCCCAACTGTTATGGAGTCATACAAGACATACAATGA
                ttttgac  putative branch site (score: 3)
                                    ttcttttttcgtgct  putative PPT
      agttaatctttttt  TA-rich tract