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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgttaaattctaattaaccatctatgctgttttatgattaaggcctgttgtcatctgatgatatttcacctgtatttacctaaatttcacttggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCTGGTTTTGATCCTGAGATTGCAAAATTGGCCCAAAGGATTCTTATCAATCCTCGTAAAATTGACT

Basic information

species Oryza sativa
transcript LOC_Os01g23610.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 4
--catgttaaattctaattaaccatctatgctgttttatgattaaggcctgttgtcatctgatgatatttcacctgtatttacctaaatttcacttggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCTGGTTTTGATCCTGAGATTGCAAAATTGGCCCAAAGGATTCTTATCAATCCTCGTAAAATTGACT
| | |||| | | | ||||| | || | | ||| | || ||||| | || ||||| ||||||||| | ||| | | |||||||||||||||||||| |||||||| || |||||||| |||||||| ||||||||||||||||| || ||||||||||| | |||||||||||||||||
tgtttcctgaattggattacatcatctct--tgatccacaattgggctttgctgtcaatagctggagtttcatctgtatttatgcattttttgatcgatcagGTTACTTTTGTTGAAGCTCTTGATCAATTAATGCCTGGGTTTGATCCCGAGATTGCAAAATTGGCGCAGAGGATTCTTATTAGTCCTCGTAAAATTGACT

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 5
catgttaaattctaattaaccatctatgctgttttatgattaaggcctgttgtcatctgatgatatttcacctgtatttacctaaatt-----tcacttggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCTGGTTTTGATCCTGAGATTGCAAAATTGGCCCAAAGGATTCTTATCAATCCTCGTAAAATTGACT
| | ||| || || ||||| | | |||||| | | || | || | | | ||| | ||| ||||| |||||| | |||||||| |||||| | |||||||| |||||||||||||| || | || || ||| || | || ||||| | || |||||||
-----ttttgtgtaaatagtagaaaataagattttaaggtaccaatctgttggtttttcgatttaaattgtagttactgatcgaaaacggaaaccttttgtgcagGTAACTTTTATAGAAGCACTGGATCAGCTAATGCCTGGATTTGATCCTGAGATCAGTAAGCTAGCTCAGAGGGTTTTGATAAATCCAAGAAAGATTGACT

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 5
catgttaaattctaattaaccatctatgctgttttatgattaaggcctgttgtcatctgatgatatttc--acctgtatttacctaaatttcacttggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCTGGTTTTGATCCTGAGATTGCAAAATTGGCCCAAAGGATTCTTATCAATCCTCGTAAAATTGACT
|||| || | || || || || | | || | || | | || | | | || | || ||| || |||||| |||||| |||| ||||| ||||| | |||||||| |||||||||||||| || |||| |||||| |||| || ||| | | ||||||||||
tcgagcaaatgggcgatagctat--attttgcttaaggtttgtgatgctctgcaactccaggaagtgaccaagctcaggggaactcttttttttttttacagGTAACTTTTATTGAGGCACTGGATCAACTAATGCCTGGATTTGATCCTGAGATCAGTAAGCTGGCTCAAAGGGTTCTAATAAATACAAGAAAAATTGACT

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 5
catgttaaattctaattaaccatctatgctgttttatgattaaggcctg-ttgtcatctgatgatatttcacctgtatttacctaaatttcacttggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCTGGTTTTGATCCTGAGATTGCAAAATTGGCCCAAAGGATTCTTATCAATCCTCGTAAAATTGACT
|||| || || ||| | || | || || || || | || || | | | | || | | | | || |||||| |||||| ||||||| ||||||||| | |||||||| |||||||||||||||| || ||||||||||| |||| || ||||| || ||||||||||
-tagttattgtcatctttgttctcttttctcataatggaacaacttacacttagaatttcattttaatgtaaatcaagttgaccataatgatattccacagGTAACTTTTATTGAAGCTCTTGATCAGCTTATGCCTGGATTTGATCCTGAGATTGGGAAGTTGGCCCAAAGAGTTCTAATAAATCCACGGAAAATTGACT

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 5
-catgttaaattctaattaaccatctatgctgtttta-tgattaaggcctgttgtcatctgatgatatttcacctgtatttacctaaatttcacttggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCTGGTTTTGATCCTGAGATTGCAAAATTGGCCCAAAGGATTCTTATCAATCCTCGTAAAATTGACT
| || | || | || || | | | ||||||| | | | | | | ||||| | ||| | | | ||| |||||||| ||||||||||| | |||||| | |||||||| |||||||||||||||| |||||||| | || |||| || |||||||| |||||||| |
ctccacttttttttggttctcttaataatctatataactgattaaatacagaatttttttatagccgagtcacc-aagctgaccacagcatta-ttgtgcagGTTACATTTGTTGAAGCTTTAGATCAGCTTATGCCTGGCTTTGATCCTGAGATTGGGAAATTGGCTCGGCGGGTTCTAATTAATCCTCGAAAAATTGATT

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 5
----------catgttaaattctaatta-accatctatgctgttttatgattaaggcctgttgtcatctgatgatatttcacctgtatttacctaaatttcacttggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCTGGTTTTGATCCTGAGATTGCAAAATTGGCCCAAAGGATTCTTATCAATCCTCGTAAAATTGACT
| || | | | | | | || | | | | | || | ||| | |||||| ||| || | || ||| | ||||| || ||||| || || |||||| ||||||||||||||||||||||||||||| || | || || ||||| | |||||||||||||||||||| |
gtaaaatttccttgcgcattattgacaataaaataaaagtggatgtgtggagtgcgtgtgtaattatctgacaataattggagctgacttcccttttctgtgggcttgcagGTCACGTTTGTCGAGGCGCTTGATGGGTTGATGCCTGGTTTTGATCCTGAGATTGGCAAGCTTGCACAGAGGATCTTGATCAATCCTCGTAAAATTGATT

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ06739 (Selaginella moellendorffii), 3'ss of exon 5
catgttaaattctaattaaccatctatgctgttttatgattaaggcctgttgtcatctgatgatatttcacctgtatttacctaaatttcact-tggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCTGGTTTTGATCCTGAGATTGCAAAATTGGCCCAAAGGATTCTTATCAATCCTCGTAAAATTGACT
| | | | ||| | ||| || | | | | || ||||| |||||||||||||| || ||||| ||||||| || ||||||||||| || | || | || || ||| | || ||||| ||||| |||||||| |
------------------------------------------------------gtttagtttttcttctttcctttttctatagaatacgcgatgtgcagGTGACTTTTGTTGAAGCTCTGGATCAACTGATGCCAGGCTTTGATCCTGAAATCGGGAAGCTTGCTCAGAGGCTCCTGATCAACCCTCGAAAAATTGATT

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|58684178|gb|CK072865.1|CK072865
EST:     GTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAG                         GTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCT
genomic: GTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaac ... acttggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgttgtcatctgatgatatttcacctgtatttacctaaatttcacttggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCTGGTTTTGATCCTGAGATTGCAAAATTGGCCCAAAGGATTCTTATCAATCCTCGTAAAATTGACT
                                  acctaaa  putative branch site (score: 3)
 tttcactt  CT-rich tract
 tatttacctaaattt  TA-rich tract