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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagatttgatccgatgtttaaccaaaataaagtatggttcaaaagcatagaagttgtaccgtatccattttctaaacatgtgttctgctctgtactcagGAAAAAGATGCAGCTCTGGGAAATGGTGGCTTGGGTAGGCTCGCATCTTGCTTTTTGGATTCGATGGCAACACTAAATTTGCCTGCTTGGGGATATGGTC

Basic information

species Oryza sativa
transcript LOC_Os01g63270.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g63270.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G085577_T01 (Zea mays), 3'ss of exon 2
-----ttagatttgatccgatgtttaaccaaaataaagtatggttcaaaagcatagaagttgtaccgtatccattttctaaacatgtgttctgc--tctgtactcagGAAAAAGATGCAGCTCTGGGAAATGGTGGCTTGGGTAGGCTCGCATCTTGCTTTTTGGATTCGATGGCAACACTAAATTTGCCTGCTTGGGGATATGGTC
| || ||| || |||| | | || |||| || | || | | || | ||| | || | | | | | |||||||||||||||||||| || ||||| |||||||||||||| |||||||||||||||||||| ||||||||| | ||||||||||||||||| ||||| |
caaggattcatggcatctgagttttactttccaattgggat--ttcataaattt-----ccataattttccaatgatgcaaattaatatttaacgattttttcacagGAAAAAGATGCAGCTCTAGGGAATGGCGGCTTGGGTAGGCTTGCATCTTGCTTTTTGGATTCAATGGCAACATTGAATTTGCCTGCTTGGGGCTATGGCC

upper sequence: LOC_Os01g63270.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G45210.1 (Glycine max), 3'ss of exon 3
----ttagatttgatccgatgtttaaccaaaataaagtatggttcaaaagcatagaagttgtaccgtatccattttctaaacatgtgttctgctctgtactcagGAAAAAGATGCAGCTCTGGGAAATGGTGGCTTGGGTAGGCTCGCATCTTGCTTTTTGGATTCGATGGCAACACTAAATTTGCCTGCTTGGGGATATGGTC
|| | | ||| || | | | ||||| || ||| | | | || | | | | | || || ||||| || |||||||| || ||||||||||| | |||||||| || ||||||||| ||||||| ||||||||||| ||||||||| ||||||| ||||||
agcattttcgaaaagtctgcatttcttcatatgtatgattggttttaatatctagtgtctaaaactcatttgctgaaccattacacatgcaactttg----cagGAGAAGGATGCAGCACTAGGAAATGGTGGTCTTGGTAGGCTTGCTTCTTGCTTTCTGGATTCCATGGCAACACTTAATTTGCCTTCTTGGGGGTATGGTT

upper sequence: LOC_Os01g63270.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA18G07480.1 (Glycine max), 3'ss of exon 2
-----ttagatttgatccgatgtttaaccaaaataaagtatggttcaaaagcatagaagttgtaccgtatccattttctaaacatgtgttctgctctgtactcagGAAAAAGATGCAGCTCTGGGAAATGGTGGCTTGGGTAGGCTCGCATCTTGCTTTTTGGATTCGATGGCAACACTAAATTTGCCTGCTTGGGGATATGGTC
|| | | ||| || | | | ||||| || ||| |||| | ||||| || || | | | ||||| || |||||||| || ||||||||||| | |||||||| || ||||||||| ||||||| ||||||||||| ||||||||| ||||||| ||||||
aagcattttccaaaagtctgcatttcttcatatgtatggttggttttaatatctag----tgtataaaactcatttgctggaccattaaacgtgcaactttgcaGGAGAAGGATGCAGCACTAGGAAATGGTGGTCTTGGTAGGCTTGCTTCTTGCTTTCTGGATTCCATGGCAACACTTAATTTGCCTTCTTGGGGGTATGGT-

upper sequence: LOC_Os01g63270.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G46970.1 (Arabidopsis thaliana), 3'ss of exon 3
ttagatttgatccgatgtttaaccaaaataaagtatggttcaaaagcatagaagttgtaccgtatccattttctaaacatgtgttctgctctgtactcagGAAAAAGATGCAGCTCTGGGAAATGGTGGCTTGGGTAGGCTCGCATCTTGCTTTTTGGATTCGATGGCAACACTAAATTTGCCTGCTTGGGGATATGGTC
| ||| | | | | || || | | | | | | | ||||| | | | | | | | || |||| |||||||||||||| ||||||||||| || || || || || || || || |||||||||||||| || |||||| ||||||||||||| ||||||
------------gtacattttaagttaccatttttctctttgaagacttgggacctaaat--aaattattttttgatc---tctccatgtttgcttgtagGAGAAAGATGCAGCTCTAGGAAATGGTGGGTTAGGGAGACTTGCCTCGTGTTTCTTGGATTCGATGGCCACCCTAAATCTGCCTGCTTGGGGTTATGGTT

upper sequence: LOC_Os01g63270.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv06s0004g06020.t01 (Vitis vinifera), 3'ss of exon 2
-----ttagatttgatccgatgtttaaccaaaataaagtatggttcaaaagcatagaagttgtaccgtatccattttctaaacatgtgttctgctctgtactcagGAAAAAGATGCAGCTCTGGGAAATGGTGGCTTGGGTAGGCTCGCATCTTGCTTTTTGGATTCGATGGCAACACTAAATTTGCCTGCTTGGGGATATGGTC
| || | ||||| |||||| | || || || | | || | ||| | | || | || | | | ||||||||||||| || || ||||||||||| |||| ||||| || || |||||| | || || ||||||||| ||||||||||||| ||||||||||||
agtctgcattcttcgattgtagtttatttgaaataatg-atatctct---gcgtttggtctcaacttttgaactttgatgattataagaaatgatatct-tatagGAAAAAGATGCGGCACTAGGAAATGGTGGACTGGGAAGGCTTGCTTCATGCTTTCTTGACTCCATGGCAACATTAAATTTGCCTGCGTGGGGATATGGTT

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|29625767|gb|CB630778.1|CB630778
EST:     CGGAGGCCGTGAAGAAGTTCGGGTACGAGCTCGAGGCCCTCGTCGGGCAG                         GAAAAAGATGCAGCTCTGGGAAATGGTGGCTTGGGTAGGCTCGCATCTTGC
genomic: CGGAGGCCGTGAAGAAGTTCGGGTACGAGCTCGAGGCCCTCGTCGGGCAGgtgagctccc ... ctgtactcagGAAAAAGATGCAGCTCTGGGAAATGGTGGCTTGGGTAGGCTCGCATCTTGC
EST: gi|29625892|gb|CB630903.1|CB630903
EST:     CGGAGGCCGTGAAGAAGTTCGGGTACGAGCTCGAGGCCCTCGTCGGGCAG                         GAAAAAGATGCAGCTCTGGGAAATGGTGGCTTGGGTAGGCTCGCATCTTGC
genomic: CGGAGGCCGTGAAGAAGTTCGGGTACGAGCTCGAGGCCCTCGTCGGGCAGgtgagctccc ... ctgtactcagGAAAAAGATGCAGCTCTGGGAAATGGTGGCTTGGGTAGGCTCGCATCTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatagaagttgtaccgtatccattttctaaacatgtgttctgctctgtactcagGAAAAAGATGCAGCTCTGGGAAATGGTGGCTTGGGTAGGCTCGCATCTTGCTTTTTGGATTCGATGGCAACACTAAATTTGCCTGCTTGGGGATATGGTC
                         ttctaaa  putative branch site (score: 2)
 ttctgctct  putative PPT
 attttctaaa  TA-rich tract