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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataacattctcttttgagtattgcacttctaagctgcactttgcaaagattttaatctattgaattttcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCTGATGCTTTTATGGTTGCAAGGGGTGATTTGGGAATGGAAATTCCGATAG

Basic information

species Oryza sativa
transcript LOC_Os01g16960.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G003883_T01 (Zea mays), 3'ss of exon 2
------gtataacattctcttttgagtattgcacttctaagctgcactttgcaaagattttaatctattgaattttcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCTGATGCTTTTATGGTTGCAAGGGGTGATTTGGGAATGGAAATTCCGATAG
       | || |||| ||||||| || |   |||  ||   |      | ||| | | | | | | |||||  | ||||||||||||||||||||||| |||||||||||||||||||||||| | ||||||||||||||||| ||||| |||||||| |||||||||||||| ||||
gtatggttctagcattttcttttgggtttcaaactagtagattttcaaattcaaggttataattgttttgaacatgcagGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCTGATGCTTTTATGGTGGCAAGAGGTGATTTAGGAATGGAAATTCCTATAG

upper sequence: LOC_Os01g16960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G26830.1 (Glycine max), 3'ss of exon 3
------------------------------------------------------------------------------------------------------------------------gtataacattctcttt-tgagtattgcacttctaagctgcact--ttgcaaagatttta---atctattgaattt-tcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCTGATGCTTTTATGGTTGCAAGGGGTGATTTGGGAATGGAAATTCCGATAG
                                                                                                                        ||| ||   | |       || |    | ||||    |  | |  |  |  | ||| ||   || | |||  ||| | ||||||| ||||||||||| || || || |||||||| || |||| | | || ||||| || ||||| ||||| |||||  |||||||||||||||| || |
gtatccatccttattctcaagtaaatgtattctgttttactttaactcttcaaataatttacagaaatgtcattttactttcactttgattctattttcaaacatacgtataagctctccgtacaagtctatgaaaacaagaaacaaagttctggcattgattaatctcccaaattgtacttatttgttgtctttgttagGTTGAAAATCAAGAGGGTGTTGCAAATTTTGATGAAATACTGGAAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG

upper sequence: LOC_Os01g16960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G07800.1 (Glycine max), 3'ss of exon 3
------------------------------gtataacattctcttttgagt-attgcacttctaagctgcactttgcaaagattttaatctattgaattttcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCTGATGCTTTTATGGTTGCAAGGGGTGATTTGGGAATGGAAATTCCGATAG
                               ||  | |   |  ||  | | |||   || | ||  || ||||        | ||  | | |||     | ||||||| ||||||||||| || || || |||||||| || |||||| | || ||||| || ||||| ||||| |||||  |||||||||||||||| || |
tgtataagttccctatacaagtctatgaaaataagaaacagttcttgtattgattaacctcccaaattgtacttatttgttgtcttcttgttttgg----ttagGTTGAAAATCAAGAGGGTGTTGCCAATTTTGATGAAATACTGGCAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG

upper sequence: LOC_Os01g16960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv08s0007g07600.t01 (Vitis vinifera), 3'ss of exon 2
gtataacattctcttttgagtattgcacttcta-agctgcacttt--gcaaagattt---taatctattgaattttcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCTGATGCTTTTATGGTTGCAAGGGGTGATTTGGGAATGGAAATTCCGATAG
||||       | |    || | |    |     |  |||| |||  | || ||| |   |||| |  ||| ||  |||||||| ||||||||||| || ||||| |||||||| || || ||| | || ||||| |||||||| || ||||||||  | ||||||||||| || || |
gtatgttgaggt-tgcaaagaactctgttgaagtatttgcatttttgggaaggatatgactaattttgtgatttggcagGTTGAAAATCAAGAGGGTGTTGCTAATTTTGATGAAATTCTTGCAAACTCAGATGCATTTATGGTGGCCAGGGGTGACCTTGGAATGGAAATCCCCATTG

upper sequence: LOC_Os01g16960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv06s0004g00130.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------------gtataacattctcttttgagtattgcacttctaagctg-cactttgcaaagattttaatctattgaattttcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCTGATGCTTTTATGGTTGCAAGGGGTGATTTGGGAATGGAAATTCCGATAG
                                         ||     |||  |  | ||||| |     ||    |||   | | | |     |||||   |||   ||   ||||||| |||||||| || ||||| || |||||||| ||||| ||| | || ||||| |||||||| ||| | |||||| ||||||||||||| || ||||
gtagcttgatttttacagaaaaaaattgaaggtttaattaagttgtgaatttacagtagagtaatctttctcatttctgatgcctggtatttgctttaaa--atttgtttggtagGTTGAAAATCAAGAAGGGGTGGCAAATTTTGATGAAATCCTTGCAAATTCAGATGCATTTATGGTGGCACGAGGTGATCTGGGAATGGAAATCCCAATAG

upper sequence: LOC_Os01g16960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S392_18V6.3 (Physcomitrella patens), 3'ss of exon 3
----------------gtataacattctcttttgagtattgcacttctaag---ctgcact----ttgcaaagattttaatctattga---att--ttcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCTGATGCTTTTATGGTTGCAAGGGGTGATTTGGGAATGGAAATTCCGATAG
                | | |  ||||||| | | || | |   ||    |   ||||| |    |||    | || | |||  ||||   ||   | ||||||||||| || || ||  |||  || || ||||| ||  ||  | |  | ||||   | ||||||||||| ||||| ||||||||||| |||||||  |
ttcattacaataatttggagacgattctctct-gtgtctcgtcttttcgtgactctgcaatgcgcttgtctcgcttctcatcatttgatggatccatgcagGTTGAGAACCAGGAAGGTCTGGTCAATTTCGATGACATTTTGAAAGAGACGGATGGAGTGATGGTTGCAAGAGGTGACTTGGGAATGGAGATTCCGACTG

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|33794571|gb|CF323172.1|CF323172
EST:     TCAGGAAGGTGCTTGGGAAGCATGCAAAGTCAATAATGCTGATGTCAAAG                         GTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCT
genomic: TCAGGAAGGTGCTTGGGAAGCATGCAAAGTCAATAATGCTGATGTCAAAGgtataacatt ... gaattttcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCT
EST: gi|218479177|gb|FG963866.1|FG963866
EST:     TCAGGAAGGTGCTTGGGAAGCATGCAAAGTCAATAATGCTGATGTCAAAG                         GTTGAGAATCAAGAG
genomic: TCAGGAAGGTGCTTGGGAAGCATGCAAAGTCAATAATGCTGATGTCAAAGgtataacatt ... gaattttcagGTTGAGAATCAAGAG
EST: gi|33804365|gb|CF328057.1|CF328057
EST:     TCACGAAGGTGCTTGGGAAGCATGCAAAGTCAATAATGCTGATGTCAAAG                         GTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCT
genomic: TCAGGAAGGTGCTTGGGAAGCATGCAAAGTCAATAATGCTGATGTCAAAGgtataacatt ... gaattttcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCT
EST: gi|33678537|gb|CF306776.1|CF306776
EST:     TCAGGAAGGTGCTTGGGAAGCATGCAAAGTCAATAATGCTGATGTCAAAG                         GTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCT
genomic: TCAGGAAGGTGCTTGGGAAGCATGCAAAGTCAATAATGCTGATGTCAAAGgtataacatt ... gaattttcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCT
EST: gi|88404025|gb|CI601435.1|CI601435
EST:     TCAGGAAGGTGCTTGGGAAGCATGCAAAGTCAATAATGCTGATGTCAAAG                         GTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCT
genomic: TCAGGAAGGTGCTTGGGAAGCATGCAAAGTCAATAATGCTGATGTCAAAGgtataacatt ... gaattttcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtattgcacttctaagctgcactttgcaaagattttaatctattgaattttcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCTGATGCTTTTATGGTTGCAAGGGGTGATTTGGGAATGGAAATTCCGATAG
                                 ttttaat  putative branch site (score: 3)
                                                ttttc  putative PPT
                            aaagattttaatctat  TA-rich tract