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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAATGGAGGAAGTATGGTCAGAAGGTCACCAAGGACAACCCCTGCCCAAGAGCCTACTTCAGATGCTCATTTGCTCCCGCCTGCCCTGTCAAGAAGAAGgtaacttaaattcctctaactaattccaaagtgatttcgtaagttttgctaaatttagtgcaaattcgagcctgtttctgaactttgttcgtggttcaaatgttgtttcag

Basic information

species Oryza sativa
transcript LOC_Os02g08440.4
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g08440.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA14G11960.1 (Glycine max), 5'ss of exon 4
CCAATGGAGGAAGTATGGTCAGAAGGTCACCAAGGACAACCCCTGCCCAAGAGCCTACTTCAGATGCTCATTTGCTCCCGCCTGCCCTGTCAAGAAGAAGgtaacttaaattcctctaactaattccaaagtgatttcgtaagttttgctaaatttagtgcaaattcgagcctgtttctgaactttgttcgtggttcaaatgttgtttcag
 ||||||||||| ||||||||||||||||| | ||| ||||| |  || || || |||||||| ||||| | ||| ||    ||||| || || ||||||||||     |||    ||| |   |  |     ||     ||| ||    | ||  | |     ||  |  |   || |  | |    | |   ||  | |  | |     
TCAATGGAGGAAATATGGTCAGAAGGTCACTAGGGATAACCCTTCTCCTAGGGCTTACTTCAGGTGCTCCTCTGCCCCAAGTTGCCCCGTGAAAAAGAAGgtaa-----attttcataatttgatttagcaccatcaataaagattacagagataaaatatgtttttcattccacttttcgattaaagttg-attttgatttctat-----

upper sequence: LOC_Os02g08440.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA13G44730.1 (Glycine max), 5'ss of exon 4
CCAATGGAGGAAGTATGGTCAGAAGGTCACCAAGGACAACCCCTGCCCAAGAGCCTACTTCAGATGCTCATTTGCTCCCGCCTGCCCTGTCAAGAAGAAGgtaacttaaattcctctaactaattccaaagtgatttcgtaagttttgctaaatttagtg--caaattcgagcctgtttctgaactttgttcgtggttcaaatgttgtttcag
 ||||||||||| ||||| || ||||| |||| ||| ||||| |  |||||||| || ||||  ||||| ||||||||   |||||| ||||| |||||||||| |  ||       | ||||||   || |        ||  |   |||| || |||      ||   || ||   |   || | || | ||  ||||| | ||  ||   
TCAATGGAGGAAATATGGACAAAAGGTGACCAGGGATAACCCTTCTCCAAGAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCGGTCAAAAAGAAGgtaaatctaac------agctaattaagaactaggcattcaaactccactaa-ttaagtaactggatcacaggctaagtt--aattgtgcttgttattcaa-tattcattag-

upper sequence: LOC_Os02g08440.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA07G02630.1 (Glycine max), 5'ss of exon 4
CCAATGGAGGAAGTATGGTCAGAAGGTCACCAAGGACAACCCCTGCCCAAGAGCCTACTTCAGATGCTCATTTGCTCCCGCCTGCCCTGTCAAGAAGAAGgtaact---taaattc-------ctctaactaattcc---aaagtgatttcgtaagttttgctaaat-ttagtgcaaattcgagcctgtttctgaactttgttcgtggttcaaatgttgtttcag
|||||||||||| ||||| || ||||| ||||  || ||||| || || ||||| || ||||  ||||| ||||||||   |||||||||||| |||||||||| |   || | ||         ||||||| |  |    || || ||| ||  | ||    | || |||||    |   |   ||    || |  ||  || ||  ||    || |  |||||
CCAATGGAGGAAATATGGGCAAAAGGTGACCAGAGATAACCCTTGTCCTAGAGCATATTTCAAGTGCTCTTTTGCTCCTAGCTGCCCTGTCAAAAAGAAGgtaaatatatataatcaaccaagtgctaactagtaactaggaaatggtttggtttggttactcacatgttagtagggaaatggatctcaagctaagtttgttttgtttttggtttggttattcag

upper sequence: LOC_Os02g08440.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA08G23380.4 (Glycine max), 5'ss of exon 4
CCAATGGAGGAAGTATGGTCAGAAGGTCACCAAGGACAACCCCTGCCCAAGAGCCTACTTCAGATGCTCATTTGCTCCCGCCTGCCCTGTCAAGAAGAAGgtaacttaaattcctctaactaattccaaagtgatttcgtaagttttgctaaatttagtgcaaattcgagcctgtttctgaactttgttcgtggttcaaatgttgtttcag
|||||||||||| ||||| || ||||| ||||  || ||||| | ||| ||||| || ||||  ||||| ||||||||   |||||||||||| ||||||||||     ||   | |||| || | | || || ||| || |   ||   |  |||   |  || | || |              | ||  |  |||   || |  |||||
CCAATGGAGGAAATATGGACAAAAGGTGACCAGAGATAACCCTTACCCTAGAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCTGTCAAAAAGAAGgtaa-----atatatataaccaagtgctaactggtttggtta---ttcacatgtttgtagggaaatggatctcaagctaagttggttttgctttttcgtttggttattcag

upper sequence: LOC_Os02g08440.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA17G33890.1 (Glycine max), 5'ss of exon 3
CCAATGGAGGAAGTATGGTCAGAAGGTCACCAAGGACAACCCCTGCCCAAGAGCCTACTTCAGATGCTCATTTGCTCCCGCCTGCCCTGTCAAGAAGAAGgtaacttaaattcctctaactaattccaaagtgatttcgtaagttttgctaaatttagtgcaaattcgagcctgtttctgaactttgttcgtggttcaaatgttgtttcag
 ||||||||||| ||||||||||| ||||| | ||| ||||| |  || ||||| |||||||| ||||| ||||| ||   |||||| || || || ||||||   ||| ||    ||| |   |  |     || ||        |    | | ||     ||     |  | ||| ||     | |   |  || |||  |  |     
TCAATGGAGGAAATATGGTCAGAAAGTCACTAGGGATAACCCTTCTCCTAGAGCTTACTTCAGGTGCTCCTTTGCCCCAAGCTGCCCCGTGAAAAAAAAGgta-tataatttttcataatttgatttagctatatatcaccgtccataaagattataagaataaaatatgtttttttttg-----tttctatattttaaaaataat-----

upper sequence: LOC_Os02g08440.4 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv09s0018g00240.t01 (Vitis vinifera), 5'ss of exon 4
CCAATGGAGGAAGTATGGTCAGAAGGTCACCAAGGACAACCCCTGCCCAAGAGCCTACTTCAGATGCTCATTTGCTCCCGCCTGCCCTGTCAAGAAGAAGgtaa-cttaaattcctctaactaattccaaagtgatttcgtaagttttgctaaatttagtgcaaattcgagcctgtttctgaactttgttcgtggttcaaatgttgtttcag---------------------
||| |||||||| ||||| || ||||||||||  ||||||||||  || ||||||||||||| |||||| ||||||||   ||||||||||||||||||||| | | |||| |   | | |  |      | |  | |  | ||              || |  |||  |         |||  |||| |     ||| ||  |  |||| |                     
CCAGTGGAGGAAATATGGCCAAAAGGTCACCAGAGACAACCCCTCTCCGAGAGCCTACTTCAAATGCTCTTTTGCTCCTAGCTGCCCTGTCAAGAAGAAGgtgagcctaaacttgacaatcccacctgtgattcgtctttttaggaacttgtgtcaaggtccggattgaaattgtccattgagttttgcttagcattctaagctgttttctgcaatttgtttcctttcttcag

upper sequence: LOC_Os02g08440.4 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv04s0008g05760.t01 (Vitis vinifera), 5'ss of exon 4
CCAATGGAGGAAGTATGGTCAGAAGGTCACCAAGGACAACCCCTGCCCAAGAGCCTACTTCAGATGCTCATTTGCTCCCGCCTGCCCTGTCAAGAAGAAGgtaacttaaattcctctaactaattccaaagtgatttcgtaagttttgctaaatttagtgcaaattcgagcctgtttctgaactttgttcgtggttcaaatgttgtttcag
||||||||| |||||||| |||||||||||||  || ||||| |  || |||||||||||||  ||||| ||||| ||  ||||||||||||| ||||||||||        || |   |  |  ||   |   |||  | |  |     | |     || |  || | |      |  | ||||| ||     |||| ||   |      
CCAATGGAGAAAGTATGGGCAGAAGGTCACCAGAGATAACCCTTCTCCCAGAGCCTACTTCAAGTGCTCCTTTGCCCCAACCTGCCCTGTCAAAAAGAAGgtaaaactccccccccccccccacccctctggtgtttgtttacctagaaaataaaatttgtagttttgggatcaaat--ggactttattt---tttcatattcag------

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|87035375|gb|CI189997.1|CI189997
EST:     GAGCCTACTTCAGATGCTCATTTGCTCCCGCCTGCCCTGTCAAGAAGAAG                         GTTCAGAGAAGCCCGGAGGACAACACGATCCTCGTGGCGACGTACGAGGGG
genomic: GAGCCTACTTCAGATGCTCATTTGCTCCCGCCTGCCCTGTCAAGAAGAAGgtaacttaaa ... gttgtttcagGTTCAGAGAAGCGCGGAGGACAACACGATCCTCGTGGCGACGTACGAGGGG
EST: gi|29659288|gb|CB655563.1|CB655563
EST:     GAGCCTACTTCAGATGCTCATTTGCTCCCGCCTGCCCTGTCAAGAAGAAG                         GTTCAGAGAAGCGCGGAGGACAACACGATCCTCGTGGCGACGTACGAGGGG
genomic: GAGCCTACTTCAGATGCTCATTTGCTCCCGCCTGCCCTGTCAAGAAGAAGgtaacttaaa ... gttgtttcagGTTCAGAGAAGCGCGGAGGACAACACGATCCTCGTGGCGACGTACGAGGGG
EST: gi|11026156|gb|AU162757.1|AU162757
EST:     GAGCCTACTTCAGATGCTCATTTGCTCCCGCCTGCCCTGTCAAGAAGAAG                         GTTCAGAGAAGCGCGGAGGACAACACGATCCTCGTGGCGACGTACGAGGGG
genomic: GAGCCTACTTCAGATGCTCATTTGCTCCCGCCTGCCCTGTCAAGAAGAAGgtaacttaaa ... gttgtttcagGTTCAGAGAAGCGCGGAGGACAACACGATCCTCGTGGCGACGTACGAGGGG
EST: gi|38475576|gb|CF959709.1|CF959709
EST:     GAGCCTACTTCAGATGCTCATTTGCTCCCGCCTGCCCTGTCAAGAAGAAG                         GTTCAGAGAAGCGCGGAGGACAACACGATCCTCGTGGCGACGTACGAGGGG
genomic: GAGCCTACTTCAGATGCTCATTTGCTCCCGCCTGCCCTGTCAAGAAGAAGgtaacttaaa ... gttgtttcagGTTCAGAGAAGCGCGGAGGACAACACGATCCTCGTGGCGACGTACGAGGGG
EST: gi|29664850|gb|CB661125.1|CB661125
EST:     GAGCCTACTTCAGATGCTCATTTGCTCCCGCCTGCCCTGTCAAGAAGAAG                         GTTCAGAGAAGCGCGGAGGACAACACGATCCTCGTGGCGACGTACGAGGGG
genomic: GAGCCTACTTCAGATGCTCATTTGCTCCCGCCTGCCCTGTCAAGAAGAAGgtaacttaaa ... gttgtttcagGTTCAGAGAAGCGCGGAGGACAACACGATCCTCGTGGCGACGTACGAGGGG
EST: gi|29646048|gb|CB651055.1|CB651055
EST:     AGCCTACTTCAGATGCTCA-TTGCTTCCCGCCTGCCCTGTCAAGAAGAAG                         GTTCAGAGAAGCGCGGAGGACAACACGATCCTCGTGGCGACGTACGAGGGG
genomic: AGCCTACTTCAGATGCTCATTTGC-TCCCGCCTGCCCTGTCAAGAAGAAGgtaacttaaa ... gttgtttcagGTTCAGAGAAGCGCGGAGGACAACACGATCCTCGTGGCGACGTACGAGGGG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAATGGAGGAAGTATGGTCAGAAGGTCACCAAGGACAACCCCTGCCCAAGAGCCTACTTCAGATGCTCATTTGCTCCCGCCTGCCCTGTCAAGAAGAAGgtaacttaaattcctctaactaattccaaagtgatttcgtaagttttgctaaatttagtgcaaattcgagcctgtttctgaactttgttcgtggttcaaatgttgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG