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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcattgatctcactgcttctgcaaattataaacatgtgactgcacattctattcatttgctagaaatatgtatacatgatggtatatcaacaatatcgtattgtgcttaaagatgtactattttcttctattgaagttttggttatttctgacagGGAAGAGTTGAAAGTGTTTTCTACAGAAGTTGTTCGCTTTGGAAACCGCTGCAAGGATCCTCAGTGGCATAACTTGGATCGCTACTTTGACAA

Basic information

species Oryza sativa
transcript LOC_Os01g65330.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G046846_T01 (Zea mays), 3'ss of exon 3
gttagc-attgatctc--actgcttctgcaaattataaacatgtgactgcacattctattcatttgctagaaatatgtatacatgatggtatatcaacaatatcgtattgtgcttaaagatgtactattttcttctattgaagttttggttatttctgacagGGAAGAGTTGAAAGTGTTTTCTACAGAAGTTGTTCGCTTTGGAAACCGCTGCAAGGATCCTCAGTGGCATAACTTGGATCGCTACTTTGACAA
|||||  | | |||||  | |  || |  ||| |||||  || || ||| ||  | | || ||||  |  |  || | ||  |    | |||||  |  | ||    ||   |||     | ||   || |  |    |||||||||  ||   ||  |||||||||||||||||||||| |||||||||||||||||||||||||| || |||||||||||||||||||| |||||||| ||||||||||| ||
gttagtgaataatctctgattctttttataaactataacaat-tgtctgaaccatttgtttattttatttatcta-gcatcaacctggttatatagaagaaatgtacttcaacttgtttttatatgcttgtagttacctgaagtttttatttggtccaacagGGAAGAGTTGAAAGTGTTCTCTACAGAAGTTGTTCGCTTTGGAAATCGTTGCAAGGATCCTCAGTGGCACAACTTGGACCGCTACTTTGATAA

upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G148773_T02 (Zea mays), 3'ss of exon 2
gttagcattgatctcactgcttctgcaaattataaacatgtgactgcacattctattcatttgctagaaatatgtatacatgatggtatatcaacaatatcgtattgtgcttaaagatgtactattttcttctattgaagttttggttatttctgacagGGAAGAGTTGAAAGTGTTTTCTACAGAAGTTGTTCGCTTTGGAAACCGCTGCAAGGATCCTCAGTGGCATAACTTGGATCGCTACTTTGACAA
                                        || ||   |  | ||||| ||| | | |      |   |||| ||| ||  |  |||    |  |  | |||             |||    || ||||||||| |||   ||  |||||||||||||||||||||||||||||||||||||||||||||||||  | |||||||||||||||||||| || ||| | ||||||||||| ||
--------------------------------------cttgcct---cgatttattcctttcccaaacccggct---catg-tggaat-cctccaacgctgggtcttcctt-------------ttttggttactgaagtttttgtttggtccaacagGGAAGAGTTGAAAGTGTTTTCTACAGAAGTTGTTCGCTTTGGAAATTGTTGCAAGGATCCTCAGTGGCACAATTTGAACCGCTACTTTGATAA

upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA20G31400.1 (Glycine max), 3'ss of exon 5
gttagcattgatctcactgcttctgcaaattataaacatgtgactgcacattctattcatttgctagaaatatgtatacatgatggtatatcaacaatatcgtattgtgcttaaagatgt-actattttcttctattgaagttttggttatttctgacagGGAAGAGTTGAAAGTGTTTTCTACAGAAGTTGTTCGCTTTGGAAACCGCTGCAAGGATCCTCAGTGGCATAACTTGGATCGCTACTTTGACAA
                        | |  |||| | |   |   | ||   || | | | | ||        | |      ||   ||| |     |  |  || ||||||||||| | | ||||| || | | |||    | ||     | | | |||| |||||||||||| | ||||||   |||||||| || |||||||| || || || |||||||| ||||| ||| |||||||||| ||||| ||
------------------------gtaggttatcatcg-atattttcatgatcaacttagtagcattctccctttgatttggagcttattttcttcagctactaatgtgcttaaagttttcactatcttatgccatt----tcttatacttctttcacagAGAAGAGTTGAAAATATTTTCTGGTGAAGTTGTGCGTTTTGGAAATCGTTGTAAAGATCCTCAATGGCACAACCTGGATCGCTATTTTGAGAA

upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA05G33040.1 (Glycine max), 3'ss of exon 2
gttagcattgatctcactgcttctgcaaattataaacatgtgactgcacattctattcatttgctagaaatatgtatacatgatggtat-atcaacaa-tatcgtattgtgcttaaagat-gtactattttcttctat-tgaagttttggttatttctgacagGGAAGAGTTGAAAGTGTTTTCTACAGAAGTTGTTCGCTTTGGAAACCGCTGCAAGGATCCTCAGTGGCATAACTTGGATCGCTACTTTGACAA
                                |||   | |      | ||   ||||  |  | ||       | |   | |||   | | |||||| |||  || | | |    |  |  ||  ||  |   || | ||   ||||| ||  |  |  |||||| ||||||||||| ||||||   || ||  |||| |||||||| || |  ||||||||||||||||| |||||||| || |||||||| ||
-------------------------------gtaacactattgaattaaatcaaattc-ctaacaaggggggcttctgtttcatgacctgaccaacaactattttagtttaccaggactttataaaatgataaactttatgtgattttgatttatgtttccagGGATGAGTTGAAAGTCTTTTCTGATGAGGTAATTCGTTTTGGAAATCGTTCAAAGGATCCTCAGTGGCACAACTTGGACCGATACTTTGAGAA

upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G00670.1 (Glycine max), 3'ss of exon 2
gttagcattgatctcactgcttctgcaaattataaacatgtgactgcacattctattcatttgctagaaatatgtatacatgatggtatatcaacaatatcgtattgtgcttaaagatgtactattttcttctattgaagttttggttatttctgacagGGAAGAGTTGAAAGTGTTTTCTACAGAAGTTGTTCGCTTTGGAAACCGCTGCAAGGATCCTCAGTGGCATAACTTGGATCGCTACTTTGACAA
|| |  |||||  | | |       ||||||   ||| |  |   ||   |||| ||    |   |     |  | || |  ||  ||  | | || ||   |||        || |||    | | | |   |||    |||    | ||||   |||||| ||||||||||| ||||||   || ||  |||| |||||||| || |  ||||||||||||||||| |||||||| || |||||||| ||
gtaactattgaattaagt-------caaattcctaac-taggggggc---ttctgttt-cataacaaggccaactttaaactattttagtttaccactactttat--------aaaatgctaaactgtgtgtgattatgattta---tgtttc---cagGGATGAGTTGAAAGTCTTTTCTGATGAGGTAATTCGTTTTGGAAATCGTTCAAAGGATCCTCAGTGGCACAACTTGGACCGATACTTTGAGAA

upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 2
gttagcattgatctcactgcttctgcaaattataaacatgtgactgcacattctat-tcatttgctagaaatatgtatacatgatggt-atatcaacaatatcgtattgtgcttaaagatgtactattttcttctattgaagttttggttatttctgacagGGAAGAGTTGAAAGTGTTTTCTACAGAAGTTGTTCGCTTTGGAAACCGCTGCAAGGATCCTCAGTGGCATAACTTGGATCGCTACTTTGACAA
                       || | | |  ||     | | |||      ||| ||||||| ||      |   |   |  |||| || |   ||||    | || | || |||  || | |  |  ||||        ||||    | || || |||||||||  ||||| | ||||||  |||||| || || ||||| || || || || |||||||||||||| |||||||| || |||||||| ||
----------------------gtgaatactgaaacagaataattgctttgattatatcatttgttaatgggctcattttttcctggttatttttccaat----tgttattct-aaaagtgaaatggtcacttc-------atttt--ccaattatggcagGGAAGAACTGAAAATTTTTTCTGGAGAAGTGGTCCGTTTTGGGAATCGATGTAAAGATCCTCAGTGGCACAACTTGGACCGTTACTTTGAGAA

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|33799472|gb|CF325594.1|CF325594
EST:     ATATCGAAAGATATGGATGAATTACTAAAGATATCTGCTGCTGACAAAAG                         GGAAGAGTTGAAAGTGTTTTCTACAGAAGTTGTTCGCTTTGGAAACCGCTG
genomic: ATATCGAAAGATATGGATGAATTACTAAAGATATATGCTGCTGACAAAAGgttagcattg ... tttctgacagGGAAGAGTTGAAAGTGTTTTCTACAGAAGTTGTTCGCTTTGGAAACCGCTG
EST: gi|33798150|gb|CF324934.1|CF324934
EST:     ATATCGAAAGATATGGATGAATTACTAAAGATATCTGCTGCTGACAAAAG                         GGAAGAGTTGAAAGTGTTTTCTACAGAAGTTGTTCGCTTTGGAAACCGCTG
genomic: ATATCGAAAGATATGGATGAATTACTAAAGATATATGCTGCTGACAAAAGgttagcattg ... tttctgacagGGAAGAGTTGAAAGTGTTTTCTACAGAAGTTGTTCGCTTTGGAAACCGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgcttaaagatgtactattttcttctattgaagttttggttatttctgacagGGAAGAGTTGAAAGTGTTTTCTACAGAAGTTGTTCGCTTTGGAAACCGCTGCAAGGATCCTCAGTGGCATAACTTGGATCGCTACTTTGACAA
                                          ttatttct  CT-rich tract
                  tattttcttctatt  TA-rich tract