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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agctagtctcatcaatgcatatttgattcattgcatgtagaaagggcatcactgctatagacaattgattctttatgacattggtgttttgcttttgcagCAACACTTGGACAGATTTTATCTAATCATGCATTGAAGCCCAGAGTATATATTGGATGCATGAAATCTGGACCTGTCCTAACTGAGAA

Basic information

species Oryza sativa
transcript LOC_Os02g06840.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G132866_T02 (Zea mays), 3'ss of exon 6
------agctagtctcatcaatgcatatttgattcattgcatgtagaa-agggcatcact-gctatagacaattgattctttatgacattggtgttttgcttttgcagCAACACTTGGACAGATTTTATCTAATCATGCATTGAAGCCCAGAGTATATATTGGATGCATGAAATCTGGACCTGTCCTAACTGAGAA
      | ||||    |  |    || | ||| ||  |||||  | || ||   || |   ||| | |  ||   | |       ||      |||  || ||||||||||| || ||||||||| | || || |||||||||||||| ||||| || || |||||||||||||||||||||||| || | || ||
ttaaaaaactagaagtacaagctgatgtgtgaatc--tgcataaaaaatagcatatgataagctctggcaaagcaact------aacgccaaagttcggcatttgcagCAACGCTCGGACAGATTCTGTCGAAACATGCATTGAAGCCGAGAGTGTACATCGGATGCATGAAATCTGGACCTGTCTTATCCGAAAA

upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA06G46230.1 (Glycine max), 3'ss of exon 7
--------------------------------------------------------------------------------------------agctagtctcatcaatgcatatttgattcat-tgcatgtagaaaggg--catcactgctatagacaattgattctttatgacattggtgttttgctt---ttgcagCAACACTTGGACAGATTTTATCTAATCATGCATTGAAGCCCAGAGTATATATTGGATGCATGAAATCTGGACCTGTCCTAACTGAGAA
                                                                                              |||     |  ||     ||  | || || |   | ||| |||    ||| |      |  |  ||  | | ||| |   | ||   | ||  ||   || |||||||||| ||||| | | ||  ||  |||  ||  || ||  |  |||| |||||||||||||||||||| ||||||||| |  | ||
gtattaatagttctaaagtttctgataatctcttactttattatgtatcaaggcatgagttttattgtaaacctcctgacactgtcttcgattcctaagtgtaaaaaaaagcatgagttttatgtttctatagtaagtaatcatgatgttgttttagtatgtactttttgtcttagtgtcatattctttcggtttcagCAACACTGGGACAAACTCTAGTTAGGCATCGATCAAAACCACGGATATACATTGGATGCATGAAATCTGGGCCTGTCCTATCCCAAAA

upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA12G10520.1 (Glycine max), 3'ss of exon 7
-------------------agctagtctc------atcaatgcata--tttgat----tcattgcatgtagaaagggcatcactgctatagacaattgattctttatgacattggtgttttgcttttgcagCAACACTTGGACAGATTTTATCTAATCATGCATTGAAGCCCAGAGTATATATTGGATGCATGAAATCTGGACCTGTCCTAACTGAGAA
                    | || ||||      || || ||||   ||| ||      || | |  ||   | |   |   |   |||   | |   ||  |  |  ||||    | || || || |||||||||| ||| | | | ||  ||  |||  ||  || ||  |  |||| |||||||||||||||||||| ||||||||| |  | ||
gtattaatagtaaagtttctgataatctcttatgtataaaagcatgagttttatgtttctatagtaaataaccatgatgttgttttaatatgtact--gtttgtcttagcattatattctttctgtttcagCAACACTGGGAGAAACTCTAGTTAGACATCGATCAAAACCACGGATATACATTGGATGCATGAAATCTGGGCCTGTCCTATCCCAAAA

upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 8
lower sequence: AT4G26940.1 (Arabidopsis thaliana), 3'ss of exon 7
----agctagtctcatcaatgcatatttgattcattgcatgtagaaagggcatcactgctatagacaattgattctttatgacattggtgttttgcttttgcagCAACACTTGGACAGATTTTATCTAATCATGCATTGAAGCCCAGAGTATATATTGGATGCATGAAATCTGGACCTGTCCTAACTGAGAA
    |  ||  ||| ||      ||| ||| |  ||   | |      | |||| |   | |   |  ||| |   || || ||| | | |||      |||||| || ||||||      ||| | |   |     |||||||| |||| || ||||| |||||||||||||||||||| ||  || ||||
gtgaatataaactc-tcttaaagtatctgaattgttttgtttctt---gtcatctcaagtttgtgcctttgctcacttctgtcatggatattt-----ctgcagCCACGCTTGGAGCAGAATTAGCAAGATACCGGATGAAGCCCCGAGTGTACATTGGTTGCATGAAATCTGGACCTGTTCTTGCTCAGAA

upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv19s0090g00560.t01 (Vitis vinifera), 3'ss of exon 7
agctagtctcatcaatgcatatttgattcattgc-atgtagaaa-gggcatcactgctatagacaattgattctttatgacattggtgttttgcttt--tgcagCAACACTTGGACAGATTTTATCTAATCATGCATTGAAGCCCAGAGTATATATTGGATGCATGAAATCTGGACCTGTCCTAACTGAGAA
    | ||| |    || |  | | ||   | || ||||||||| |      | |||| |     ||   ||   ||||   ||  | |||| | ||  |||||||||||| |||   | |||| | |  ||    |  || || ||  | || |||||||||||||||||||||||||| ||| || | ||
---gattcttactcttgaaagtatcatatgtggccatgtagaaatgaatgctattgct-tcctttatccttttcatatggggttcatcttttacattgctgcagCAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAA

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|29682551|gb|CB678826.1|CB678826
EST:     GGATGCAGACTTTTATGTGAAGGTTGATGATGACGTGCACGTAAACATAG                         CAACACTTGGCCAGATTTTATCTAATCATGCATTGAAGCCCAGAGTATATA
genomic: GGATGCAGACTTTTATGTGAAGGTTGATGATGACGTGCATGTAAACATAGgtaaatctcc ... gcttttgcagCAACACTTGGACAGATTTTATCTAATCATGCATTGAAGCCCAGAGTATATA
EST: gi|2799316|gb|AA752305.1|AA752305
EST:     GGATGCAGACTTTTATGTGAAGGTTGATGATGACGTGCATGTAAACATAG                         CAACACTTGGACAGATTTTATCCAACCATGCATTGAAGCCCAGAGTATATA
genomic: GGATGCAGACTTTTATGTGAAGGTTGATGATGACGTGCATGTAAACATAGgtaaatctcc ... gcttttgcagCAACACTTGGACAGATTTTATCTAATCATGCATTGAAGCCCAGAGTATATA
EST: gi|2799246|gb|AA753771.1|AA753771
EST:     GGATGCAGACTTTTATGTGAAGGTTGATGATGACGTGCATGTAAACATAG                         CAACACTTGGACAGATTTTATCCAACCATGCATTGAAGCCCAGAGTATATA
genomic: GGATGCAGACTTTTATGTGAAGGTTGATGATGACGTGCATGTAAACATAGgtaaatctcc ... gcttttgcagCAACACTTGGACAGATTTTATCTAATCATGCATTGAAGCCCAGAGTATATA
EST: gi|29657303|gb|CB653578.1|CB653578
EST:     GGATGCAGACTTTTATGTGAAGGTTGATGATGACGTGCATGTAAACATAG                         CAACACTTGGACAGATTTTATCTAATCATGCATTGAAGCCCAGAGTATATA
genomic: GGATGCAGACTTTTATGTGAAGGTTGATGATGACGTGCATGTAAACATAGgtaaatctcc ... gcttttgcagCAACACTTGGACAGATTTTATCTAATCATGCATTGAAGCCCAGAGTATATA
EST: gi|87006638|gb|CI295021.1|CI295021
EST:     GGATGCAGACTTTTATGTGAAGGTTGATGATGACGTGCATGTAAACATAG                         CAACACTTGGACAGATTTTATCTAATCATGCATTGAAGCCCAGAGTATATA
genomic: GGATGCAGACTTTTATGTGAAGGTTGATGATGACGTGCATGTAAACATAGgtaaatctcc ... gcttttgcagCAACACTTGGACAGATTTTATCTAATCATGCATTGAAGCCCAGAGTATATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatcactgctatagacaattgattctttatgacattggtgttttgcttttgcagCAACACTTGGACAGATTTTATCTAATCATGCATTGAAGCCCAGAGTATATATTGGATGCATGAAATCTGGACCTGTCCTAACTGAGAA
                 aattgat  putative branch site (score: 4)
                                         ttttgctttt  putative PPT
                 aattgattctttat  TA-rich tract