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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taggacattttgcacataatatgaaaatcatcacggcaataataacaagttgacgatttttcctcaaaaaagttaacgattgatccatcttctttttcagATATACTCTGAAATGATTGGTAATGTTATGACTGATGCACGCTCAACCGGGAAGTACTACCACT

Basic information

species Oryza sativa
transcript LOC_Os06g13810.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 6
---------------------------------------------------------------------------------------taggacattttgcacataatatgaaaatca--tcacggcaataataacaagttgac--gatttttcctcaaaaaagt-taacgattgatccatcttctttttcagATATACTCTGAAATGATTGGTAATGTTATGACTGATGCACGCTCAACCGGGAAGTACTACCACT
                                                                                        |   |   | |  |||  | | ||  | |  | | |||| |    |||  |  |   ||     | |||  ||  | | | ||   |   ||| | |||||||||||||||||||||||||||| |||||||||||||||||  | || || || || ||||||||||
gtatctaattcttgattgttgactatgtatgaagtctcagtctaggtttttaattagctacaatggtgatgggctaattgctcaccgcacacctgctcgagcattctttcaatttgaaattaaggcattctacacagatgcatttgaaaacccatcatgaatatatcatgac-aaggaatcatatttttcagATATACTCTGAAATGATTGGCAATGTTATGACTGATGCGAGATCCACTGGAAAATACTACCACT

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 6
taggacattttgcacataatatgaaaatcatcacggcaataataacaagttgacgatttttcctcaaaaaagttaacgattgatccatcttcttttt---------cagATATACTCTGAAATGATTGGTAATGTTATGACTGATGCACGCTCAACCGGGAAGTACTACCACT
        ||   | ||  ||| | ||| || ||     || |   |  |  | | |   |  | | |  | || || |||   |  | ||  | ||         |||||||| |||||||||||||| ||||||||||  ||||| || ||||| || || || ||||| |
-------attgctaaatgttat-ataatgat-acccttttagttttacatacatggtgcatgattacatgacttgactattttcctctttttatgttaatgtgatgcagATATATTCTGAAATGATTGGAAATGTTATGATAGATGCCCGATCAACTGGAAAATATTACCATT

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 6
taggacattttgcacataatatgaaaatcatcacggcaataataacaagttg-acgatttttcctcaaaaaagttaacgattgatccatcttcttt--ttcagATATACTCTGAAATGATTGGTAATGTTATGACTGATGCACGCTCAACCGGGAAGTACTACCACT
 |     ||||||| ||  | |  | | | |    |   ||   ||| | || | ||||      |   |  |||  |   || |     |  | |  | |||||||| |||||||||||||| ||||||||||  ||||| || ||||| || || || ||||| |
-atttagttttgcatat--tttctatacccttttagttttagatacatggtgcatgattacatgacttgattgttttcctatgtttatgttaatgtaatgcagATATATTCTGAAATGATTGGAAATGTTATGATAGATGCCCGATCAACTGGAAAATATTACCATT

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 6
taggacattttgcacataatatgaaaatcatcacggcaataata-acaagttgacgatttttcctcaaaaaagttaacgattgatccatcttctttttcagATATACTCTGAAATGATTGGTAATGTTATGACTGATGCACGCTCAACCGGGAAGTACTACCACT
                      | || | |       | | ||  | || ||     | |||    | || |  |  |  ||  |   | |     |  |||||||||| ||||||||||| ||||||||||  ||||| || || || || || ||||| ||||
----------------------gtaagtaactttaaaatttatgcataacttagttgtctttttatagaagaccttccattttgtgattatatacatgtagATATACTCAGAAATGATTGGAAATGTTATGATCGATGCGCGTTCCACGGGAAAATACTATCACT

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|58598594|gb|CK009122.1|CK009122
EST:     TGAAATGCAAGGAGGTTCCA-CACGCTTTGGGTTTGACACTGCTTGCAAG                         ATATACTCTGAAATGAT
genomic: TGAAATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCTTGCAAGgtatcaggtt ... tctttttcagATATACTCTGAAATGAT
EST: gi|29689204|gb|CB685479.1|CB685479
EST:     CAACAAGCTTTGGGTTTGACACTGCTTGCAAG                         ATATACTCTGAAATGATTGGTAATGTTATGACTGATGCACGCTCAACCGGG
genomic: CAACAAGCTTTGGGTTTGACACTGCTTGCAAGgtatcaggtt ... tctttttcagATATACTCTGAAATGATTGGTAATGTTATGACTGATGCACGCTCAACCGGG
EST: gi|218497540|gb|FG953486.1|FG953486
EST:     TGAAATGCGAGGAGGTTCCAACAAGCTTTGGGTTAGACACTGCTTGCAAG                         ATATACTCTGAAATGATTGGTAATGTAATGACTGATGCACGCTCA
genomic: TGAAATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCTTGCAAGgtatcaggtt ... tctttttcagATATACTCTGAAATGATTGGTAATGTTATGACTGATGCACGCTCA
EST: gi|58657805|gb|CK046485.1|CK046485
EST:     AATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCTTGCAAG                         ATATACTCTGAAATGATTGGTAATGTTATGACTGATGCACGCTCAACCGGG
genomic: AATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCTTGCAAGgtatcaggtt ... tctttttcagATATACTCTGAAATGATTGGTAATGTTATGACTGATGCACGCTCAACCGGG
EST: gi|58675628|gb|CK064315.1|CK064315
EST:     TGAAATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCTTGCAAG                         ATATACTCTGAAATGATTGGTAATGTTATGACTGATGCACGCTCAACCGGG
genomic: TGAAATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCTTGCAAGgtatcaggtt ... tctttttcagATATACTCTGAAATGATTGGTAATGTTATGACTGATGCACGCTCAACCGGG
EST: gi|33796706|gb|CF324221.1|CF324221
EST:     TGAAATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCTTGCAAG                         ATATACTCTGAAATGATTGGTAATGTTATGACTGATGCACGCTCAACCGGG
genomic: TGAAATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCTTGCAAGgtatcaggtt ... tctttttcagATATACTCTGAAATGATTGGTAATGTTATGACTGATGCACGCTCAACCGGG
EST: gi|5003496|gb|AU068645.1|AU068645
EST:     TGAAATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCTTGCAAG                         ATATACTCTGAAATGATTGGTAATGTTATGACTGATGCACGCTCAACCGGG
genomic: TGAAATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCTTGCAAGgtatcaggtt ... tctttttcagATATACTCTGAAATGATTGGTAATGTTATGACTGATGCACGCTCAACCGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagttgacgatttttcctcaaaaaagttaacgattgatccatcttctttttcagATATACTCTGAAATGATTGGTAATGTTATGACTGATGCACGCTCAACCGGGAAGTACTACCACT
                                      tccatcttctttttc  CT-rich tract
                    aaaaaagttaa  TA-rich tract