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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actcatctttaaaattggaaagcctctggtgaaggaagattttgtaactgattatgactgaagagcaatgatatactaattgaccaatgttgatttttagGTCCTTGTGCGGAATATACCGCCTGATCCTGATGAATCAATTGGTGAGCTTGTGGAACATTTCTTCCTTGTAAACCATCCTGACCATTATCTTACGCACC

Basic information

species Oryza sativa
transcript LOC_Os01g35050.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G021194_T01 (Zea mays), 3'ss of exon 4
----------------------------------------------------------------------------------------actcatctttaaaattggaaag-----cctctggtgaaggaagattttgtaactgattatgactgaagagcaatgatatactaa------ttgaccaatgttgat-ttttagGTCCTTGTGCGGAATATACCGCCTGATCCTGATGAATCAATTGGTGAGCTTGTGGAACATTTCTTCCTTGTAAACCATCCTGACCATTATCTTACGCACC
                                                                                        ||  |  |||  |   |  ||       || |  |     ||  |  |  |   |||| ||     |  |  ||||  | ||        ||   ||||| | || ||||||||||||||||||||||||||||||||||| |||||||||||| |||||||||||||||||||||| ||||| || |||||||  || ||||| || || |
gtatgactaacctatgattgagttatgccttgaacacatagtgctatccagatacttaaagttgaaatttgtactgttactgcatttcacatagattttgaggcgagaacacgtttcttttttcccctaaactgatcaagtggattttgttgttatgggtatgacttgctgtatgcgcttactcaatgattatattttagGTCCTTGTGCGGAATATACCGCCTGATCCAGATGAATCAATTAGTGAGCTTGTGGAACATTTCTTTCTTGTGAATCATCCTGGTCACTATCTGACACATC

upper sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G163334_T01 (Zea mays), 3'ss of exon 3
----------------------------------------------------------------------------------------actcatctttaaaattggaaag-----cctctggtgaaggaagattttgtaactgattatgactgaagagcaa--tgatatactaattgac-caatgttgat-ttttagGTCCTTGTGCGGAATATACCGCCTGATCCTGATGAATCAATTGGTGAGCTTGTGGAACATTTCTTCCTTGTAAACCATCCTGACCATTATCTTACGCACC
                                                                                        ||  |  |||  |   |  ||       || |  |     ||  |  |  |   |||| ||      |    |  || | ||     | || ||||| | || ||||||||||||||||||||||||||||||||||| |||||||||||| |||||||||||||||||||||| ||||| || |||||||  || ||||| || || |
gtatgactaacctatgattgagttatgccttgaacacatagtgctatccagacacttaaagttgaaatttgtactgttactgcatttcacatagattttgaggcgagaacacgtttcttttttcccctaaactgatcaagtggattttgttatgggtatgacttgttgtatgcgcttactcaatgattatattttagGTCCTTGTGCGGAATATACCGCCTGATCCAGATGAATCAATTAGTGAGCTTGTGGAACATTTCTTTCTTGTGAATCATCCTGGTCACTATCTGACACATC

upper sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G43910.2 (Glycine max), 3'ss of exon 4
actcatctttaaaattggaaagcctctggtgaaggaagattttgtaactgattatgactgaagagcaatgata--tactaattgac-caatgttgattttt--agGTCCTTGTGCGGAATATACCGCCTGATCCTGATGAATCAATTGGTGAGCTTGTGGAACATTTCTTCCTTGTAAACCATCCTGACCATTATCTTACGCACC
    | |||   |  |  |||   | | | | |  ||  |||   ||   | | |  ||   |       ||   | ||  || |  |||| |  |||| |  |||| |||||  | ||| |||| |||||||||||||||||  |  ||||||| ||||||||||||||  | || || ||||| || || ||||| || || |
----accttcctacctttaaaaa-tatagaggaaaaacttttgacaataaactttatcttgtgtttccccatgcttgctccttcatgcaatttacatttgtgcagGTACTTGTTAGAAATGTACCACCTGATCCTGATGAATCGGTCAGTGAGCTAGTGGAACATTTCTTTTTGGTCAATCATCCAGATCACTATCTCACTCAGC

upper sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G11960.1 (Arabidopsis thaliana), 3'ss of exon 4
actcatctttaaaattggaaagcctctggtgaaggaagattttgtaactgattatgactgaagagcaatgatatactaattgaccaatgttgatttttagGTCCTTGTGCGGAATATACCGCCTGATCCTGATGAATCAATTGGTGAGCTTGTGGAACATTTCTTCCTTGTAAACCATCCTGACCATTATCTTACGCACC
                            || ||| ||   | ||| |    || ||  |   ||     ||       | ||| | |  |   ||   ||||  | ||  ||||  ||||  | || || ||||| || ||| ||||   ||||||||||||||| || || |||||||| ||||||||||||||||| |
----------------------------gtaaagcaattatatgtgatcagttttgtttcttgatgttagaaccttggactgagccagttactttcccagGTTTTGGTTAGGAACGTACCAGCGGACCCAGATGAGTCCATTAGTGACAGTGTGGAACATTTCTTTCTAGTTAACCATCCGGACCATTATCTTACGCATC

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|58609230|gb|CK037263.1|CK037263
EST:     TGCGTCTGCGCTTTCTTGCATCAGAGAAGCGCCGCCCAGATCAGTTCACG                         GTCCTTGTGCGGAATATACCGCCTGATCCTGATGAATCAATTGGTGAGCTT
genomic: TGCGTCTGCGCTTTCTTGCATCAGAGAAGCGCCGCCCAGATCAGTTCACGgtatgatctt ... tgatttttagGTCCTTGTGCGGAATATACCGCCTGATCCTGATGAATCAATTGGTGAGCTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactgattatgactgaagagcaatgatatactaattgaccaatgttgatttttagGTCCTTGTGCGGAATATACCGCCTGATCCTGATGAATCAATTGGTGAGCTTGTGGAACATTTCTTCCTTGTAAACCATCCTGACCATTATCTTACGCACC
                                                ttttt  CT-rich tract
                     aatgatatactaatt  TA-rich tract