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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggctttctctttcctttttctattgtgtccattcaatttaacaaagtcagtttttgcctagtagtttctgtaaatatgtttggggccaacagatatcttccatgctgttcatcctcatccaatgaatgataaatagcataacatgtatgaaattatttatattatagaatgatcttattcacttagtggtaatgcagGAGTTGCTGGCTATTCAGCAACAGGGACCGCGGGCTATAGGTTTTTTTGGTACCCGTAACATGGGGTTTATGCATCAACAGCTTATTGAGATCCTGAGCT

Basic information

species Oryza sativa
transcript LOC_Os01g23680.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g23680.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G081653_T02 (Zea mays), 3'ss of exon 2
gtggctttctctttcctttttctattgtgtccattcaatttaacaaagtcagtttttgcctagtagtttctgtaaatatgtttggggccaacagatatcttccatgctgttcatcctcatccaatgaatgataaatagcata----acatgtatgaaattatttatattatagaatgatcttattcacttagtggtaatgcagGAGTTGCTGGCTATTCAGCAACAGGGACCGCGGGCTATAGGTTTTTTTGGTACCCGTAACATGGGGTTTATGCATCAACAGCTTATTGAGATCCTGAGCT
||   ||| |||   | |||| || ||      ||   ||||  |||     |||  |  || | |||  |  |||  | ||    |                || |  |      ||    |||||||| ||  ||||||     |  | |||||| | ||||||  |||  | ||  || ||| | || ||||| ||| ||||| |||||||||||||||| || ||||| || || |||||||| ||||| ||||| |||||||| |||||||| |||||||||||||||||||||||||
gtacttttttctgatcattttatactgaactgtttt--tttattaaa----atttaagtttaatggttctt--aaacct-ttcaaagttggtg--------tgatacaatcagaaatccaataatgaatgctacttagcatgtatgagctttatgaattgatttatcctatgaagtggactcatttattttgtggtcatgaagGAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGAACCCGCAACATGGGATTTATGCACCAACAGCTTATTGAGATCCTGAGCT

upper sequence: LOC_Os01g23680.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S134_28V6.1 (Physcomitrella patens), 3'ss of exon 2
gtggctttctctttcctttttctattgtgtccattcaatttaacaaagtcagtttttgcctagtagtttctgtaaatatgtttggggccaacagatatcttccatgctgttcatcctcatccaatgaatgataaatagcataacatgtatgaaattatttatattatagaatgat-cttattcacttagtggtaatgcagGAGTTGCTGGCTATTCAGCAACAGGGACCGCGGGCTATAGGTTTTTTTGGTACCCGTAACATGGGGTTTATGCATCAACAGCTTATTGAGATCCTGAGCT
                                                                                             ||   |||       |||||   |   | ||||| | ||   |     |  | || |    || ||| | |||| ||| ||| |  |    ||  |||||  | |||||| | || || ||||| ||  | |||||  |||||||||| |||||||| || || ||||||||||| ||||| || || || |||||||| || || |
---------------------------------------------------------------------------------------------gagggctttttcaaggttcaaatt---ctaatgacttatttgtgttgcactacgttttggcttgtttcttttat-gaacgatgcacacctgct--gtggtt-ttcagGAGCTTCTAGCAATTCAACAGAATGGACCAAGGGCTATAGGCTTTTTTGGAACTCGGAACATGGGGTTCATGCACCAGCAACTCATTGAGATTCTTAGTT

upper sequence: LOC_Os01g23680.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S323_60V6.1 (Physcomitrella patens), 3'ss of exon 2
gtggctttctctttcctttttctattgtgtccattcaatttaacaaagtcagtttttgcctagtagtttctgtaaatatgtttggggccaacagatatcttccatgctgttcatcctcatccaatgaatgataaatagcataacatgtatgaaattatttatattatagaatgatcttattcacttagtggtaatgcagGAGTTGCTGGCTATTCAGCAACAGGGACCGCGGGCTATAGGTTTTTTTGGTACCCGTAACATGGGGTTTATGCATCAACAGCTTATTGAGATCCTGAGCT
                                                                                                |  ||  |||  | |||      |        |  |     |||  || | | ||   || ||| | || |  |        |    ||  ||| |  | |||||| | || || ||||||||  | |||||  |||||||||| ||||||||||| || || |||||||| ||||| || || || |||||||| || || |
-----------------------------------------------------------------------------------------------aaggttttatgaagatcaagacttttagggtgtttgtgcgctgcactacgtatttggc-ttgtttct-ttgttaacaagctacagctgct--gtgttttttcagGAGCTTCTAGCCATTCAGCAGAATGGACCAAGGGCTATAGGGTTTTTTGGTACTCGGAATATGGGGTTCATGCACCAGCAACTCATTGAGATTCTTAGTT

upper sequence: LOC_Os01g23680.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ38716 (Selaginella moellendorffii), 3'ss of exon 1
gtggctttctctttcctttttctattgtgtccattcaatttaacaaagtcagtttttgcctagtagtttctgtaaatatgtttggggccaacagatatcttccatgctgttcatcctcatccaatgaatgataaatagcataacatgtatgaaattatttatattatagaa-tgatcttattcacttagtggtaatgcagGAGTTGCTGGCTATTCAGCAACAGGGACCGCGGGCTATAGGTTTTTTTGGTACCCGTAACATGGGGTTTATGCATCAACAGCTTATTGAGATCCTGAGCT
                                                                                                                       |    |    | |   | | |   | |||      || ||| | ||   | | |  |  | ||    |  |  |    |||||  | || || || || ||||| || ||  | ||||| || || || || || || |||||||| || ||||||||||||||||||||||| || || |
----------------------------------------------------------------------------------------------------------------------gtaagttcttagttctctcgaaactcttgttccttcttctttgtttttcgggagttcttatgtttttctcttcctttctcagGAACTTCTCGCGATCCAACAACAAGGGCCAAGAGCTATCGGCTTCTTCGGAACGCGAAACATGGGATTCATGCATCAACAGCTTATTGAGATACTTAGTT

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|29659908|gb|CB656183.1|CB656183
EST:     CGGTTGCTACTCCAGAGTATAAGTCGATTCCAGATCTAGATTACCTGCAG                         GAGTTGCTGGCTATTCAGCAACAGGGACCGCGGGCTATAGGNNNNNNNGGT
genomic: CGGTTGCTACTCCAGAGTATAAGTCGATTCCAGATCTAGATTACCTGCAGgtggctttct ... ggtaatgcagGAGTTGCTGGCTATTCAGCAACAGGGACCGCGGGCTATAGGTTTTTTTGGT
EST: gi|29658365|gb|CB654640.1|CB654640
EST:     CGGTTGCTACTCCAGAGTATAAGTCGATTCCAGATCTAGATTACCTGCAG                         GAGTTGCTGGCTATTCAGCAACAGGGACCGCGGGCTATAGGNNNNNNNGGT
genomic: CGGTTGCTACTCCAGAGTATAAGTCGATTCCAGATCTAGATTACCTGCAGgtggctttct ... ggtaatgcagGAGTTGCTGGCTATTCAGCAACAGGGACCGCGGGCTATAGGTTTTTTTGGT
EST: gi|163923267|gb|EG711076.1|EG711076
EST:     CGGTTGCTACTCCAGAGTATAAGTCGATTCCAGATCTAGATTACCTGCAG                         GAGTTGCTGGCTATTCAGCAACAGGGACCGCGGGCTATAGGNNNNNNNGGT
genomic: CGGTTGCTACTCCAGAGTATAAGTCGATTCCAGATCTAGATTACCTGCAGgtggctttct ... ggtaatgcagGAGTTGCTGGCTATTCAGCAACAGGGACCGCGGGCTATAGGTTTTTTTGGT
EST: gi|29657705|gb|CB653980.1|CB653980
EST:     CGGTTGCTACTCCAGAGTATAAGTCGATTCCAGATCTAGATTACCTGCAG                         GAGTTGCTGGCTATTCAGCAACAGGGACCGCGGGCTATAGGNNNNNNNGGT
genomic: CGGTTGCTACTCCAGAGTATAAGTCGATTCCAGATCTAGATTACCTGCAGgtggctttct ... ggtaatgcagGAGTTGCTGGCTATTCAGCAACAGGGACCGCGGGCTATAGGTTTTTTTGGT
EST: gi|29660019|gb|CB656294.1|CB656294
EST:     CGGTTGCTACTCCAGAGTATAAGTCGATTCCAGATCTAGATTACCTGCAG                         GAGTTGCTGGCTATTCAGCAACAGGGACCGCGGGCTATAGGNNNNNNNGGT
genomic: CGGTTGCTACTCCAGAGTATAAGTCGATTCCAGATCTAGATTACCTGCAGgtggctttct ... ggtaatgcagGAGTTGCTGGCTATTCAGCAACAGGGACCGCGGGCTATAGGTTTTTTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtatgaaattatttatattatagaatgatcttattcacttagtggtaatgcagGAGTTGCTGGCTATTCAGCAACAGGGACCGCGGGCTATAGGTTTTTTTGGTACCCGTAACATGGGGTTTATGCATCAACAGCTTATTGAGATCCTGAGCT
       aaattatttatattat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggctttctctttcctttttctattgtgtccattcaatttaacaaagtcagtttttgcctagtagtttctgtaaatatgtttggggccaacagatatcttccatgctgttcatcctcatccaatgaatgataaatagcataacatgtatgaaattatttatattatagaatgatcttattcacttagtggtaatgcagGAGTTGCTGGCTATTCAGCAACAGGGACCGCGGGCTATAGGTTTTTTTGGTACCCGTAACATGGGGTTTATGCATCAACAGCTTATTGAGATCCTGAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC