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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatctgtgtttgggtttaactagacttggttggataaataacttgtccttttgttcacagtaattcctcactgttattgtttttgtacattatcacttctcacactcttccataacgcaaattctgtttctatttttcagAGATTAAACTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAACCATATCCTCGTGGAGAAATCTGTGTTAGGGGACCTACGATATTCTGTGG

Basic information

species Oryza sativa
transcript LOC_Os12g04990.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 7
gtaagatctgtgtttgggtttaactagacttggttggataaataacttgtccttttgttcacagtaattcctcactgttattgtttttgtacattatcacttctcacactcttccataacgcaaattct---gtttctatttttcagAGATTAAACTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAACCATATCCTCGTGGAGAAATCTGTGTTAGGGGACCTACGATATTCTGTGG
                                       ||  || |        | | || | |||||      ||   ||||  || |  |||||         |||  || | ||| |   ||  |   ||||| ||||| ||||| | ||||| ||||||||||||||||||||||| || ||||| ||| |||| ||||||||||||||||| |||||||| |||||||  ||||||   ||
---------------------------------------aatcaaatgacatccatatccaaaataattgggtg-tgcctttgtgcttttgtattattgt------cacagtttcgtaatgtggatctttgtgtttccatttt-cagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGG

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 16
gtaagatctgtgtttgggtttaactagacttggttggataaataacttgtccttttgttcacagtaattcctcactgttattgtttttgtacattatcacttctcacactcttcca--taacgcaaa---ttctgtttctatttttcagAGATTAAACTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAACCATATCCTCGTGGAGAAATCTGTGTTAGGGGACCTACGATATTCTGTGG
                                                 ||||||| |  | || | ||      ||  ||| | |||      | |||  | |  |  | ||     ||  || ||   || ||||  | | |||||||||| |||||||||||||| ||||||||||| || || ||||| ||| | ||  |||| ||||| ||||| ||||| ||||| ||     | ||  | ||
------------------------------------------------ctccttttatgaa-agaatttaaaagatgaaattatgtttaatttatgtcagctgtagctttgttatgcctagtgccaacagttttgttcttttgtttcagAGATAAAACTAGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCCTTGTTTTTCGAGG

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 16
gtaagatctgtgtttgggtttaactagacttggttggataaataacttgtccttttgttcacagtaattcctcactgttattgtttttgtacattatcacttctcacactcttcca--taacgcaaa---ttctgtttctatttttcagAGATTAAACTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAACCATATCCTCGTGGAGAAATCTGTGTTAGGGGACCTACGATATTCTGTGG
                                                   |||||  |   || | ||      ||   || | |||      | |||  | |  |  ||||     ||  || ||   || ||||  | | |||||||||| ||||| |||||||| ||||||||||| || || ||||| ||| | ||  |||| ||||| ||||| ||||| ||||| || |   | ||  | ||
-------------------------------------------------cactttttatggaagaatttaaaagatgaagttatatttaatttatgtcatctgtagctttcttatgcctagtgccaagagttttgttcttttgtttcagAGATAAAACTTGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCATTGTTTTTCGGGG

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 15
lower sequence: AT5G27600.1 (Arabidopsis thaliana), 3'ss of exon 16
gtaagatctgtgtttgggtttaactagacttggttggataaataacttgtccttttgttcacagta-attcctcactgttattgtttttgtacatta-tcacttctcacactcttccataacgcaaattctgtttctatttttcagAGATTAAACTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAACCATATCCTCGTGGAGAAATCTGTGTTAGGGGACCTACGATATTCTGTGG
                                      |||  ||  |||  ||||    |||||  ||   |||   |      |||||||    | |    |  |    | ||   |   | ||||  | |||||  || | |||| | ||||| |||||||| || |||||||||||||| || || ||| ||||||| || ||||| ||||||||||| || ||||| |  || |||   ||
-------------------------------------gtaagcaatgtgttattttaaagacagtgtatatatcagaatccaaacttttgtatccaaattgtatgactggtttttgtgttttgaaaatgttttttct--ttcttagAGGTAAAACTTGTGGATGTTCCCGAAATGAATTACACATCAGACGATCAACCATACCCACGTGGTGAAATCTGTGTAAGAGGACCAATCATCTTCAAAGG

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 15
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 16
gtaagatctgtgtttgggtttaactagacttggttggataaataacttgtccttttgttcacagtaattcctcactgttattgt--ttttgtac--attatcacttctcacactcttccataacgcaaattctgtttctatttttcagAGATTAAACTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAACCATATCCTCGTGGAGAAATCTGTGTTAGGGGACCTACGATATTCTGTGG
                                              |   | ||||  | ||  |      | |    ||  ||  ||| | ||  | |||| | | | | | |  |     |   ||  |   ||||||| |||||||  | || || |||||||||||||||||||| || || || | |||| | ||  |||| ||||| ||||| ||||||||||| ||||  || ||    ||
---------------------------------------------gtgagctttttactgactctgcgatatgataagtagagtaatttggaactaaatatc-cattttaaattgctttgggatttaatatgcatttctatatttcagAAGTAAAGCTTGTGGATGTCCCAGAAATGAACTATACATCAGCGGATCAGCCCCATCCCCGTGGCGAAATATGTGTTAGGGGTCCTATCATTTTTACAGG

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv14s0128g00720.t01 (Vitis vinifera), 3'ss of exon 16
gtaagatctgtgtttgggtttaactagacttggttggataaataacttgtccttttgttcacagtaattcctcactgttattgtttttgtacattatcacttctcacactcttccataacgcaaattctgtttctatttttcagAGATTAAACTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAACCATATCCTCGTGGAGAAATCTGTGTTAGGGGACCTACGATATTCTGTGG
                                        |||  |  |   | ||    | | |  |   ||||   || ||   |  | || |   | || |     |  |   |    |     || || ||   ||||||| || || || |||||||| || |||||||||||||||||||||||| | || |||||||| || ||||| ||||| ||||| ||     | |||   ||
---------------------------------------taattgccggatgtctttaagaaaatggtat-tcacaactaatgaactaattcactg--agttgtgtggattctggttgctccctgcccttttcct--ctttcagAAATAAAGCTTGTGGATGTTCCTGAAATGAATTACACCTCTGAGGATCAGCCCTATCCTCGCGGTGAAATATGTGTCAGGGGTCCCGTTCTCTTCCAAGG

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 16
gtaagatctgtgtttgggtttaactagacttggttggataaataacttgtc-cttttgttcacagtaattc-ctcactgttattgtttttgtacattatcacttctcacactcttccataacgcaaattctgtttctatttttcagAGATTAAACTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAACCATATCCTCGTGGAGAAATCTGTGTTAGGGGACCTACGATATTCTGTGG
                                     | ||  ||  |||  ||  ||   |||  ||||  ||  |  || | || | ||     | |   ||   | |   ||     | |  |||| |||     | |||||||  | || || |||||||| || |||||||| ||||| ||||||||| | || ||||||||||| |||||||||||| |||| || |   | ||    ||
------------------------------------aacaagaaaaatgtggctcctgagtacaacaattttctttccattgtggtctgtgc-tgctctattttgggataaattt-----atgttaatt-tgtcc---tctttcagAAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGCCCTATCCTCGTGGTGAAATCTGTGTTCGGGGTCCCATTCTTTTTCTAGG

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|568356|gb|D39204.1|D39204
EST:     TATTGGTGATAGGTTAATTGGTCATGTCGGATCTCCAAATCCATCTTGTG                         AGATTAAACTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAAC
genomic: TATTGGTGATAGGTTAATTGGTCATGTCGGATCTCCAAATCCATCTTGTGgtaagatctg ... tatttttcagAGATTAAACTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAAC
EST: gi|58602340|gb|CK012868.1|CK012868
EST:     TATTGGTGATAGGTTAATTGGTCATGTCGGATCTCCAAATCCATCTTGTG                         AGATTAAACTAATGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAAC
genomic: TATTGGTGATAGGTTAATTGGTCATGTCGGATCTCCAAATCCATCTTGTGgtaagatctg ... tatttttcagAGATTAAACTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAAC
EST: gi|58693358|gb|CK082045.1|CK082045
EST:     TATTGGTGATAGGTTAATTGGTCATGTCGGATCTCCAAATCCATCTTGTG                         AGATTAAACTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAAC
genomic: TATTGGTGATAGGTTAATTGGTCATGTCGGATCTCCAAATCCATCTTGTGgtaagatctg ... tatttttcagAGATTAAACTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAAC
EST: gi|58659745|gb|CK048425.1|CK048425
EST:     TATTGGTGATAGGTTAATTGGTCATGTCGGATCTCCAAATCCATCTTGTG                         AGATTAAACTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAAC
genomic: TATTGGTGATAGGTTAATTGGTCATGTCGGATCTCCAAATCCATCTTGTGgtaagatctg ... tatttttcagAGATTAAACTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAAC
EST: gi|313081138|gb|HO213724.1|HO213724
EST:     TATTGGTGATAGGTTAATTGGTCATGTCGGATCTCCAAATCCATCTTGTG                         AGATTAAACTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAAC
genomic: TATTGGTGATAGGTTAATTGGTCATGTCGGATCTCCAAATCCATCTTGTGgtaagatctg ... tatttttcagAGATTAAACTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacattatcacttctcacactcttccataacgcaaattctgtttctatttttcagAGATTAAACTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAACCATATCCTCGTGGAGAAATCTGTGTTAGGGGACCTACGATATTCTGTGG
                                    ttctgtttctattttt  CT-rich tract
                                         tttctattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatctgtgtttgggtttaactagacttggttggataaataacttgtccttttgttcacagtaattcctcactgttattgtttttgtacattatcacttctcacactcttccataacgcaaattctgtttctatttttcagAGATTAAACTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAACCATATCCTCGTGGAGAAATCTGTGTTAGGGGACCTACGATATTCTGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA