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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttgtttatactctcatgatctttttctgatttattcttatagaattcaattaattcctactaaattagttctgttttgtatgaaaagcactactgctaatacaaatgtagaaacaaactaatccaattgtgtcataggaagaggagcttacaggattttttttattccttgctgttacgttgcagTTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGTGGCCATCTCGTAAGATAAAGAAGGTAAACCGATCCCTAAAGAAGATCCA

Basic information

species Oryza sativa
transcript LOC_Os11g16290.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g16290.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G42160.1 (Glycine max), 3'ss of exon 6
gtaatttgtttatactctcatgatctttttctgatttattcttatagaattcaattaattcctactaaattagttctgttttgtatgaaaagcactactgctaatacaaatgtagaaacaaactaatccaattgtgtcataggaagaggagcttacaggattttttttattccttgctgttacgttgcagTTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGTGGCCATCTCGTAAGATAAAGAAGGTAAACCGATCCCTAAAGAAGATCCA
                                                                     | | ||   || |  |  |||     |      ||||    || |   |      ||| |  |||| | || |||| |  || |||     || ||   |    || ||  |  | | ||||||| || || || |||||||||||||||||||||||||||||  ||||||||||||| || ||||| || || || || |||||  | |||||||| ||
--------------------------------------------------------------------ttcaatttcattgtccaaaaaagatgtt-----caatatttctgaaagga------aattc--ttgt-taattggaaaa--agttta-----ttcttaacaaatgtttcttctttgat-cagTTTGCCCAACGACTCTGAAAAGGATATGCAGACAACATGGAATTCCAAGGTGGCCATCCCGCAAGATTAATAAAGTGAATCGATCATTGAAGAAGATACA

upper sequence: LOC_Os11g16290.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA11G13390.1 (Glycine max), 3'ss of exon 4
gtaatttgtttatactctcatgatctttttctgatttattcttatagaattcaattaattcctactaaattagttctgttttgtatgaaaagcactactgctaatacaaatgtagaaacaaactaatccaattgtgtcataggaagaggagcttacaggattttttttattccttgctgttacgttgcagTTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGTGGCCATCTCGTAAGATAAAGAAGGTAAACCGATCCCTAAAGAAGATCCA
                                                                         |    |||| | | |||   |  |    ||| |||  | |  ||   ||    || | ||       |  ||||     |||  |     ||   |  | || ||  |  |   ||||||| || || || || |||||||||||||||||||||||||| ||||| |||||||| || |||||||| || || || || ||  |||||||||| ||
-------------------------------------------------------------------------tatgattttatcttaaagttaagatg--taagacatttctgaaaggtaat---tctagtta------ataaagacagatttatcg-----ttaacaaacatttcttctttga-acagTTTGCCCAACAACTCTAAAAAGGATATGCAGACAACATGGAATTTCAAGATGGCCATCCCGAAAGATAAATAAAGTGAATCGTTCGTTAAAGAAGATACA

upper sequence: LOC_Os11g16290.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA12G05390.1 (Glycine max), 3'ss of exon 6
gtaatttgtttatactctcatgatctttttctgatttattcttatagaattcaattaattcctactaaattagttctgttttgtatgaaaagcactactgctaatacaaatgtagaaacaaactaatccaattgtgtcataggaagaggagcttacaggattttttttattccttgctgttacgttgcagTTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGTGGCCATCTCGTAAGATAAAGAAGGTAAACCGATCCCTAAAGAAGATCCA
                                                             |||  |  |||  |     || | | |||  || | |||  ||   || | |||     ||| ||  |   | |||| |            | |||    ||||||||||                ||||||| || || || || |||||||||||||| ||||||||||| ||||| |||||||| || |||||||| || || ||||| ||  | |||||||| ||
------------------------------------------------------------tctatgattttatcttaaagttatgttaaa--catttctga-aaggtaattctag---ttaacaaagacggatttgtcgt------------taacaaacatttttttatttga------------acagTTTGCCCAACAACTCTAAAAAGGATATGCAGGCAACATGGAATTTCAAGATGGCCATCCCGCAAGATAAATAAAGTGAACCGTTCTTTGAAGAAGATACA

upper sequence: LOC_Os11g16290.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G03220.1 (Glycine max), 3'ss of exon 7
gtaatttgtttatactctcatgatctttttctgatttattcttatagaattcaattaattcctactaaattagttctgttttgtatgaaaagcactactgctaatacaaatgtagaaacaaactaatccaattgtgtcataggaagaggagcttacaggattttttttattccttgctgttacgttgcagTTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGTGGCCATCTCGTAAGATAAAGAAGGTAAACCGATCCCTAAAGAAGATCCA
                                                                         | |  |||  |     ||  | ||     ||||    || |   | |  ||  |  |||||          | |  || |||     | ||    | | |||  | ||   |  ||||||| || || || ||||||||||||||||| |||||||||||  ||||||||||||| || ||||| || || || || |||||  | |||||||| ||
-------------------------------------------------------------------------tgcaatttcattgtccaaaaaatatgttcaatatttctgaaaggaaattcttgtt-aattg----------aaaaaagtttat----tcttgacaaatgcttcttctttgat--cagTTTGCCCAACAACTCTGAAAAGGATATGCAGGCAACATGGAATTCCAAGGTGGCCATCCCGCAAGATTAATAAAGTCAATCGATCATTGAAGAAGATACA

upper sequence: LOC_Os11g16290.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G59580.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaatttgtttatactctcatgatctttttctgatttattcttatagaattcaattaattcctactaaattagttctgttttgtatgaaaagcactactgctaatacaaatgtagaaacaaactaatccaattgtgtcataggaagaggagcttacaggattttttttattccttgctgttacgttgcagTTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGTGGCCATCTCGTAAGATAAAGAAGGTAAACCGATCCCTAAAGAAGATCCA
                                                                                     ||| ||  |||| | ||| ||    | |     |    |   |  |     | ||   ||  |  | |    |||| |||||   |  ||||| |     |||||||||||| ||||| || ||||||||||| |||||||| |||||    || ||||||||||| ||||| || || || ||  | || |||| ||| || ||
------------------------------------------------------------------------------------gtgagaa--actagtactagtagtgctcttt--gcttgtttcccttacaagattattc-aattgctgatccttggatgttttt--ctttttgctttctttctgcagTTTGTCCGACTACACTAAAAAGGATATGTAGACAACACGGAATTATGAGATGGCCATCTCGAAAGATTAACAAAGTGAATAGGTCACTAAGGAAAATACA

upper sequence: LOC_Os11g16290.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G43500.2 (Arabidopsis thaliana), 3'ss of exon 6
gtaatttgtttatactctcatgatctttttctgatttattcttatagaattcaattaattcctactaaattagttctgttttgtatgaaaagcactactgctaatacaaatgtagaaacaaactaatccaattgtgtcataggaagaggagcttacaggattttttttattc---cttgctgttacgttgcagTTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGTGGCCATCTCGTAAGATAAAGAAGGTAAACCGATCCCTAAAGAAGATCCA
                                                                                                                                                     |||  |||   | | |     ||    | | | ||    |||||||||||| |||||  ||||| |||||||||| |||||||| ||    |||||||||||||||||||| || || || ||| | || |||| ||| || ||
--------------------------------------------------------------------------------------------------------------------------------------------------gttagcacacaaactatctgaccctcgacttggattttcttctgcagTTTGTCCAACTACATTGAAACGGATATGCAGGCAACATGGGATCATGAGGTGGCCATCTCGTAAGATTAACAAAGTGAACAGGTCACTAAGGAAAATACA

upper sequence: LOC_Os11g16290.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv05s0094g00020.t01 (Vitis vinifera), 3'ss of exon 4
gtaatttgtttatactctcatgatctttttctgatttattcttatagaattcaattaattcctactaaattagttctgttttgtatgaaaagcactactgctaatacaaatgtagaaacaaactaatccaattgtgtcataggaagaggagcttacaggattttttttattccttgctgttacgttgcagTTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGTGGCCATCTCGTAAGATAAAGAAGGTAAACCGATCCCTAAAGAAGATCCA
                                                                                         |  | | ||  ||| || ||||  |||    |  |     ||     |   |    | | ||  |     |||  ||||  |  ||    ||   || ||||||| || ||||| || ||||| || |||||||||||||| |||||||| ||||| || || ||||| || ||||| ||| |||| || | |||||| ||
--------------------------------------------------------------------------------------agtagtcccaacaactagtataaata-agatgttatttggaagaagaagttggcaaactgtgtagtct--gatattgattttgatt-ttatctttgttttacagTTTGCCCCACTACACTCAAAAGAATCTGCAGACAACATGGGATATCAAGATGGCCGTCCCGCAAGATCAACAAGGTGAACAGATCACTGAGGAAGATACA

upper sequence: LOC_Os11g16290.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S302_9V6.1 (Physcomitrella patens), 3'ss of exon 2
gtaatttgtttatactctcatgatctttttctgatttattcttatagaattcaattaattcctactaaattagttctgttttgtatgaaaagcactactgctaatacaaatgtagaaacaaactaatccaattgtgtcataggaagaggagcttacaggattttttttattccttgctgttacgttgcagTTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGTGGCCATCTCGTAAGATAAAGAAGGTAAACCGATCCCTAAAGAAGATCCA
                                                                        |||   |||     ||  ||  |     ||| |   ||| |      ||  |  || | || | | |              | || | ||  | || || |    || |   ||||||| ||||| || ||||| || || ||||| |||||||| ||||| ||||||||||| ||||| || || || || || |  |||||  | || ||  | ||
------------------------------------------------------------------------gttgcttttgagccgagtagtccagt--ctactctcaatatgttgggaattttttctatttttctgac-------------tccatgtttactgttgttgc--aatgat-ttttgcagTATGTCCAACAACGCTCAAGAGAATATGTAGACAACACGGAATCTCAAGGTGGCCTTCTCGAAAAATCAATAAAGTTAGTCGATCGTTGAAAAAATTGCA

upper sequence: LOC_Os11g16290.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ35275 (Selaginella moellendorffii), 3'ss of exon 3
gtaatttgtttatactctcatgatctttttctgatttattcttatagaattcaattaattcctactaaattagttctgttttgtatgaaaagcactactgctaatacaaatgtagaaacaaactaatccaattgtgtcataggaagaggagcttacaggattttttttattccttgctgttacgttgcagTTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGTGGCCATCTCGTAAGATAAAGAAGGTAAACCGATCCCTAAAGAAGATCCA
                                                                                                                         ||        || ||||   ||  |      ||      |||| |  | | | |    ||      ||||||||||||| |||||||||| ||| ||||||||||| || ||     | ||||| || || ||| | |||||| |  | ||     | |||||||||||
-----------------------------------------------------------------------------------------------------------------------gtacgcgcttcgtt-tgtctctggctg------tttttttcttttctgaactgcatttgtttgttcgacagTTTGTCCTACGACGCTGAAAAAGATCTGCAGACAACACGGGATTGACCGCTGGCCGTCACGCAAGCTCAAGAAGATTGATCGGCAAGTTAAGAAGATCCA

upper sequence: LOC_Os11g16290.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ24209 (Selaginella moellendorffii), 3'ss of exon 3
gtaatttgtttatactctcatgatctttttctgatttattcttatagaattcaattaattcctactaaattagttctgttttgtatgaaaagcactactgctaatacaaatgtagaaacaaactaatccaattgtgtcataggaagaggagcttacaggattttttttattccttgctgttacgttgcagTTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGTGGCCATCTCGTAAGATAAAGAAGGTAAACCGATCCCTAAAGAAGATCCA
                                                                                                                                 |   |  || |  |    ||   ||      |||| |  | | | |    ||      ||||||||||||| |||||||||| ||| ||||||||||| || ||     | ||||| || || ||| | |||||| |  | ||     | |||||||||||
-------------------------------------------------------------------------------------------------------------------------------gtacgcgcttcgttcgtcttggctgttttttc-ttttctgaactgcatttgtttgttcgacagTTTGTCCTACGACGCTGAAAAAGATCTGCAGACAACACGGGATTGATCGCTGGCCGTCACGCAAGCTCAAGAAGATTGATCGGCAAGTTAAGAAGATCCA

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|29685065|gb|CB681340.1|CB681340
EST:     CCAGCAGTACTTCTCTGGCAGCCTGAAAGATGCTGCAAAGAGTATTGGTG                         TTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGT
genomic: CCAGCAGTACTTCTCTGGCAGCCTGAAAGATGCTGCAAAGAGTATTGGTGgtaatttgtt ... tacgttgcagTTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGT
EST: gi|88688917|gb|CI732493.1|CI732493
EST:     CCAGCAGTACTTCTCTGGCAGCCTGAAAGATGCTGCAAAGAGTATTGGTG                         TTTGTCCTACTACGCTGAAAAG
genomic: CCAGCAGTACTTCTCTGGCAGCCTGAAAGATGCTGCAAAGAGTATTGGTGgtaatttgtt ... tacgttgcagTTTGTCCTACTACGCTGAAAAG
EST: gi|29670811|gb|CB667086.1|CB667086
EST:     CCAGCAGTACTTCTCTGGCAGCCTGAAAGATGCTGCAAAGAGTATTGGTG                         TTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGT
genomic: CCAGCAGTACTTCTCTGGCAGCCTGAAAGATGCTGCAAAGAGTATTGGTGgtaatttgtt ... tacgttgcagTTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGT
EST: gi|58687769|gb|CK076456.1|CK076456
EST:     CCAGCAGTACTTCTCTGGCAGCCTGAAAGATGCTGCAAAGAGTATTGGTG                         TTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGT
genomic: CCAGCAGTACTTCTCTGGCAGCCTGAAAGATGCTGCAAAGAGTATTGGTGgtaatttgtt ... tacgttgcagTTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGT
EST: gi|29669189|gb|CB665464.1|CB665464
EST:     CCAGCAGTACTTCTCTGGCAGCCTGAAAGATGCTGCAAAGAGTATTGGTG                         TTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGT
genomic: CCAGCAGTACTTCTCTGGCAGCCTGAAAGATGCTGCAAAGAGTATTGGTGgtaatttgtt ... tacgttgcagTTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGT
EST: gi|88688760|gb|CI732336.1|CI732336
EST:     CCAGCAGTACTTCTCTGGCAGCCTGAAAGATGCTGCAAAGAGTATTGGTG                         TTTGTCCTACTACGCTGAA
genomic: CCAGCAGTACTTCTCTGGCAGCCTGAAAGATGCTGCAAAGAGTATTGGTGgtaatttgtt ... tacgttgcagTTTGTCCTACTACGCTGAA
EST: gi|58610755|gb|CK038467.1|CK038467
EST:     CCAGCAGTACTTCTCTGGCAGCCTGAAAGATGCTGCAAAGAGTATTGGTG                         TTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGT
genomic: CCAGCAGTACTTCTCTGGCAGCCTGAAAGATGCTGCAAAGAGTATTGGTGgtaatttgtt ... tacgttgcagTTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcataggaagaggagcttacaggattttttttattccttgctgttacgttgcagTTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGTGGCCATCTCGTAAGATAAAGAAGGTAAACCGATCCCTAAAGAAGATCCA
              agcttac  putative branch site (score: 3)
                         ttttttttattccttg  putative PPT
                        attttttttattcctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttgtttatactctcatgatctttttctgatttattcttatagaattcaattaattcctactaaattagttctgttttgtatgaaaagcactactgctaatacaaatgtagaaacaaactaatccaattgtgtcataggaagaggagcttacaggattttttttattccttgctgttacgttgcagTTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGTGGCCATCTCGTAAGATAAAGAAGGTAAACCGATCCCTAAAGAAGATCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG