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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgtgttagataagaaaatgtttatgcctatcttacacttcgttattgtattttagttttcatttgttctcatttattaatatcactatgattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCTTCAAATCGTATAGGTTCAAATGCTGGTGCAAATGACATCAAGCAACATT

Basic information

species Oryza sativa
transcript LOC_Os04g23890.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g23890.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G032351_T01 (Zea mays), 3'ss of exon 19
-------------------------------------------------------------------------------catgtgttag-ataagaaaatgttt-atgcctatcttacacttcgttattgtattttagttttcatttgttctcatttattaatatcactatgatt-ctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCTTCAAATCGTATAGGTTCAAATGCTGGTGCAAATGACATCAAGCAACATT
                                                                               ||| || | | |||  || | ||||     |||||| ||| |   || |   |  |      |  ||| ||||  |    || || ||  ||| || ||||||||||||| ||| || |||||||||||||||||||| || ||||||||||| ||   |||  | ||||||| ||||| |||||| || |||||||||||| 
gtaagaaatttcatccttatttttgttacctacaattgcatgtaaatctggtcaaatttgcctgtgtttgtgcagttaacatttgatggtatagaaataagttttgaaactatct-acaatgttttgtaccacatacaacgttgtttattctgttcacctattaacaa-atgtttactccagGTTAGTCCTGCGGCTAAGCAATTAATCCATGGATTGCTACAGAGAGATCCCTCTTCTCGACTTGGTTCAAGTGCTGCTGCAAACGATATCAAGCAACATC
















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|86481914|gb|CI124547.1|CI124547
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|38478618|gb|CF962751.1|CF962751
EST:     TTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: TTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29613428|gb|CB618441.1|CB618441
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29618974|gb|CB623986.1|CB623986
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29612811|gb|CB617824.1|CB617824
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|25806004|gb|CA761965.1|CA761965
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCTGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29618297|gb|CB623309.1|CB623309
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29626656|gb|CB631667.1|CB631667
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29619193|gb|CB624205.1|CB624205
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29620201|gb|CB625213.1|CB625213
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29630592|gb|CB635601.1|CB635601
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29615866|gb|CB620878.1|CB620878
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29679663|gb|CB675938.1|CB675938
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29685421|gb|CB681696.1|CB681696
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29646470|gb|CB651477.1|CB651477
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|86861209|gb|CI326647.1|CI326647
EST:     CATTTTATAACATAC-GCACAAAGACC-TACATTTCCCAGTAGCATTCCGG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCC
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCC-Ggtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCC
EST: gi|33381050|gb|CF196393.1|CF196393
EST:     CATTTTATAACATACTGCACNNNGACCTTACATTTCCCAGTAGCATTCCG                         GNNAGTCTTGCAGCAAAG
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAG
EST: gi|29685192|gb|CB681467.1|CB681467
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29619194|gb|CB624206.1|CB624206
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtattttagttttcatttgttctcatttattaatatcactatgattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCTTCAAATCGTATAGGTTCAAATGCTGGTGCAAATGACATCAAGCAACATT
                              tattaat  putative branch site (score: 2)
                                               ttctcc  putative PPT
     attttagttttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgtgttagataagaaaatgtttatgcctatcttacacttcgttattgtattttagttttcatttgttctcatttattaatatcactatgattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCTTCAAATCGTATAGGTTCAAATGCTGGTGCAAATGACATCAAGCAACATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA