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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccttttaaatatcctttttgaatttctgtactttcaccatacaaagtttctgttaaggtattctaaaatatttttatttgaatgctcattctgcttcagCAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTTTCAAAAGATAATGGATTTGAAATAGTTACGGTGAACCCAGCAATGGTCA

Basic information

species Oryza sativa
transcript LOC_Os01g34480.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g34480.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G179981_T01 (Zea mays), 3'ss of exon 3
tccttttaaatatcctttttgaatttctgtact--ttcaccatacaaagtttctgttaaggtattctaaaatatttttatttgaatgctcattctgctt--cagCAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTTTCAAAAGATAATGGATTTGAAATAGTTACGGTGAACCCAGCAATGGTCA
       |||      |||     |  | |||   |    ||  | |  ||  | || |  |  ||     || |||  | |  | |   |  ||  ||  |||||||||||| || |||||||||| || ||||||||||||||||||||||| ||||  ||||||||| ||||||| |||||  | |||||||| ||||| |
----agcaaagtctgatttcattgtcttataccaatgtctcaagctatattgttatttattttatcattgctactttattctctaagtctacactatttggcagCAATGGTATATTTTGTCCAAGACGCTGGCAGAGGAGGCTGCTTGGAAGTTCTCAAGGGATAATGGACTTGAAATCGTTACTATAAACCCAGCGATGGTTA
















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|568053|gb|D38888.1|D38888
EST:     TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAG                         CAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
genomic: TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAGgtaatatgcc ... tctgcttcagCAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
EST: gi|29640618|gb|CB645627.1|CB645627
EST:     TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAG                         CAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
genomic: TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAGgtaatatgcc ... tctgcttcagCAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
EST: gi|44671842|gb|CR285276.1|CR285276
EST:     TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAG                         CAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
genomic: TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAGgtaatatgcc ... tctgcttcagCAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
EST: gi|29616459|gb|CB621471.1|CB621471
EST:     TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAG                         CAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
genomic: TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAGgtaatatgcc ... tctgcttcagCAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
EST: gi|218497240|gb|FG957726.1|FG957726
EST:     TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAG                         CAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
genomic: TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAGgtaatatgcc ... tctgcttcagCAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
EST: gi|117221000|gb|CT845506.1|CT845506
EST:     TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAG                         CAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
genomic: TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAGgtaatatgcc ... tctgcttcagCAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
EST: gi|11026105|gb|AU162706.1|AU162706
EST:     TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAG                         CAATGGTATGTTCTGTCCAAGACCCTAACAGAGGAGGCTGCTTGGAAGTTT
genomic: TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAGgtaatatgcc ... tctgcttcagCAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
EST: gi|2312785|gb|C28940.1|C28940
EST:     TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAG                         CAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
genomic: TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAGgtaatatgcc ... tctgcttcagCAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTT
EST: gi|84117052|gb|CD150819.1|CD150819
EST:     TTGTTGATGAGACATGGGGTTCAGTTCCAGAGATTTGTGAAAAGCATCAG                         CAATGGTATGTTCTGTCCAAGACCCTATCAGAGGAGGCTGCTTGGAA
genomic: TTGTTGATGAGACATGGTTTTCAGTTCCAGAGATTTGTGAAAAGCATCAGgtaatatgcc ... tctgcttcagCAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttctgttaaggtattctaaaatatttttatttgaatgctcattctgcttcagCAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTTTCAAAAGATAATGGATTTGAAATAGTTACGGTGAACCCAGCAATGGTCA
                ttctaaa  putative branch site (score: 2)
                                            ttctgcttc  putative PPT
        ttaaggtattctaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccttttaaatatcctttttgaatttctgtactttcaccatacaaagtttctgttaaggtattctaaaatatttttatttgaatgctcattctgcttcagCAATGGTATGTTCTGTCCAAGACCCTAGCAGAGGAGGCTGCTTGGAAGTTTTCAAAAGATAATGGATTTGAAATAGTTACGGTGAACCCAGCAATGGTCA

- - - - - - - - - - - - ttctgta
- - - - - - - - - - - - - - - - - - -ccataca
- - - - - - - - - - - - - - - - - - - - - - - - ttctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatgct