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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtctccccctatacagacacaaaaatatctattcattcgggtatatttagttagctttccactaaaagaaaattttaatcagcttgagtgtaacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGAGGACTACGGTTCTGCGTTGGAGCAGACTTCAGCAAGCTACAATTGGCTA

Basic information

species Oryza sativa
transcript LOC_Os04g48210.2
intron # 6
splice site 3'
intron type U2

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|88666016|gb|CI716172.1|CI716172
EST:     ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAG                         GATAAACCAGAGATAAACCGTGGATCAAAACANTTCA
genomic: ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAGgtttgataat ... taacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCA
EST: gi|88671466|gb|CI725582.1|CI725582
EST:     ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAG                         GATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCG
genomic: ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAGgtttgataat ... taacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCG
EST: gi|88673589|gb|CI727702.1|CI727702
EST:     ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAG                         GATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
genomic: ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAGgtttgataat ... taacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
EST: gi|88972545|gb|CI717285.1|CI717285
EST:     ATCCATATATTTATCCGGATCCTCCCACCTTCATCCCTTCACGGTTTAAG                         GATAAACCAGAGATAAACCGTGG
genomic: ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAGgtttgataat ... taacatgcagGATAAACCAGAGATAAACCGTGG
EST: gi|88904595|gb|CI711894.1|CI711894
EST:     ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAG                         GATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
genomic: ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAGgtttgataat ... taacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
EST: gi|88954725|gb|CI720204.1|CI720204
EST:     ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAG                         GATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
genomic: ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAGgtttgataat ... taacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
EST: gi|88688393|gb|CI731969.1|CI731969
EST:     ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAG                         GATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCG
genomic: ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAGgtttgataat ... taacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCG
EST: gi|88675847|gb|CI729419.1|CI729419
EST:     ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAG                         GATAAACCAGAGATAAACCGTGGATCAAAANACTTCATGGCATTCGGCGGA
genomic: ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAGgtttgataat ... taacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
EST: gi|88593610|gb|CI713564.1|CI713564
EST:     ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAG                         GATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
genomic: ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAGgtttgataat ... taacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
EST: gi|88671660|gb|CI725458.1|CI725458
EST:     ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAG                         GATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
genomic: ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAGgtttgataat ... taacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
EST: gi|88691724|gb|CI733802.1|CI733802
EST:     ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAG                         GATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
genomic: ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAGgtttgataat ... taacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
EST: gi|88525439|gb|CI453445.1|CI453445
EST:     TCCTCTCACCTTCATCCCTTCAAGGTTTAAG                         GATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
genomic: TCCTCTCACCTTCATCCCTTCAAGGTTTAAGgtttgataat ... taacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
EST: gi|86484064|gb|CI126697.1|CI126697
EST:     CCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAG                         GATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
genomic: CCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAGgtttgataat ... taacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
EST: gi|88693843|gb|CI735420.1|CI735420
EST:     ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAG                         GATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
genomic: ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAGgtttgataat ... taacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
EST: gi|88693862|gb|CI735439.1|CI735439
EST:     ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAG                         GATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
genomic: ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAGgtttgataat ... taacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
EST: gi|88905628|gb|CI712927.1|CI712927
EST:     ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAG                         GATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
genomic: ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAGgtttgataat ... taacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
EST: gi|88672624|gb|CI726740.1|CI726740
EST:     ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAG                         GATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
genomic: ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAGgtttgataat ... taacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
EST: gi|88972283|gb|CI717024.1|CI717024
EST:     ATCNATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAG                         GATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
genomic: ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAGgtttgataat ... taacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
EST: gi|86500214|gb|CI142847.1|CI142847
EST:     ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAG                         GATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
genomic: ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAGgtttgataat ... taacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
EST: gi|88973865|gb|CI718273.1|CI718273
EST:     ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAG                         GATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
genomic: ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAGgtttgataat ... taacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
EST: gi|88674089|gb|CI728202.1|CI728202
EST:     ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAG                         GATAAACCACAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
genomic: ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAGgtttgataat ... taacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
EST: gi|88669475|gb|CI723393.1|CI723393
EST:     ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAG                         GATAAACCAGAGATAAACCGTGGATCAAAANACTTCATGGCATTCGGCGGA
genomic: ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAGgtttgataat ... taacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
EST: gi|88593797|gb|CI713751.1|CI713751
EST:     ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAG                         GATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
genomic: ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAGgtttgataat ... taacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
EST: gi|88687952|gb|CI731528.1|CI731528
EST:     ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAG                         GATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA
genomic: ATCCATATATTTATCCGGATCCTCTCACCTTCATCCCTTCAAGGTTTAAGgtttgataat ... taacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagttagctttccactaaaagaaaattttaatcagcttgagtgtaacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGAGGACTACGGTTCTGCGTTGGAGCAGACTTCAGCAAGCTACAATTGGCTA
               actaaaagaaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctccccctatacagacacaaaaatatctattcattcgggtatatttagttagctttccactaaaagaaaattttaatcagcttgagtgtaacatgcagGATAAACCAGAGATAAACCGTGGATCAAAACACTTCATGGCATTCGGCGGAGGACTACGGTTCTGCGTTGGAGCAGACTTCAGCAAGCTACAATTGGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - acagaca
- - - - - - - - - - aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagcttg