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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacttgcttaaatggtacacctaagctatttatactatatgctgtttttaatgccattattatctaatcttaattcctttgctttttttgtcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGCTAAACGTAGAAGGGAAAAATACCAAAAACAATCATCTCTCTTGTCAAAG

Basic information

species Oryza sativa
transcript LOC_Os06g13820.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM5G811223_T01 (Zea mays), 3'ss of exon 8
gacttgcttaa--atggtacacctaagctatttatactatatgct-gtttttaatgccattattatctaatcttaattcctttgctttttttgtcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGCTAAACGTAGAAGGGAAAAATACCAAAAACAATCATCTCTCTTGTCAAAG
    || | ||   ||||     ||   |   |||    ||||||  |||||   |    | ||   ||   || ||   ||   |  ||   ||  |||||| ||||||||||| || || |||||||||||||| |||||||| ||||||||||| || |||||||| || ||||||||||||||||||||| ||||||| 
tttctgatcaattgtggttgctatatattgaatatggcttatgcttattttttgggtacattttgaatagcttttatattttcaatcatt---tctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGCTAAGCGCAGAAGGGAGAAGTACCAAAAACAATCATCTCTCCTGTCAAAA

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 20
gacttgcttaaatggt-acacctaagctatttatactatatgctgtttttaatgccattattatctaatcttaattcctttgctttttttgtcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGCTAAACGTAGAAGGGAAAAATACCAAAAACAATCATCTCTCTTGTCAAAG
 |  |   | |  | |      |    ||| |  | |||    | | |||| |   | ||   | | |      ||  | |     |  | || ||||||| |||||||||||||| || ||||||||||| || |||||||||||||||||||| || |||||||| || ||||||||||||||||||||| ||||||| 
-atatttctgatcgattgtggttgccatatattcagtatggcttatgtttatttttagtacattttgaatagcttttgtatttcaatcatttctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGCTAAGCGCAGAAGGGAGAAGTACCAAAAACAATCATCTCTCCTGTCAAAA
















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|29662868|gb|CB659143.1|CB659143
EST:     GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAG                         TGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
genomic: GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAGgttgatgaat ... tcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
EST: gi|29614012|gb|CB619025.1|CB619025
EST:     GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAG                         TGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
genomic: GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAGgttgatgaat ... tcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
EST: gi|29657562|gb|CB653837.1|CB653837
EST:     GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAG                         TGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
genomic: GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAGgttgatgaat ... tcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
EST: gi|86482222|gb|CI124855.1|CI124855
EST:     GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAG                         TGGGCAAAGCAATGCAAAAATTGAAGAGCTTCCTGCAAGAGGACCATAATG
genomic: GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAGgttgatgaat ... tcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTT-CTGCAAGAGGACCATAATG
EST: gi|29625430|gb|CB630441.1|CB630441
EST:     AGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAG                         TGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
genomic: AGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAGgttgatgaat ... tcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
EST: gi|218497504|gb|FG955306.1|FG955306
EST:     GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAG                         TGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
genomic: GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAGgttgatgaat ... tcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
EST: gi|29622848|gb|CB627859.1|CB627859
EST:     GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAG                         TGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
genomic: GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAGgttgatgaat ... tcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
EST: gi|25798429|gb|CA754390.1|CA754390
EST:     GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAG                         TGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
genomic: GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAGgttgatgaat ... tcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
EST: gi|87040350|gb|CI194972.1|CI194972
EST:     GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAG                         TGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
genomic: GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAGgttgatgaat ... tcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
EST: gi|86898985|gb|CI296187.1|CI296187
EST:     GAAGATATGCTAAACCAGCTATATAGTTCAATAAG                         TGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
genomic: GAAGATATGCTAAACCAGCTATATAGTTCAATAAGgttgatgaat ... tcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaatgccattattatctaatcttaattcctttgctttttttgtcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGCTAAACGTAGAAGGGAAAAATACCAAAAACAATCATCTCTCTTGTCAAAG
                      tcttaat  putative branch site (score: 3)
                            ttcctttgcttttttt  CT-rich tract
          attattatctaatctt  TA-rich tract