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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttaactactgataatccccaattccccaagaacctacttgaccaccattaaacacatagttctgttgatttatcaattaacatggaattctagcttattctctgataaatcatctatattggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAGACTGCAAATTGAAAATATGTGATTTCGGACTTGCCCGAGCATCATTCAA

Basic information

species Oryza sativa
transcript LOC_Os06g49430.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g49430.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G306028_T02 (Zea mays), 3'ss of exon 2
gtaagc---ttaactactgataatccc-caattccccaagaaccta-cttgaccaccattaaacacat---agttctgttgatttatcaattaacatggaattctagcttattctc-tgataa----------atcatctatattggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAGACTGCAAATTGAAAATATGTGATTTCGGACTTGCCCGAGCATCATTCAA
|||||    |||| || |   || | | || | ||     || ||| |  |||     ||  |    |   | |  ||| |  | |||  ||  |||||   || || ||||| |    ||||          ||  ||||||  ||  ||||||||||||||||||| || ||||||||||||||||||||||| ||||| ||||||||| ||||||||||||| || || |||||||| |||||||| ||
gtaagtatattaattagtaccaaccacacagtacctatccaatctagcaagacagtttttgtatttgtcaaattgttgtgggctcatctgtt--catggttatccagtttattattacaataatgtgatctttatgttctataccggtgcagCTAATGTATTTCATCGTGACCTAAAGCCCAAGAATATACTGGCTAACTCGGACTGCAAACTGAAAATATGTGACTTTGGTCTTGCCCGTGCATCATTTAA

upper sequence: LOC_Os06g49430.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G135904_T01 (Zea mays), 3'ss of exon 2
-------------gtaagcttaactac-tgataatc-cccaattccccaaga----------acctacttgaccaccattaaacacatagttctgttgattta-tcaattaacatggaattctagcttattctctgataaatcatctatattggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAGACTGCAAATTGAAAATATGTGATTTCGGACTTGCCCGAGCATCATTCAA
              ||     ||| || || ||     || ||   |||||           |  |    |||     |    ||  |  |  || | || || |   ||   |||  ||  ||   || | |           ||||||||||  ||||||||||||| ||||| |||||||||||||||||||||||||| ||||| ||||||||| ||||||||||||| || ||||||||||| |||||||||||
gtaagtatattagctagtaccaaccacatggtacctatcccatgtaccaaggcagtttatatatttgtcagactgttgtggttcatctgctcatggttatctagtttgttgttatgatatattatgataatgtgctccttgcggtctatattggtgcagCTAATGTATTCCATCGTGATCTAAAGCCCAAGAATATACTGGCTAACTCGGACTGCAAACTGAAAATATGTGACTTTGGACTTGCCCGTGCATCATTCAA

upper sequence: LOC_Os06g49430.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 2
gtaagcttaactactgataatccccaattccccaagaacctacttgaccaccattaaacacatagttctgttgatttatcaattaacatggaattctagcttattctctgataaatcatctatattggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAGACTGCAAATTGAAAATATGTGATTTCGGACTTGCCCGAGCATCATTCAA
                                  | ||  ||  |      ||  ||  | |  |   | |    | || |||     |    || | | |  |    || |      |   |  ||    |||||||||||||||||||||||| ||||| |||||| || |||||||| | || |||||  ||||||| |||||||| |||||||| || |   | |||| 
--------------------------------tgaaaatgtaactatatttcaagaagaatagtggattatgatctaatgaatgtgtgtctcgtt-tggatgttgacgtgcttctatttgggtgatgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG

upper sequence: LOC_Os06g49430.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S80_71V6.2 (Physcomitrella patens), 3'ss of exon 2
gtaagcttaactactgataatccccaattccccaagaacctacttgaccaccattaaacacatagttctgttgatttatcaattaacatggaattctagcttattctctgataaatcatctatattggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAGACTGCAAATTGAAAATATGTGATTTCGGACTTGCCCGAGCATCATTCAA
              | | ||  | ||  |   ||| |  ||  | |       |         | ||||||   ||| |         |||| |  |  | | |||            | |    | |  |||||||||| ||||||||||| || ||||| |||||  |  |||||||| | ||||| ||| ||||||| ||||| || |||||||| ||||   | || | 
--------------tcacaactctca-ctgtacaaaagactgatgggatgtggtcctttttggatttctgtctgttttt--------gtgga-tgttgacgtcttca---------tgtttgggattgttcagCTAATGTGTTTCATCGCGACCTGAAGCCAAAGAACGTGTTGGCAAACGCTGACTGTAAACTGAAAATTTGTGACTTTGGACTTGCTCGAGTGGCCTTTAG

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|29645354|gb|CB650361.1|CB650361
EST:     CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAG                         CTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
genomic: CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAGgtaagcttaa ... attggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
EST: gi|29664602|gb|CB660877.1|CB660877
EST:     CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAG                         CTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
genomic: CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAGgtaagcttaa ... attggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
EST: gi|33795692|gb|CF323716.1|CF323716
EST:     CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAG                         CTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
genomic: CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAGgtaagcttaa ... attggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
EST: gi|58687543|gb|CK076230.1|CK076230
EST:     CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAG                         CTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
genomic: CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAGgtaagcttaa ... attggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
EST: gi|33676627|gb|CF304866.1|CF304866
EST:     CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAG                         CTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
genomic: CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAGgtaagcttaa ... attggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
EST: gi|58652759|gb|CK041439.1|CK041439
EST:     AGTTTTTCCTGTACCAACGTTCGTCCGTGCTCTCAAGTACATCCATGCAG                         CTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
genomic: AGTTTTTCCTGTACCAAC-TTC-TCCGTGCTCTCAAGTACATCCATGCAGgtaagcttaa ... attggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
EST: gi|58663889|gb|CK052575.1|CK052575
EST:     CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAG                         CTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
genomic: CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAGgtaagcttaa ... attggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
EST: gi|58668308|gb|CK056994.1|CK056994
EST:     CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAG                         CTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
genomic: CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAGgtaagcttaa ... attggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
EST: gi|29633813|gb|CB638822.1|CB638822
EST:     CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAG                         CTAATGTATTTCATCGCGATCTAAAGCC
genomic: CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAGgtaagcttaa ... attggcacagCTAATGTATTTCATCGCGATCTAAAGCC
EST: gi|33675107|gb|CF303346.1|CF303346
EST:     CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAG                         CTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
genomic: CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAGgtaagcttaa ... attggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
EST: gi|29632340|gb|CB637349.1|CB637349
EST:     CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAG                         CTAATGTATTTCATCGCGATCTAA
genomic: CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAGgtaagcttaa ... attggcacagCTAATGTATTTCATCGCGATCTAA
EST: gi|66913253|gb|CX100101.1|CX100101
EST:     CCAGGTGTTCCTGTACCAACTTCTTCGTGCTCTCAAGTACATCCATGCAG                         CTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
genomic: CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAGgtaagcttaa ... attggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
EST: gi|29627483|gb|CB632494.1|CB632494
EST:     CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAG                         CTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
genomic: CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAGgtaagcttaa ... attggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
EST: gi|33675390|gb|CF303629.1|CF303629
EST:     CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAG                         CTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
genomic: CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAGgtaagcttaa ... attggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
EST: gi|58668784|gb|CK057470.1|CK057470
EST:     CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAG                         CTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG
genomic: CCAGTTTTTCCTGTACCAACTTCTCCGTGCTCTCAAGTACATCCATGCAGgtaagcttaa ... attggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaattaacatggaattctagcttattctctgataaatcatctatattggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAGACTGCAAATTGAAAATATGTGATTTCGGACTTGCCCGAGCATCATTCAA
                                ataaatcatctatatt  TA-rich tract