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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgcatgtgtggttattatcgatttaaagtatgtagcttttgacaatgataggcatgacatttttgtgctcatcgatccatctgcttaattacgtgcagCTGGACGACTGGGTGCTCTGCCGGATCTACAAGAAGTCCGGCCAGGCGTCGCCGATGATGCCGCCGCTCGCCGCCGACTACGACCACGACGAGCCGTCCG

Basic information

species Oryza sativa
transcript LOC_Os07g48450.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g48450.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G042494_T01 (Zea mays), 3'ss of exon 3
catgcatgtgtggttattatcgatttaaagtatgtagcttttgacaatgataggcatgacatttttgtgctcatcgatccatctgcttaat-tacg-----tgcagCTGGACGACTGGGTGCTCTGCCGGATCTACAAGAAGTCCGGCCAGGCGTCGCCGATGATGCCGCCGCTCGCCGCCGACTACGACCACGACGAGCCGTCCG
   |  ||| || |   | |  ||   |  | |||||| || ||  ||  ||| |   |||| |       ||   ||| |||  || ||| | ||     ||||||||||||||||||| || |||||||||||||||||| || |||| | | ||||||||  |  |||||    | ||||| |||| || |||||||| | ||
--cgattgt-tgatccatctgcatccgatctgtgtagcatt-gattattttagtctccacatatcctcttcca--aatctatcatctcaatctgcgcatggtgcagCTGGACGACTGGGTTCTGTGCCGGATCTACAAGAAGGCCAGCCACGTGCCGCCGATGGCGGTGCCGCCGCTCTCCGACCACGAGCAGGACGAGCCCTGCG

upper sequence: LOC_Os07g48450.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G011598_T01 (Zea mays), 3'ss of exon 2
-catgcatgtgtggttattatcgatttaaagtatgtagcttttgacaatgataggcatgacatttttgtgctcatcgatccatctgcttaattacgtgcagCTGGACGACTGGGTGCTCTGCCGGATCTACAAGAAGTCCGGC---CAGGCGTCGCCGATGATGCCG---CCGCTCGCCGCCGACTACGACCACGACGAGCCGTCCG
  ||  |||  || | ||   |  ||     |   |   || ||  |  |||    ||      | || || | |         || |    | |||||||||||||||||||||||| |||||||||||||||||| || ||   |||| | || |||||  | ||   ||||    | ||||| ||||||| |||||||      
atatatatgcatgat-atatcctcttcttcctggtttatttgtgcgatggattattattgatcgtctgcgcgcgtacgcgtgcgtggtgtggtgcgtgcagCTGGACGACTGGGTGCTGTGCCGGATCTACAAGAAGGCCAGCTGCCAGGTGCCGGCGATGGCGGCGGTGCCGCAGCTCTCCGACCACGACCAGGACGAGC------

upper sequence: LOC_Os07g48450.2 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ36823 (Selaginella moellendorffii), 3'ss of exon 1
catgcatgtgtggttattatcgatttaaagtatgtagcttttgacaatgataggcatgacatttttgtgctcatcgatccatctgcttaattacgtgcagCTGGACGACTGGGTGCTCTGCCGGATCTACAAGAAGTCCGGCCAGGCGTCGCCGATGATGCCGCCGCTCGCCGCCGACTACGACCACGACGAGCCGTCCG
   | | || |   |     | | |    | ||  ||   |  | | ||      |  |||           |   |        |    | | | |  |    |  |   | ||   | |    |   ||||  || |  |    ||| || | ||   |  | |   || |    |     | ||    ||  | |  
---gtaagtttcaattcctccaagtagttgcata-agtcctgcatattggggaaaaaaacaaaaaaaaaaaaaaaaaagagagctcgagctcatgagtggtattaaaaaccgatggcttact---ttggcaagctgttcttcttt-cgttgcagCTGG-ACGACTGGGTGCTGT--GCCGGATCTACAGAAAGAAGACA-

upper sequence: LOC_Os07g48450.2 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ07271 (Selaginella moellendorffii), 3'ss of exon 1
-----------------------------------------------catgcatgtgtggttatt-atcgattt------aaagtatgtagcttttgacaatgataggcatgacatttttgtgctcatcgatccatctgcttaattacgtgcagCTGGACGACTGGGTGCTCTGCCGGATCTACAAGAAGTCCGGCCAGGCGTCGCCGATGATGCCGCCGCTCGCCGCCGACTACGACCACGACGAGCCGTCCG
                                                ||| || |||| |  |  ||| || |      |  |   ||   ||| | ||||    ||   |   ||  || | |      | | ||  |||  ||  |  ||||||||||||||||| |||||||||||||||||||||  |   |  |||      |     |||| ||                                 
gtaagtgatagagccttgtgtgttcttgagcgttctatgttatattatatggatctgtgttcttggatcaatctctcgcgagggagagttcttttcggcaatcgcgggatgggttttgatgggttt-----ttcttcctctttcttttggtcagCTGGACGACTGGGTTCTCTGCCGGATCTACAAGAAG--CAATCGAGCGATTGGAAGAGCCCCGCGGCCTCA-----------------------------

upper sequence: LOC_Os07g48450.2 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ07841 (Selaginella moellendorffii), 3'ss of exon 1
-----------------------------------------------catgcatgtgtggttatt-atcgatttaaagtatgt---agcttttgacaatgataggcatgacatttttgtgctcatcgatccatctgcttaattacgtgcagCTGGACGACTGGGTGCTCTGCCGGATCTACAAGAAGTCCGGCCAGGCGTCGCCGATGATGCCGCCGCTCGCCGCCGACTACGACCACGACGAGCCGTCCG--
                                                ||| || |||| |  |  ||| || |   |   |    || ||||  |    || | |  ||    ||| || |      | | ||  |||  ||  |  ||||||||||||||||| |||||||||||||||||||||  |   |  |||      |     |||| ||    |    |   | |   ||      |||     
gtaagtgatagagccttgtgttttcttgagcgttctatgttatattatatggatctgtgttcttggatcaatctctcgcgagggagaggttttttcggcaatcg-cgggatgggttt-tgatgggtttttcttcctctttcttttggtcagCTGGACGACTGGGTTCTCTGCCGGATCTACAAGAAG--CAATCGAGCGATTGGAAGAGCCCCGCGGCCTCACAAGAAGCGCCAAGCCGCGAGAACGTGAAAA

upper sequence: LOC_Os07g48450.2 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ27849 (Selaginella moellendorffii), 3'ss of exon 1
catgcatgtgtggttattatcgatttaaagtatgtagcttttgacaatgataggcatgacatttttgtgctcatcgatccatctgcttaattacgtgcagCTGGACGACTGGGTGCTCTGCCGGATCTACAAGAAGTCCGGCCAGGCGTCGCCGATGATGCCGCCGCTCGCCGCCGACTACG-ACCACGACGAGCCGTCCG----------
   | | || |   |     | | |    | ||  ||   |  | | ||      |  |||           |   |   |       ||  | | ||    |  |   || ||| | |     | | |           | || ||    |   |   |  || ||| | |   ||||  |  |   | ||   |  | |          
---gtaagtttcaattcctccaagtagttgcatccagtcctgcatattggggaaaaaaaca-----aaaaaaacaaaaaaaaaaaaaaaagaaagagcga--gagctcgtgagtggtattaaaaaccgatggcttactttggcaagctgttcttctttcgttgcagCTGGAC---GACTGGGTGCTGTGCCGGATCTACAGAAAGAAGACA

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|29644294|gb|CB649301.1|CB649301
EST:     ACACCTACAAGCCCTCCTCCTCCTCCCGATTCCGCAACGTCTCCATGAGG                         CTGGACGACTGGGTGCTCTGCCGGATCTACAAGAAGTCCGGCCAGGCGTCG
genomic: ACACCTACAAGCCCTCCTCCTCCTCCCGATTCCGCAACGTCTCCATGAGGgtatgtacct ... ttacgtgcagCTGGACGACTGGGTGCTCTGCCGGATCTACAAGAAGTCCGGCCAGGCGTCG
EST: gi|29668046|gb|CB664321.1|CB664321
EST:     ACACCTACAAGCCCTCCTCCTCCTCCCGATTCCGCAACGTCTCCATGAGG                         CTGGACGACTGGGTGCTCTGCCGGATCTACAAGAAGTCCGGCCAGGCGTCG
genomic: ACACCTACAAGCCCTCCTCCTCCTCCCGATTCCGCAACGTCTCCATGAGGgtatgtacct ... ttacgtgcagCTGGACGACTGGGTGCTCTGCCGGATCTACAAGAAGTCCGGCCAGGCGTCG
EST: gi|58593268|gb|CF991576.1|CF991576
EST:     ACACCTACAAGCCCTCCTCCTCCTCCCGATTCCGCAACGTCTCCATGAGG                         CTGGACGACTGGGTGCTCTGCCGGATCTACAAGAAGTCCGGCCAGGCGTCG
genomic: ACACCTACAAGCCCTCCTCCTCCTCCCGATTCCGCAACGTCTCCATGAGGgtatgtacct ... ttacgtgcagCTGGACGACTGGGTGCTCTGCCGGATCTACAAGAAGTCCGGCCAGGCGTCG
EST: gi|88763642|gb|CI773089.1|CI773089
EST:     ACACCTACAAGCCCTCCTCCTCCTCCCGATTCCGCAACGTCTCCATGAGG                         CTGGACGACTGGGTGCTCTGCCGGATCTACAAGAAGTCCGGCCAGGCGTCG
genomic: ACACCTACAAGCCCTCCTCCTCCTCCCGATTCCGCAACGTCTCCATGAGGgtatgtacct ... ttacgtgcagCTGGACGACTGGGTGCTCTGCCGGATCTACAAGAAGTCCGGCCAGGCGTCG
EST: gi|29679145|gb|CB675420.1|CB675420
EST:     ACACCTACAAGCCCTCCTCCTCCTCCCGATTCCGCAACGTCTCCATGAGG                         CTGGACGACTGGGTGCTCTGCCGGATCTACAAGAAGTCCGGCCAGGCGTCG
genomic: ACACCTACAAGCCCTCCTCCTCCTCCCGATTCCGCAACGTCTCCATGAGGgtatgtacct ... ttacgtgcagCTGGACGACTGGGTGCTCTGCCGGATCTACAAGAAGTCCGGCCAGGCGTCG
EST: gi|29629414|gb|CB634423.1|CB634423
EST:     ACACCTACAAGCCCTCCTCCTCCTCCCGATTCCGCAACGTCTCCATGAGG                         CTGGACGACTGGGTGCTCTGCCGGATCTACAAGAAGTCCGGCCAGGCGTCG
genomic: ACACCTACAAGCCCTCCTCCTCCTCCCGATTCCGCAACGTCTCCATGAGGgtatgtacct ... ttacgtgcagCTGGACGACTGGGTGCTCTGCCGGATCTACAAGAAGTCCGGCCAGGCGTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgataggcatgacatttttgtgctcatcgatccatctgcttaattacgtgcagCTGGACGACTGGGTGCTCTGCCGGATCTACAAGAAGTCCGGCCAGGCGTCGCCGATGATGCCGCCGCTCGCCGCCGACTACGACCACGACGAGCCGTCCG
                                       gcttaat  putative branch site (score: 4)
                                         ttaatta  TA-rich tract