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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcgcccaaaaaaatgttacaatatttcttgacagaaacctcccagattttctgaaacctggcaagaagatttgatgcaaatttgttctttttccattcagGTCAAAACAACATCACCAAGGAAGTATTTCGTCCGGCCGAACGCGAACATCGTCCAGCCATGGGATTCTTGCACAATAACAA

Basic information

species Oryza sativa
transcript LOC_Os02g43594.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g43594.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G074173_T01 (Zea mays), 3'ss of exon 3
----------------------------------gcgcccaaaaaaatgttacaatatttcttgacagaaacctc-ccagattttctgaaacctggcaaga----------------agatttgatgc---aaatttgttctttttccattcagGTCAAAACAACATCACCAAGGAAGTATTTCGTCCGGCCGAACGCGAACATCGTCCAGCCATGGGATTCTTGCACAATAACAA
                                   ||||  | ||  |       | || ||||   ||||||   |||| |    ||    |||    ||                || | || |     |||||||  |  ||  | ||||||||||||| |||||||| ||||||||||| |||||||||||||||| ||||||||||||||||||||||||||||||||| |
gtccgtagcttcggctatcgcattcgcgtgatgttcgcctcagaatttccgcgttttttgcttgctggaaaccaagccaggtggcttggtgtctgaggggagaagaaaaactaaactaggtctggttggtgaaatttgcccgattcactttcagGTCAAAACGACATCACCGAGGAAGTATTTTGTCCGGCCGAACGCGAGCATCGTCCAGCCATGGGATTCTTGCACAATAACGA

upper sequence: LOC_Os02g43594.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G171406_T06 (Zea mays), 3'ss of exon 2
-------------------------gcgcccaaaaaaatgttacaatatttcttgacagaaacctc-ccagattttctga-aacctggcaagaagatttgatg---------caaatttgttctttttccattcagGTCAAAACAACATCACCAAGGAAGTATTTCGTCCGGCCGAACGCGAACATCGTCCAGCCATGGGATTCTTGCACAATAACAA
                         |  | |   | ||| |     | || || |    ||| |   |||| |||  ||   |  ||  ||||| | | ||           ||||||||  |  |||   ||||||||||||||||||| || |||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| |
gtccatgtcttccctgtcccgtgaagttcacctcagaatctccgcgttttgctcgctgaaaatcgaaccaggtttgatgttgagatgagaagaaaactagactaggtctggtcaaatttgccccatttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATCGTCCAGCCATGGGATTCTTGCACAATAACGA
















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|88728659|gb|CI752169.1|CI752169
EST:     ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTTGCATTCAAG                         GTCAAAACAACATCACCAAGGAAGTATTTCGTCCGGCCGAACGCGAACATC
genomic: ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTTGCATTCAAGgtatctatcg ... ttccattcagGTCAAAACAACATCACCAAGGAAGTATTTCGTCCGGCCGAACGCGAACATC
EST: gi|88401755|gb|CI591082.1|CI591082
EST:     ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTTGCATTCAAG                         GTCAAAACAACATCACCAAGGAAGTATTTCGTCCGGCCGAACGCGAACATC
genomic: ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTTGCATTCAAGgtatctatcg ... ttccattcagGTCAAAACAACATCACCAAGGAAGTATTTCGTCCGGCCGAACGCGAACATC
EST: gi|88389102|gb|CI595336.1|CI595336
EST:     ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTTGCATTCAAG                         GTCAAAACAACATCACCAAGGAAGTATTTCGTCCGGCCGAACGCGAACATC
genomic: ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTTGCATTCAAGgtatctatcg ... ttccattcagGTCAAAACAACATCACCAAGGAAGTATTTCGTCCGGCCGAACGCGAACATC
EST: gi|88405086|gb|CI685534.1|CI685534
EST:     ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTTGCATTCAAG                         GTCAAAACAACATCACCAAGGAAGTATTTCGTCCGGCCGAACGCGAACATC
genomic: ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTTGCATTCAAGgtatctatcg ... ttccattcagGTCAAAACAACATCACCAAGGAAGTATTTCGTCCGGCCGAACGCGAACATC
EST: gi|88581198|gb|CI698173.1|CI698173
EST:     ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTTGCATTCAAG                         GTCAAAACAACATCACCAAGGAAGTATTTCGTCCGGCCGAACGCGAACATC
genomic: ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTTGCATTCAAGgtatctatcg ... ttccattcagGTCAAAACAACATCACCAAGGAAGTATTTCGTCCGGCCGAACGCGAACATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttctgaaacctggcaagaagatttgatgcaaatttgttctttttccattcagGTCAAAACAACATCACCAAGGAAGTATTTCGTCCGGCCGAACGCGAACATCGTCCAGCCATGGGATTCTTGCACAATAACAA
                       atttgat  putative branch site (score: 5)
                                   tttgttctttttccat  putative PPT
                                aaatttgttcttttt  TA-rich tract