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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctataattaggtaatgaaaatataataaaatggaagatctacatattattgtaccgtgttgaataaattcatcattaactatttttttctcaatttatagACAATGAAGAATCACAAGAACCTACCAAACGACGTAATAGATTGGGTCCAGCAGGCCTTGCACTGCATTACGCCAATATCATCAGTCAGATCGATACTCT

Basic information

species Oryza sativa
transcript LOC_Os01g65330.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G046846_T01 (Zea mays), 3'ss of exon 8
-ctataattaggtaatgaaaatataataaaatggaagatctacatattattgtacc-gtgttgaataaattcatcattaactatttttttctcaatttatagACAATGAAGAATCACAAGAACCTACCAAACGACGTAATAGATTGGGTCCAGCAGGCCTTGCACTGCATTACGCCAATATCATCAGTCAGATCGATACTCT
 |  |          ||| | |||| ||  |  |      |      || ||||    || |  || | || |      | |||     |  || | |  ||||| |||||||||||| |||||||||||||||||||||||||||||||||||||| |||||||||||||| || ||||||||||||||||| ||||||||
tccttccccgaacgctgaca-tatattatgaccgttttcttcaccggtactgtatttatgatttatca-ttgactgaagattatcaccctaacactatgcagACAGTGAAGAATCACAGGAACCTACCAAACGACGTAATAGATTGGGTCCAGCAGGTCTTGCACTGCATTATGCAAATATCATCAGTCAGATTGATACTCT

upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G148773_T02 (Zea mays), 3'ss of exon 7
---ctataattagg-taatgaaaatataataaaatggaagatctacatattattgtaccgtgttgaataaattcatcattaactatttttttctcaatttatagACAATGAAGAATCACAAGAACCTACCAAACGACGTAATAGATTGGGTCCAGCAGGCCTTGCACTGCATTACGCCAATATCATCAGTCAGATCGATACTCT
     |  |||| | ||  |    | | | |  |||   | | |    |  |  |||| || || |  |  || |     || |    |  |  || | |  ||||| |||||||||||| ||||||||||| ||||| |||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||
ccttaaccattatgctagaggccctttcacatcatgattgtttttttcacca--gtactgtatttacca--ttgactggaaattgccatcctaacactatgcagACAGTGAAGAATCACAGGAACCTACCAAGCGACGCAATAGATTGGGTTCAGCAGGCCTTGCACTGCATTACGCCAATATCATCAGTCAGATCGATACTCT
















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|29680203|gb|CB676478.1|CB676478
EST:     CATTGTGCATTTCTTACATTTGGAGATCCATAATGCCTTTGGGCGCTCAG                         ACAATGAAGAATCACAAGAACCTACCAAACGACGTAATAGATTGGGTCCAG
genomic: CATTGTGCATTTCTTACATTTGGAGATCCATAATGCCTTTGGGCGCTCAGgtattaggct ... caatttatagACAATGAAGAATCACAAGAACCTACCAAACGACGTAATAGATTGGGTCCAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattgtaccgtgttgaataaattcatcattaactatttttttctcaatttatagACAATGAAGAATCACAAGAACCTACCAAACGACGTAATAGATTGGGTCCAGCAGGCCTTGCACTGCATTACGCCAATATCATCAGTCAGATCGATACTCT
                           cattaac  putative branch site (score: 2)
                                    tttttttctcaattt  putative PPT
                aataaattcatcatta  TA-rich tract