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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGCTCGATAGCGAGATTAAGTCATGGCTTGCTTTTGCTGCCCAAAAAGTGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtactcttttttgccctttatctattctcacctcttaattagagcctgagcatagtactcattactcaatagcatttgaagaaacttctgctcatttatacatttgtgaacaatattgtacag

Basic information

species Oryza sativa
transcript LOC_Os12g42884.3
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g42884.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G149751_T06 (Zea mays), 5'ss of exon 5
CAAGCTCGATAGCGAGATTAAGTCATGGCTTGCTTTTGCTGCCCAAAAAGTGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtactcttttttgccctttatctattctcacctcttaattagagcctgagcatagtactcattactcaatagcatttga-agaaacttctgctcatttatacattt-gtgaacaatattgtacag
 ||||| || |||||||||||||| |||||||||||||||||||| || || ||||||||  |||| |||||||||||||||||||| || |||||||||||||||   | |  ||   | |||    ||||| | ||  |  || | |  |   | |  | | | | |  || |  |  || | | |||||| | |    ||  | ||||  || |||           
TAAGCTTGACAGCGAGATTAAGTCTTGGCTTGCTTTTGCTGCCCAGAAGGTTGTTGAGGTTGATGCTCTTGCTAAGGCATTGGCTGGTCAAAAGGATGAGgtatggctgtgtagttc-tcattttctgattcttaactagtcctttgcgttt---cttttttcccttcatacattttcccttcatacaaacttattcattcttgcaaatttcatgtacag----------
















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|300215517|gb|HO088143.1|HO088143
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACACTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|218492493|gb|FG951515.1|FG951515
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACACTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACACTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|300216253|gb|HO088038.1|HO088038
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACACTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|29620902|gb|CB625913.1|CB625913
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACACTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|29637650|gb|CB642659.1|CB642659
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACACTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACACTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|29675799|gb|CB672074.1|CB672074
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACACTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACACTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|58613186|gb|CK040898.1|CK040898
EST:     GGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACACTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: GGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACACTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|218483058|gb|FG951439.1|FG951439
EST:     GCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACACTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: GCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACACTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|428283|gb|D24431.1|D24431
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACACTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACACTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|29615679|gb|CB620691.1|CB620691
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACGCTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACACTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|29635138|gb|CB640147.1|CB640147
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACACTGCTGCTCAAGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACACTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|4881161|gb|AU065460.1|AU065460
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACACTGCTGCTCANGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACACTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
EST: gi|33800724|gb|CF326232.1|CF326232
EST:     TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAG                         GCTTACTTTGCAGCAAACACTGCTGCTCAGGCCTCCAGGAGGTCATCACCT
genomic: TGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtact ... tattgtacagGCTTACTTTGCAGCAAACACTGCTGCTCAGGCCTCCAGGAGGTCATCACCT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGCTCGATAGCGAGATTAAGTCATGGCTTGCTTTTGCTGCCCAAAAAGTGGTTGAGGTGAATGCCCTTGCTAAGGCATTGGCTGGACAGAAGGATGAGgtatggtactcttttttgccctttatctattctcacctcttaattagagcctgagcatagtactcattactcaatagcatttgaagaaacttctgctcatttatacatttgtgaacaatattgtacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG