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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttgatcaagaatatattggaatgtacagacttgccattttgtaaacaaactgttaacctggtttccatattcagGTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTTGGTGACCATAGAGTGGCTTCCATTCAACAACAGCTTGCATCTTTAAAAC

Basic information

species Oryza sativa
transcript LOC_Os02g32350.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 13
lower sequence: AC207890.3_FGT002 (Zea mays), 3'ss of exon 13
gtttgttgatcaagaatatattggaatgtacagacttgccattttgtaaacaaactgttaacctggttt-ccatattcagGTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTTGGTGACCATAGAGTGGCTTCCATTCAACAACAGCTTGCATCTTTAAAAC
||||||| || ||| |||| || ||| | |    |     |||| |  |   || |  |  | ||  |  |  |||| |||||||||| || ||||| ||||||||||| ||||| ||||| || ||| | |||||||| || |||||||| |||||||| |||||||||||||| ||||
gtttgttaatgaaggatatttttgaa-gcatgtcccatttatttgggtag--aattaatttcttgactgactctatttagGTTGTTGTCACGGAAGTTCTTGGTGGTGGGAAGTTTTATGTTCAGACAATGGGTGACCAGAGGGTGGCTTCAATTCAACAGCAGCTTGCATCTTTGAAAC

upper sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G136296_T01 (Zea mays), 3'ss of exon 14
gtttgttgatcaagaatatattggaatgtacagacttgccattttgtaaacaaactgttaacctggtttccatattcagGTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTTGGTGACCATAGAGTGGCTTCCATTCAACAACAGCTTGCATCTTTAAAAC
||||||  || ||| |||| || |||       | ||       |||||  ||  | || ||    |  |  |||| ||||||| |  || ||||| ||||||||||| ||||| ||||| || ||||| |||||||| || |||||||| |||||||| |||||||||||||| ||||
gtttgtccatgaaggatatttttgaagcactccatttctttgggtgtaattaacttcttgac----tcactctatttagGTTGTCGCCACGGAAGTTCTTGGTGGTGGGAAGTTTTATGTTCAGACAGTGGGTGACCAGAGGGTGGCTTCAATTCAACAGCAGCTTGCATCTTTGAAAC
















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|2799427|gb|AA752416.1|AA752416
EST:     AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAG                         GTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
genomic: AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAGgtttgttgat ... ccatattcagGTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
EST: gi|2311450|gb|C27605.1|C27605
EST:     AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAG                         GTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
genomic: AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAGgtttgttgat ... ccatattcagGTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
EST: gi|29622581|gb|CB627592.1|CB627592
EST:     AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAG                         GTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
genomic: AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAGgtttgttgat ... ccatattcagGTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
EST: gi|29674464|gb|CB670739.1|CB670739
EST:     AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAG                         GTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
genomic: AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAGgtttgttgat ... ccatattcagGTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
EST: gi|163928125|gb|EG712993.1|EG712993
EST:     AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAG                         GTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
genomic: AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAGgtttgttgat ... ccatattcagGTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
EST: gi|218498571|gb|FG951792.1|FG951792
EST:     AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAG                         GTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
genomic: AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAGgtttgttgat ... ccatattcagGTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
EST: gi|29623578|gb|CB628589.1|CB628589
EST:     AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAG                         GTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
genomic: AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAGgtttgttgat ... ccatattcagGTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
EST: gi|66916134|gb|CX102982.1|CX102982
EST:     AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAG                         GTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
genomic: AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAGgtttgttgat ... ccatattcagGTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
EST: gi|88329612|gb|CI650071.1|CI650071
EST:     AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAG                         GTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
genomic: AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAGgtttgttgat ... ccatattcagGTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
EST: gi|58684252|gb|CK072939.1|CK072939
EST:     AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAG                         GTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
genomic: AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAGgtttgttgat ... ccatattcagGTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
EST: gi|13420819|gb|AU174909.1|AU174909
EST:     AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAG                         GTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
genomic: AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAGgtttgttgat ... ccatattcagGTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
EST: gi|29627293|gb|CB632304.1|CB632304
EST:     AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAG                         GTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
genomic: AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAGgtttgttgat ... ccatattcagGTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
EST: gi|29631512|gb|CB636521.1|CB636521
EST:     AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAG                         GTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
genomic: AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAGgtttgttgat ... ccatattcagGTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
EST: gi|38565897|gb|CK085350.1|CK085350
EST:     AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAG                         GTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
genomic: AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAGgtttgttgat ... ccatattcagGTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
EST: gi|218500523|gb|FG958817.1|FG958817
EST:     AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAG                         GTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
genomic: AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAGgtttgttgat ... ccatattcagGTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
EST: gi|29644259|gb|CB649266.1|CB649266
EST:     AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAG                         GTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
genomic: AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAGgtttgttgat ... ccatattcagGTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
EST: gi|58692787|gb|CK081474.1|CK081474
EST:     AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAG                         GTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT
genomic: AAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAGgtttgttgat ... ccatattcagGTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 72 (upstream exon), 73 (downstream exon)
Score: 124

ATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAGgtttgttgat ... ccatattcagGTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTTGGTGACCATAGAGTGGCTTCCATTCAACAACAGCTTGCATCTTTAAAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtacagacttgccattttgtaaacaaactgttaacctggtttccatattcagGTTGTTGTAACTGAAGTCCTTGGTGGTGGAAAGTTCTATGTCCAAACAGTTGGTGACCATAGAGTGGCTTCCATTCAACAACAGCTTGCATCTTTAAAAC
                               tgttaac  putative branch site (score: 124)
                                          tttccat  putative PPT
                attttgtaaacaaa  TA-rich tract