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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcttattttcttcttggttgcagagtttttgatgtatttttatttacagcaaactgtacctataaaggaaaaagatgctgacctatttatctcctgtagGTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAG

Basic information

species Oryza sativa
transcript LOC_Os03g17120.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17120.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G044237_T03 (Zea mays), 3'ss of exon 11
atcttattttcttcttggttgcagagtttt-tgatgtatttttatttac--agcaaac-----tgtacctataaaggaaaaagatgctgacctatttatctcctgtagGTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAG
      | || ||||  |   |  |  | | |    || ||||  |  |  |||  ||     | ||||| | |||   |   |||||||| ||||  |  | |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||| |||||||||
------tattgttctcagcaacgcatctctgtaccttagttttgctccctaagccgacactgttttacctgttaagttcat--atgctgacttattccttccttgtagGTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAG

upper sequence: LOC_Os03g17120.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA13G19450.1 (Glycine max), 3'ss of exon 12
atcttattttcttcttggttgcag-agtttttgatgtatttttatttacagcaaactgtacctataaaggaaaaagatgctgacctatttatctcctgtagGTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAG
 || |  ||| |||     | |   || | |     || |||  | | ||  |      |   | |||     ||| |  |||  |  || |    |  ||||||||||||||||||| ||||| ||||| |||||||| || || |||||||| ||  |||||
gtcatcctttattccaacctccttcagatgtaagcataatttattcttcaaaagtgcccagtcagaaaatgtgaag-ttttgagttgattgttctttccagGTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGGGAAGGAGCAACATGCCTCGTTGAG

upper sequence: LOC_Os03g17120.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA10G05090.1 (Glycine max), 3'ss of exon 11
--atcttattttcttct-tggttgcagagtttttgatgtatttttatttacagcaaactgtacctataaaggaaaaagatgctgacctatttatctcctgtagGTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAG
   |   || ||||||  ||||| |   |      ||||| |||  | | ||  |     |    | |||     ||| |  |||  |  || |    |  ||||||||||||||||||| ||||| ||||| |||||||| || ||||||||||| ||  |||||
cctttagatcttcttccatggttacctcgagac--atgtaatttattcttcaaaagtgcctggtcagaaaatgtgaag-ttttgagttgattgttctttccagGTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGAGAAGGTGCAACATGCCTCGTTGAG

upper sequence: LOC_Os03g17120.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT2G37500.2 (Arabidopsis thaliana), 3'ss of exon 12
atcttattttcttcttggttgcagagtttttgatgtatttttatttacagcaaactgtacctataaaggaaaaagatgctgacctatttatctcctgtagGTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAG
                       |  | | || | | ||  ||| | |  | ||| ||   |  ||  |    |  |            ||||  |  |||| |||||||| ||||| ||||| ||||| ||||||||||| ||||| |||||||| || |||
-----------------------gtatgtatgttattttgctatcttc--ctaacagt-tgttcaagagctggacttaacatggagcccatctttttcagGTGATGCAAGGACTTGCTAAATCAATAGCTTGGGATGGTGAAGGTGCTACATGTCTCATCGAG

upper sequence: LOC_Os03g17120.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv08s0040g03320.t01 (Vitis vinifera), 3'ss of exon 12
-atcttattttcttcttggttgcagagtttttgatgtatttttatttacagcaaactgtacctataaaggaaaaagatgctgacctatttatctcctgtagGTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAG
 |     ||  ||  |  | |  ||||  ||  || |  |  ||||     ||  || |   |  ||       || |  | ||  || |   |  |  |||||||||| |||||||||||||| |||||||||||||| || || |||||||| |||||||||
aagtcagttggctcatgaggtttagaggcttgaat-ttctactattatggacagcctttgggtccaatctggtcagttcttaacaaatgtccttttttcagGTAATGCAGGGTCTTGCAAAATCAATAGCATGGGATGGAGAAGGAGCAACATGCCTAATTGAG

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|27546388|gb|CA767223.2|CA767223
EST:     TTACTCATGATAGCACTGAAGCTCAACAGTTCCAAGCATGCTTAGATGCT                         GTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACA
genomic: TTACTCATGATAGCACTGAAGCTCAACAGTTCCAAGCATGCTTAGATGCTgtaagtttta ... tctcctgtagGTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACA
EST: gi|218494800|gb|FG943469.1|FG943469
EST:     TACTCAAGATAGCACTGAAGCTCAACAGTTCCAAGCATAGCTTAGATGCT                         GTAATACAAGGTCTTGCAAAATCCATAGCATGGGAT
genomic: TACTCATGATAGCACTGAAGCTCAACAGTTCCAAGCAT-GCTTAGATGCTgtaagtttta ... tctcctgtagGTAATGCAAGGTCTTGCAAAATCCATAGCATGGGAT
EST: gi|29613227|gb|CB618240.1|CB618240
EST:     TTACTCATGATAGCACTGAAGCTCAACAGTTCCAAGCATGCTTAGATGCT                         GTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACA
genomic: TTACTCATGATAGCACTGAAGCTCAACAGTTCCAAGCATGCTTAGATGCTgtaagtttta ... tctcctgtagGTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACA
EST: gi|29670993|gb|CB667268.1|CB667268
EST:     TTACTCATGATAGCACTGAAGCTCAACAGTTCCAAGCATGCTTAGATGCT                         GTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACA
genomic: TTACTCATGATAGCACTGAAGCTCAACAGTTCCAAGCATGCTTAGATGCTgtaagtttta ... tctcctgtagGTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacagcaaactgtacctataaaggaaaaagatgctgacctatttatctcctgtagGTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAG
                               tgctgac  putative branch site (score: 2)
                                     cctatttatctcct  CT-rich tract
                                       tatttatct  TA-rich tract