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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcaattattctttaatgcaagatatgcacttattttgttccatcgtccagataaaacataatttgcttctggatgaacatgaataacttattctg...

Basic information

species Oryza sativa
transcript LOC_Os12g03470.5
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03470.5 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G006130_T06 (Zea mays), 5'ss of exon 3
GAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcaattattctttaatgcaagatatgcacttattttgttccatcgtccagataaaacataatttgcttctggatgaacatgaataacttattctg------------------
|| ||||||||||||||||||||||| |||||||| || ||||| ||||||||||||||  ||  ||||||| ||| |    |   |  ||      |  |    | ||  ||      ||  |||| | || ||   |||   ||  | ||                     
GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAGgtaccccagctattcttgaattctgtgtgc-cttttgaaacatcactagatgcacttattttgaaagctgctgccgg-tgttgatgttcaaggttttggagctggatttttacttcag

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G077299_T01 (Zea mays), 5'ss of exon 3
GAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcaattattctttaatgcaagatatgcacttattttg--------ttccatcg---tccagataaaac------ataatttgcttctgg--atgaacat--gaataacttattctg-------------------------------------------------------------------------
|| |||||||||||||| |||||||| ||||||||||||||||||||||||||||||  ||||   || | |         | |||| ||| |||||         | ||  |   |||  | |  |       | |||||| || |||  |  | | |  |||||  | || ||                                                                          
GAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAGgtgattcagccatgcct--gcttttcacatgcccttgttttgagcgtaagcttcaaagggttccgaaaatgatgaactgaaaatttgtttttggggacaagcttttgaatagatcatactaggcttttccccttcggaagcttctgtcagatgtcaaacctggattttatgcataaactgcatttatgctgcag

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G077299_T02 (Zea mays), 5'ss of exon 3
GAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcaattattctttaatgcaagatatgcacttattttg--------ttccatcg---tccagataaaac------ataatttgcttctgg--atgaacat--gaataacttattctg-------------------------------------------------------------------------
   |||||||||||||| |||||||| ||||||||||||||||||||||||||||||  ||||   || | |         | |||| ||| |||||         | ||  |   |||  | |  |       | |||||| || |||  |  | | |  |||||  | || ||                                                                          
---ATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAGgtgattcagccatgcct--gcttttcacatgcccttgttttgagcgtaagcttcaaagggttccgaaaatgatgaactgaaaatttgtttttggggacaagcttttgaatagatcatactaggcttttccccttcggaagcttctgtcagatgtcaaacctggattttatgcataaactgcatttatgctgcag

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA19G30150.1 (Glycine max), 5'ss of exon 3
GAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcaattattctttaatgcaagatatgcactt--attt---tgttccatcgtccagataaaacataatttgcttctggatgaacatgaataacttattctg
|||||||| |||||||||||||| ||| | |||||||| ||||| || || ||||||  || |  | ||||| ||       |      ||  ||||   | | | |  |  ||   | | | | |  | |   |   | |  |  |||  |    || |
GAAATCAATCATGCAGGAGCTGGGGGATTGTGGGCTGAGCTTGTGAGGAATAGAGgtcatttacgtgttcttaaaattctccttcatgtttggatttagatatgcaaatgctcaatgagatcttgacgt-cactttctttattaaaaatttcacgctcag

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G10740.1 (Arabidopsis thaliana), 5'ss of exon 3
GAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcaattattctttaatgcaa--gatatgcacttattttgttccatcgtccagataaaacataatttgcttctggatgaacatgaata----acttattctg----------------------
|| ||||||||||| || || |||||| ||||||| ||||||||||| |||||||||   |   || |   ||  | | |  || || ||      |   ||  | ||   | |  |   |  ||   | |  |||||  |  |||     | | | | |                       
GAGATCAACCATGCTGGTGCCGGTGGATTATGGGCCGAACTTGTTAGCAACAGAGgttagttttttttagcttgttactactgaaatccatgggaatcaatc-gttgtttggcttcattttctttctttacatgatgagaaaaaatgtggtagtaacttttaaggaaaaactttggtttccag

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G26120.1 (Arabidopsis thaliana), 5'ss of exon 3
GAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtactt-caattattctttaatgcaagatatgcacttattttgttccatcgtccagataaaacataa-tttgcttctggatgaacatgaataacttattctg
||||| || ||||| ||||| |||||| ||||||||||||||||||| || ||||||  ||   ||| |   ||   |     |||  |  | |||  ||  |  |    |  || | | |  |||| || | |                       
GAAATAAATCATGCTGGAGCAGGTGGACTATGGGCTGAACTTGTTAGCAATAGAGgtttttgtgattttatcttggagttttctataaagct-tttcattaaaaagaatggtgaataaaaatctttggttatag-----------------------

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv08s0040g00320.t01 (Vitis vinifera), 5'ss of exon 4
GAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcaattattctttaatgcaagatatgcacttattttgttccatcgtccagataaaacataatttgcttctggatgaacatgaataacttattctg
|| |||||||||||||||||||||||| | ||||| || ||||| || |||||||||  ||     ||   ||  |   |||||   |           | |   |  |         || |  || | |   |   |||||  |    | |   
GAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAACAGAGgtcatttctaaatctcttgttttcagataacaaggacaaaaacccgaatatttaatgtttttgtattcagcatttctgtatgcatgagaatagaactaga

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|29627933|gb|CB632944.1|CB632944
EST:     CAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG                         GTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcaat ... ttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
EST: gi|29624170|gb|CB629181.1|CB629181
EST:     CAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG                         GTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcaat ... ttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
EST: gi|29624168|gb|CB629179.1|CB629179
EST:     CAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG                         GTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcaat ... ttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
EST: gi|29627193|gb|CB632204.1|CB632204
EST:     CAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG                         GTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcaat ... ttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
EST: gi|88327708|gb|CI657748.1|CI657748
EST:     CAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG                         GTTTTGAAGCTGGAGGCCCTCATACCCC
genomic: CAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcaat ... ttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCC
EST: gi|29667031|gb|CB663306.1|CB663306
EST:     CAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG                         GTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA
genomic: CAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcaat ... ttatgcacagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAGgtacttcaattattctttaatgcaagatatgcacttattttgttccatcgtccagataaaacataatttgcttctggatgaacatgaataacttattctg

- - - - - - -  GGAGCT
- - - - - - - - - - TGGTGG
- - - - - - - - - -  GGTGGA