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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattcctattgagcttatttttaatttcgacatattgtttggtccttgctgatgtaatgatgaatacctttttattggtccatttggatttttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAAGAACTTATTGAAGCTTGCAAACCAGCACTTGAATCAGAATATGTCACCA

Basic information

species Oryza sativa
transcript LOC_Os01g38620.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g38620.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G142984_T02 (Zea mays), 3'ss of exon 2
gattcctattgagcttatttttaatttcgac---atattgtttggtccttgctgatgtaatgatga-atacctttttattggtccatttggatttttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAAGAACTTATTGAAGCTTGCAAACCAGCACTTGAATCAGAATATGTCACCA
      |  |   ||| || || |  | |     | | |||    ||  | |   ||  ||  |||  | |  |  | || ||    |||  |   | || ||| ||||||| ||||| ||||||||| |||||||||||||||||||||| |||||||||||| ||||||| || || |||||||| || ||  || ||||||
---atatgcttgtcttgttcttgaggttgttcctaaagtgtccactctctacatttgagatcctgatgtgctatactttttgtt-ggttgtctacatattgcagCTTGCATTCCCTGATGCTGTTTACCTAGTTGATGCTATTGAGGGTGGAAAAGAACTTATTCAAGCTTGTAAGCCCGCACTTGAGTCTGATCATATCACCA

upper sequence: LOC_Os01g38620.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G081924_T01 (Zea mays), 3'ss of exon 2
---------gattcctattgagcttatttttaatttcgacatattgtttggtccttgctgatgtaatgatgaatacctttttattggtccatttggatttttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAAGAACTTATTGAAGCTTGCAAACCAGCACTTGAATCAGAATATGTCACCA
           || || ||||| || |  | || |    ||| |   |   ||   | |  ||  ||||   |   |||||| |||||     ||   || | || ||| ||||||| ||||||||||||||| |||||||||||||||||||||| |||||||||||| ||||||| || || |||||||| || ||  || ||||||
atatacttgacttgctcttgaggttgtcctaaagtgtc-catctctctacatctaagatactgacatgacata---ctttttgttggt-----tgtcgttatattgcagCTTGCATTCCCTGACGCTGTTTACCTAGTTGATGCTATTGAGGGTGGAAAAGAACTTATTCAAGCTTGTAAGCCCGCACTTGAGTCTGATCATATCACCA

upper sequence: LOC_Os01g38620.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G142984_T01 (Zea mays), 3'ss of exon 2
gattcctattgagcttatttttaatttcgac---atattgtttggtccttgctgatgtaatgatga-atacctttttattggtccatttggatttttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAAGAACTTATTGAAGCTTGCAAACCAGCACTTGAATCAGAATATGTCACCA
      |  |   ||| || || |  | |     | | |||    ||  | |   ||  ||  |||  | |  |  | || ||    |||  |   | || ||| ||||||| ||||| ||||||||| |||||||||||||||||||||| |||||||||||| ||||||                                 
---atatgcttgtcttgttcttgaggttgttcctaaagtgtccactctctacatttgagatcctgatgtgctatactttttgtt-ggttgtctacatattgcagCTTGCATTCCCTGATGCTGTTTACCTAGTTGATGCTATTGAGGGTGGAAAAGAACTTATTCAAGCTT---------------------------------

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|218487804|gb|FG952787.1|FG952787
EST:     ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAG                         ATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
genomic: ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAGgtgagttcaa ... tttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
EST: gi|58594793|gb|CF993101.1|CF993101
EST:     --TGTGAAGGCGTA-ACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAG                         ATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
genomic: ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAGgtgagttcaa ... tttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
EST: gi|218504651|gb|FG960768.1|FG960768
EST:     ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAG                         ATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
genomic: ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAGgtgagttcaa ... tttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
EST: gi|58655403|gb|CK044083.1|CK044083
EST:     ATGGTGCTCTCTGTATCATGCAG                         ATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
genomic: ATGGTGCTCTCTGTATCATGCAGgtgagttcaa ... tttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
EST: gi|27577966|gb|CB000661.1|CB000661
EST:     ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAG                         ATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
genomic: ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAGgtgagttcaa ... tttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
EST: gi|38473357|gb|CF957489.1|CF957489
EST:     ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAG                         ATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
genomic: ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAGgtgagttcaa ... tttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
EST: gi|58588638|gb|CF986946.1|CF986946
EST:     ATTGTGAAGGCGTAGACCTTTGCCGACATGGTGCTCTCTGTATCATGCAG                         ATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
genomic: ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAGgtgagttcaa ... tttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
EST: gi|313080792|gb|HO213589.1|HO213589
EST:     ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAG                         ATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
genomic: ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAGgtgagttcaa ... tttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
EST: gi|58598824|gb|CK009352.1|CK009352
EST:     ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAG                         ATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
genomic: ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAGgtgagttcaa ... tttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
EST: gi|218483500|gb|FG948234.1|FG948234
EST:     ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAG                         ATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
genomic: ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAGgtgagttcaa ... tttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
EST: gi|218502513|gb|FG958404.1|FG958404
EST:     TTGTGAAGGCGTAGA-CTTTGCCGCCAATGGTGC-CTCTGTAT-ATGCAG                         ATTGCA-TTCCTGACGCTGTTTA-TTAGTTGATGCTATTGAGGGTGGGAAA
genomic: TTGTGAAGGCGTAGACCTTTGCCGCC-ATGGTGCTCTCTGTATCATGCAGgtgagttcaa ... tttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctgatgtaatgatgaatacctttttattggtccatttggatttttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAAGAACTTATTGAAGCTTGCAAACCAGCACTTGAATCAGAATATGTCACCA
 tgctgat  putative branch site (score: 3)
                                           tttttttttc  putative PPT
                                    atttggattttttttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattcctattgagcttatttttaatttcgacatattgtttggtccttgctgatgtaatgatgaatacctttttattggtccatttggatttttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAAGAACTTATTGAAGCTTGCAAACCAGCACTTGAATCAGAATATGTCACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC