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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagtactatgatctaccacctgttagtgcataaaagagatatcaaattatacatgtggtgaactggtgattgatagtccagcattttcattctcttgtagGAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGTCCATTAGTGCCAGTGATCATTGGCTAGGAATAGGTGCTGCTGACAACTC

Basic information

species Oryza sativa
transcript LOC_Os01g39380.1
intron # 30
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g39380.1 (Oryza sativa), 3'ss of exon 30
lower sequence: GRMZM2G074466_T01 (Zea mays), 3'ss of exon 10
cagtactatgatctaccacctgttagtgcataaaagagatatcaaattatacatgtgg----tgaac-tggtgattgatagtccagcattttcat-tctcttgtagGAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGTCCATTAGTGCCAGTGATCATTGGCTAGGAATAGGTGCTGCTGACAACTC
      | |  | |    ||||||| |   |   |    ||| || |    | | | |    || || |||      | | |  |||||||   | ||| ||  ||||||||||| ||| |||||||| ||||| |||||| | ||||| |||||||||||||||||||||||||| |||||||  || ||||||||||| || ||
------ttttttttctttcctgttatttttttggaagtttataaagtctatcctttagctactgcacatggcctaaaaaactaaagcatttcgttctcttttacagGAGGAATAAAATGCGTCAAGAATCTTACACTTCACACAGCATCCGTTCTGTCCATTAGTGCCAGTGATCACTGGCTAGCGATTGGTGCTGCTGATAATTC
















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|86504094|gb|CI146727.1|CI146727
EST:     GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG                         GAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGT
genomic: GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAGgtgagatctt ... tctcttgtagGAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGT
EST: gi|29628945|gb|CB633956.1|CB633956
EST:     GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG                         GAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGT
genomic: GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAGgtgagatctt ... tctcttgtagGAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGT
EST: gi|29641895|gb|CB646902.1|CB646902
EST:     GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG                         GAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGT
genomic: GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAGgtgagatctt ... tctcttgtagGAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGT
EST: gi|86257231|gb|CI004049.1|CI004049
EST:     GATGGGCTTATACGTTTTTGGGAAAATGAAG                         GAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGT
genomic: GATGGGCTTATACGTTTTTGGGAAAATGAAGgtgagatctt ... tctcttgtagGAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGT
EST: gi|29639658|gb|CB644667.1|CB644667
EST:     GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG                         GAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGT
genomic: GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAGgtgagatctt ... tctcttgtagGAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGT
EST: gi|58694575|gb|CK083262.1|CK083262
EST:     GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG                         GAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGT
genomic: GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAGgtgagatctt ... tctcttgtagGAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGT
EST: gi|27547319|gb|CA765549.2|CA765549
EST:     GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG                         GAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGT
genomic: GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAGgtgagatctt ... tctcttgtagGAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGT
EST: gi|22304904|gb|BQ906126.1|BQ906126
EST:     GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG                         GAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGT
genomic: GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAGgtgagatctt ... tctcttgtagGAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGT
EST: gi|325493716|gb|JG458240.1|JG458240
EST:     GTTCCTCTGATGGGCTTATACGTTTATGGGAAAATGAAG                         GAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGT
genomic: GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAGgtgagatctt ... tctcttgtagGAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGT
EST: gi|88845811|gb|CI084541.1|CI084541
EST:     GGGAAAATGAAG                         GAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGT
genomic: GGGAAAATGAAGgtgagatctt ... tctcttgtagGAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGT
EST: gi|38476896|gb|CF961029.1|CF961029
EST:     GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG                         GAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGT
genomic: GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAGgtgagatctt ... tctcttgtagGAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatacatgtggtgaactggtgattgatagtccagcattttcattctcttgtagGAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGTCCATTAGTGCCAGTGATCATTGGCTAGGAATAGGTGCTGCTGACAACTC
                      gattgat  putative branch site (score: 4)
                                    cattttcattctctt  putative PPT
                                     attttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagtactatgatctaccacctgttagtgcataaaagagatatcaaattatacatgtggtgaactggtgattgatagtccagcattttcattctcttgtagGAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGTCCATTAGTGCCAGTGATCATTGGCTAGGAATAGGTGCTGCTGACAACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - cacctgt
- - - - - - - - - - - - -gtgcata
- - - - - - - - - - - - - - - - -aagagata
- - - - - - - - - - - - - - - - - - - - - - - - atacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctggtga