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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttaagctaatatgcctacttataacattgtcagttttacacgtatgtgtcacctttccgtatcccttacttgtttcaatgtgttttttctgaagtctagGTACAAGGAAGCGGAGGGTGACTATAGCAAATACCTGGAGCTAAAACCTGGGAGTTCTTCTGTGGAAAAGGAATTATCTCAACTGCTTCAGGCTCAAAAT

Basic information

species Oryza sativa
transcript LOC_Os01g74580.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g74580.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G341404_T01 (Zea mays), 3'ss of exon 3
gttaagctaatatgcctacttataacattgtcagttttacacgtatgtgtcacctttcc---gtatcccttacttgtttcaatgtgttttttctgaagtctagGTACAAGGAAGCGGAGGGTGACTATAGCAAATACCTGGAGCTAAAACCTGGGAGTTCTTCTGTGGAAAAGGAATTATCTCAACTGCTTCAGGCTCAAAAT
   |||   | ||| ||||  | | | |||||| |||||||| |     | || | | |   | ||  ||||  ||   |  | || ||||  | ||||| || ||| ||||||| ||| | ||||||| |||| ||||||||||||  ||||||  | |||| ||||  ||||||||||| || || || ||||||||||||
-gaaagaggacatgtctaccaaaatccttgtca-ttttacacctgc-cattacttattccttgcatgtcttatgtgcaactgtatgcttttcttaaagtccagATACGAGGAAGCTGAGAGGGACTATAACAAACACCTGGAGCTAAGTCCTGGGTCTGCTTCAGTGGTGAAGGAATTATCCCAGCTTCTGCAGGCTCAAAAT
















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|33678961|gb|CF307200.1|CF307200
EST:     CACTCAGAAGCTTACAGGCAGCGTGCATCTGTGCTTCGTCACAAGTGCAG                         GTACAAGGAAGCGGAGGGTGACTATAGCAAATACCTGGAGCTAAAACCTGG
genomic: CACTCAGAAGCTTACAGGCAGCGTGCATCTGTGCTTCGTCACAAGTGCAGgtaaaaaatt ... tgaagtctagGTACAAGGAAGCGGAGGGTGACTATAGCAAATACCTGGAGCTAAAACCTGG
EST: gi|218484052|gb|FG943456.1|FG943456
EST:     CACTCAGAAGCTTACAGGCAGCGTGCATCTGTGCTTCGTCACAAGTGCAG                         GTACAAGGAAGCGGAGGGTGACTATAGCAAATACCTGGAGCTAAAACCTGG
genomic: CACTCAGAAGCTTACAGGCAGCGTGCATCTGTGCTTCGTCACAAGTGCAGgtaaaaaatt ... tgaagtctagGTACAAGGAAGCGGAGGGTGACTATAGCAAATACCTGGAGCTAAAACCTGG
EST: gi|29616879|gb|CB621891.1|CB621891
EST:     CACTCAGAAGCTTACAGGCAGCGTGCATCTGTGCTTCGTCACAAGTGCAG                         GTACAAGGAAGCGGAGGGTGACTATAGCAAATACCTGGAGCTAAAACCTGG
genomic: CACTCAGAAGCTTACAGGCAGCGTGCATCTGTGCTTCGTCACAAGTGCAGgtaaaaaatt ... tgaagtctagGTACAAGGAAGCGGAGGGTGACTATAGCAAATACCTGGAGCTAAAACCTGG
EST: gi|5004270|gb|AU069419.1|AU069419
EST:     CACTCAGAAGCTTACAGGCAGCGTGCATCTGTGCTTCGTCACAAGTGCAG                         GTACAAGGAAGCGGAGGGTGACTATAGCAAATACCTGGAGCTAAAACCTGG
genomic: CACTCAGAAGCTTACAGGCAGCGTGCATCTGTGCTTCGTCACAAGTGCAGgtaaaaaatt ... tgaagtctagGTACAAGGAAGCGGAGGGTGACTATAGCAAATACCTGGAGCTAAAACCTGG
EST: gi|117246981|gb|CT843770.1|CT843770
EST:     CACTCAGAAGCTTACAGGCAGCGTGCATCTGTGCTTCGTCACAAGTGCAG                         GTACAAGGAAGCGGAGGGTGACTATAGCAAATACCTGTAGCTAAAACCTGG
genomic: CACTCAGAAGCTTACAGGCAGCGTGCATCTGTGCTTCGTCACAAGTGCAGgtaaaaaatt ... tgaagtctagGTACAAGGAAGCGGAGGGTGACTATAGCAAATACCTGGAGCTAAAACCTGG
EST: gi|58677217|gb|CK065904.1|CK065904
EST:     CACTCAGAAGCTTACAGGCAGCGTGCATCTGTGCTTCGTCACAAGTGCAG                         GTACAAGGAAGCGGAGGGTGACTATAGCAAATACCTGGAGCTAAAACCTGG
genomic: CACTCAGAAGCTTACAGGCAGCGTGCATCTGTGCTTCGTCACAAGTGCAGgtaaaaaatt ... tgaagtctagGTACAAGGAAGCGGAGGGTGACTATAGCAAATACCTGGAGCTAAAACCTGG
EST: gi|2310536|gb|C26691.1|C26691
EST:     CACTCAGAAGCTTACAGGCAGCGTGCATCTGTGCTTCGTCACAAGTGCAG                         GTACAAGGAAGCGGAGGGTGACTATAGCAAATACCTGGAGCTAAAACCTGG
genomic: CACTCAGAAGCTTACAGGCAGCGTGCATCTGTGCTTCGTCACAAGTGCAGgtaaaaaatt ... tgaagtctagGTACAAGGAAGCGGAGGGTGACTATAGCAAATACCTGGAGCTAAAACCTGG
EST: gi|33676606|gb|CF304845.1|CF304845
EST:     CACTCAGAAGCTTACAGGCAGCGTGCATCTGTGCTTCGTCACAAGTGCAG                         GTACAAGGAAGCGGAGGGTGACTATAGCAAATACCTGGAGCTAAAACCTGG
genomic: CACTCAGAAGCTTACAGGCAGCGTGCATCTGTGCTTCGTCACAAGTGCAGgtaaaaaatt ... tgaagtctagGTACAAGGAAGCGGAGGGTGACTATAGCAAATACCTGGAGCTAAAACCTGG
EST: gi|29679525|gb|CB675800.1|CB675800
EST:     CACTCAGAAGCTTACAGGCAGCGTGCATCTGTGCTTCGTCACAAGTGCAG                         GTACAAGGAAGCGGAGGGTGACTATAGCAAATACCTGGAGCTAAAACCTGG
genomic: CACTCAGAAGCTTACAGGCAGCGTGCATCTGTGCTTCGTCACAAGTGCAGgtaaaaaatt ... tgaagtctagGTACAAGGAAGCGGAGGGTGACTATAGCAAATACCTGGAGCTAAAACCTGG
EST: gi|33677524|gb|CF305763.1|CF305763
EST:     CACTCAGAAGCTTACAGGCAGCGTGCATCTGTGCTTCGTCACAAGTGCAG                         GTACAAGGAAGCGGAGGGTGACTATAGCAAATACCTGGAGCTAAAACCTGG
genomic: CACTCAGAAGCTTACAGGCAGCGTGCATCTGTGCTTCGTCACAAGTGCAGgtaaaaaatt ... tgaagtctagGTACAAGGAAGCGGAGGGTGACTATAGCAAATACCTGGAGCTAAAACCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtcacctttccgtatcccttacttgtttcaatgtgttttttctgaagtctagGTACAAGGAAGCGGAGGGTGACTATAGCAAATACCTGGAGCTAAAACCTGGGAGTTCTTCTGTGGAAAAGGAATTATCTCAACTGCTTCAGGCTCAAAAT
                  cccttac  putative branch site (score: 3)
                                    tgttttttct  putative PPT
                                    tgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaagctaatatgcctacttataacattgtcagttttacacgtatgtgtcacctttccgtatcccttacttgtttcaatgtgttttttctgaagtctagGTACAAGGAAGCGGAGGGTGACTATAGCAAATACCTGGAGCTAAAACCTGGGAGTTCTTCTGTGGAAAAGGAATTATCTCAACTGCTTCAGGCTCAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - tgcctac
- - - - - - - - - - - - - - - - - - - - - gtatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgttt