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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggttactagaaatagtctatagtagttgtgtttggttacaaataagtcaaattgtaccactcattcatttatttattccttccatcattgtgtttgattttggttccagGTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAACTGTTTCTGACGAAG

Basic information

species Oryza sativa
transcript LOC_Os08g26870.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g26870.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G146355_T01 (Zea mays), 3'ss of exon 6
gtaaggttactagaaatagtctatagtagttgtgtttggttacaaataagtcaaattgtaccactcattcatttatttattccttccatcattgtgtttgattttggttccagGTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAACTGTTTCTGACGAAG
      ||||| | ||   | | ||| || | || ||  ||        |||||   | |    | |||||| |  ||   ||||| |||||  || | | |||||| | ||||||||||| ||| || |||| |||||||||||||||||||||||||| ||||| | | | || |||
---tttttacttgtaagcatttgtagcagatatgcttacttg-------gtcaaggagaa--gttaattcatcttattgccccttctatcatgatggt-ggttttgggttcagGTAAAACTTGTTAGGGTAAACAAAAGAATTCAAGAAGCATACTGTGCCGAACTTTATTTAACAAAG

upper sequence: LOC_Os08g26870.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G148892_T01 (Zea mays), 3'ss of exon 4
---gtaaggttactagaaatagtctatagtagttgtgtttggttacaaataagtcaaattgtaccactcattcatttatttattccttccatcattgtgtttgattttggttccagGTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAACTGTTTCTGACGAAG---
    ||   ||||| | ||   | | ||| || | || ||  ||        |||||   | |    | |||||| |  ||   ||||| |||||  || | | |||||| | |||||||||||  || |  |||| ||||||||||||||||| |||||||||||||| | | | || |||   
gtaatatttttacttgtaagcatttgtagcagatatgcttacttg-------gtcaaggagaa--gttaattcatcttattgccccttctatcatgatggt-ggttttgggttcagGTAAAACTTATTAGTGTAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAGGTA

upper sequence: LOC_Os08g26870.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G377595_T01 (Zea mays), 3'ss of exon 5
---gtaaggttactagaaatagtctatagtagttgtgtttggttacaaataagtcaaattgtaccactcattcatttatttattccttccatcattgtgtttgattttggttccagGTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAACTGTTTCTGACGAAG
    |    ||||| | ||   | | ||| || | || ||  ||        |||||   | |    | |||||| |  ||   ||||| |||||  || | | |||||| | ||||||||||| ||| || |||| ||||||||||||||||||||||||||||| || | | | || |||
gtaatctttttacttgtaagcatttgtagcagatatgcttacttg-------gtcaaggagaa--gttaattcatattattgccccttctatcatgatggt-ggttttgggttcagGTAAAACTTGTTAGGGTAAACAAAAGAATTCAAGAAGCATACTGTGCTGATCTTTATTTAACAAAG

upper sequence: LOC_Os08g26870.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G053531_T02 (Zea mays), 3'ss of exon 5
---gtaaggttactagaaatagtctatagtagttgtgtttggttacaaataagtcaaattgtaccactcattcatttatttattccttccatcattgtgtttgattttggttccagGTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAACTGTTTCTGACGAAG
    |    ||||| | ||   | | ||| || | || ||  ||        |||||   | |    | |||||| |  ||   ||||| |||||  || | | |||||| | ||||||||||| ||| || |||| ||||||||||||||||| |||||||||||||| | | | || |||
gtaatctttttacttgtaagcatttgtagcagatatgcttacttg-------gtcaaggagaa--gttaattcatcttattgccccttctatcatgatggt-ggttttgggttcagGTAAAACTTGTTAGGGTAAACAAAAGAATTCAAGAAGCCTACTGTGCTGAACTTTATTTAACAAAG

upper sequence: LOC_Os08g26870.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G006468_T05 (Zea mays), 3'ss of exon 4
gtaaggtta-ctagaaatagtctatagtagttgtgtttggttacaaataagtcaaattgtaccactcattcatttatttattccttccatcattgtgtttgattttggttccagGTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAACTGTTTCTGACGAAG
||||  |||  | | ||   | | | | |||| || ||  |||  |  |||   || |  ||   | |||||| |  |||| ||||  ||| |  || | | |||||| | ||||||||||| |||||| |||| ||||||||||||||||| |||||||||||||| | ||| || |||
gtaatcttaattcgtaagcctttgttgcagttatgcttattta--atcaaggagaagttaac--ttaattcatcttcttatcccttttatcttgatggt-ggttttgggttcagGTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAACTTTGTCTAACAAAG

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|29659232|gb|CB655507.1|CB655507
EST:     CAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGTTATGAG                         GTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAA
genomic: CAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGTTATGAGgtaaggttac ... ttggttccagGTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAA
EST: gi|109974602|gb|DT806998.1|DT806998
EST:     CAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGTTATGAG                         GTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAA
genomic: CAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGTTATGAGgtaaggttac ... ttggttccagGTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAA
EST: gi|84117164|gb|CD150931.1|CD150931
EST:     CAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGTTATGAG                         GTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAA
genomic: CAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGTTATGAGgtaaggttac ... ttggttccagGTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAA
EST: gi|58687907|gb|CK076594.1|CK076594
EST:     CAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGTTATGAG                         GTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAA
genomic: CAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGTTATGAGgtaaggttac ... ttggttccagGTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAA
EST: gi|218495687|gb|FG969804.1|FG969804
EST:     CAACCATATATCACGTTGTGAAGGAGATGATTGATAAGATGGGTTATGAG                         GTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAA
genomic: CAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGTTATGAGgtaaggttac ... ttggttccagGTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAA
EST: gi|58692668|gb|CK081355.1|CK081355
EST:     CAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGTTATGAG                         GTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAA
genomic: CAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGTTATGAGgtaaggttac ... ttggttccagGTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAA
EST: gi|29629366|gb|CB634377.1|CB634377
EST:     CAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGTTATGAG                         GTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAA
genomic: CAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGTTATGAGgtaaggttac ... ttggttccagGTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAA
EST: gi|33683462|gb|CF311701.1|CF311701
EST:     CAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGTTATGGG                         GTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAA
genomic: CAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGTTATGAGgtaaggttac ... ttggttccagGTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAA
EST: gi|58605333|gb|CK033366.1|CK033366
EST:     CAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGTTATGAG                         GTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAA
genomic: CAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGTTATGAGgtaaggttac ... ttggttccagGTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccactcattcatttatttattccttccatcattgtgtttgattttggttccagGTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAACTGTTTCTGACGAAG
                                     gtttgat  putative branch site (score: 5)
      tcattcatttatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggttactagaaatagtctatagtagttgtgtttggttacaaataagtcaaattgtaccactcattcatttatttattccttccatcattgtgtttgattttggttccagGTAAAACTGGTTCGGATAAATAAAAGAATTCAAGAAGCATACTGTGCTGAACTGTTTCTGACGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC