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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctcataaacttatattgtgcatccgggttggcttcagcagtacttcatattccaaaacattatttacctaacaataatcgatctctgtaactgatacagATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCGGAGCTGCTGCACCGCAGATTCCACAGGCGTTGATTGAGCAGCTAAAGCC

Basic information

species Oryza sativa
transcript LOC_Os08g44280.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44280.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G423027_T01 (Zea mays), 3'ss of exon 4
tctcataaacttatattgtgcatccgggttggcttcagcagtacttcatattccaaa-acattatttacctaa--caataatcgatctctgtaactgatacagATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCGGAGCTGCTGCACCGCAGATTCCACAGGCGTTGATTGAGCAGCTAAAGCC
   | ||   |   | | ||   |     ||  ||||||| |  |   | ||| | | ||  |    || | |  ||  ||  ||| | |  ||  ||| |||||||||| |||||||||||||| || ||||||||||| ||||||||||| |||||||| ||||||||||| ||  ||||| |||| |||||||| |||||
--ccttagtttggcactctg-gccttatgtgcattcagcattgttggttgttctatatacccttaacacttgatgcaccaagagatgtttaaaatggatgcagATGGCAGGGAAGGTTGGCCAGAACTGGCACCCTATGAAGCCATCCATGTTGGAGCTGCAGCACCGCAGATCCCCGAGGCGCTGATCGAGCAGCTGAAGCC
















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|86601157|gb|CI356914.1|CI356914
EST:     TATACATATTACCG                         ATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
genomic: TATACATATTACCGgtaagtagcg ... actgatacagATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
EST: gi|12405081|gb|AU166682.1|AU166682
EST:     GTATACATATTACCG                         ATGGCAAAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
genomic: GTATACATATTACCGgtaagtagcg ... actgatacagATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
EST: gi|86822716|gb|CI251801.1|CI251801
EST:     TTAACTGATGGATCCCTCAGTATACATATTACCG                         ATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
genomic: TTAACTGATGGATCCCTCAGTATACATATTACCGgtaagtagcg ... actgatacagATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
EST: gi|33814509|gb|CF333119.1|CF333119
EST:     TGCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCG                         ATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
genomic: TGCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCGgtaagtagcg ... actgatacagATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
EST: gi|86538317|gb|CI178523.1|CI178523
EST:     TGCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCG                         ATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
genomic: TGCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCGgtaagtagcg ... actgatacagATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
EST: gi|88224333|gb|CI224182.1|CI224182
EST:     ATACATATTACCG                         ATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
genomic: ATACATATTACCGgtaagtagcg ... actgatacagATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
EST: gi|27547530|gb|CA765568.2|CA765568
EST:     TGCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCG                         ATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
genomic: TGCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCGgtaagtagcg ... actgatacagATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
EST: gi|86507775|gb|CI150408.1|CI150408
EST:     TGCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCG                         ATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
genomic: TGCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCGgtaagtagcg ... actgatacagATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
EST: gi|87016037|gb|CI281780.1|CI281780
EST:     TGCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCG                         ATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
genomic: TGCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCGgtaagtagcg ... actgatacagATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
EST: gi|88224109|gb|CI223958.1|CI223958
EST:     TGCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCG                         ATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
genomic: TGCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCGgtaagtagcg ... actgatacagATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
EST: gi|55414903|gb|CV727279.1|CV727279
EST:     CAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCG                         ATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTTG
genomic: CAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCGgtaagtagcg ... actgatacagATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
EST: gi|86598094|gb|CI278484.1|CI278484
EST:     TGCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCG                         ATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
genomic: TGCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCGgtaagtagcg ... actgatacagATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
EST: gi|33817249|gb|CF334461.1|CF334461
EST:     GCAGCGGCTCCACAGTTAACTGATGGATCCCTCACGTATACATATTACCG                         ATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
genomic: GCAGCGGCTCCACAGTTAACTGATGGATCCCTCA-GTATACATATTACCGgtaagtagcg ... actgatacagATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
EST: gi|9866234|gb|AU101984.1|AU101984
EST:     GCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACCATATTACCG                         ATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
genomic: GCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATA-CATATTACCGgtaagtagcg ... actgatacagATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
EST: gi|86824521|gb|CI263016.1|CI263016
EST:     TGCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCG                         ATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
genomic: TGCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCGgtaagtagcg ... actgatacagATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
EST: gi|86534228|gb|CI174434.1|CI174434
EST:     TGCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCG                         ATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
genomic: TGCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCGgtaagtagcg ... actgatacagATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
EST: gi|88216795|gb|CI216397.1|CI216397
EST:     TGCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCG                         ATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
genomic: TGCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCGgtaagtagcg ... actgatacagATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
EST: gi|89197889|gb|CI013879.1|CI013879
EST:     TGCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCG                         ATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
genomic: TGCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCGgtaagtagcg ... actgatacagATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
EST: gi|29689479|gb|CB685754.1|CB685754
EST:     TGCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCG                         ATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG
genomic: TGCAGCGGCTCCACAGTTAACTGATGGATCCCTCAGTATACATATTACCGgtaagtagcg ... actgatacagATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatattccaaaacattatttacctaacaataatcgatctctgtaactgatacagATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCGGAGCTGCTGCACCGCAGATTCCACAGGCGTTGATTGAGCAGCTAAAGCC
         aaaacattattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctcataaacttatattgtgcatccgggttggcttcagcagtacttcatattccaaaacattatttacctaacaataatcgatctctgtaactgatacagATGGCAGAGAAGGTTGGCCAGAGCTCGCACCCTATGATGCCATCCATGTCGGAGCTGCTGCACCGCAGATTCCACAGGCGTTGATTGAGCAGCTAAAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- -cataaac
- - - - - - - - - tgcatcc
- - - - - - - - - - - - - - - - cttcagc
- - - - - - - - - - - - - - - - - - - - - - - - - -tccaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaata