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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGAATGGTCTCGGAGGGTTCTTAGCTGGCTTTTCGATTGGATTAGCAGCAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgctgttctttcaccttgtatgtgtggattgttcagatgttacctgtgttgttgtctctgtcgtccgatggacgggtccgtgtgattgtgttcg...

Basic information

species Oryza sativa
transcript LOC_Os04g51400.5
intron # 1
splice site 5'
intron type U2

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|29643914|gb|CB648921.1|CB648921
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAG                         TTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... tcatttccagTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
EST: gi|29676636|gb|CB672911.1|CB672911
EST:     CAGCCGGGTCACACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAG                         TTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... tcatttccagTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
EST: gi|29622172|gb|CB627183.1|CB627183
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGTCATTTCCAG                
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGG--A---A-----AGgttggccgct ... t
EST: gi|29671276|gb|CB667551.1|CB667551
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAG                         TTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... tcatttccagTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
EST: gi|427890|gb|D24032.1|D24032
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTNCCGCAGAAGGGAGAAGGAAAG                         TTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... tcatttccagTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
EST: gi|58689183|gb|CK077870.1|CK077870
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAG                         TTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... tcatttccagTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
EST: gi|29688856|gb|CB685131.1|CB685131
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAG                         TTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... tcatttccagTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
EST: gi|88407370|gb|CI583828.1|CI583828
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAG                         TTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... tcatttccagTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
EST: gi|58594947|gb|CF993255.1|CF993255
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAG                         TTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... tcatttccagTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
EST: gi|88370919|gb|CI595031.1|CI595031
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAG                         TTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... tcatttccagTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
EST: gi|87006839|gb|CI285873.1|CI285873
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAG                         TTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... tcatttccagTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
EST: gi|29676638|gb|CB672913.1|CB672913
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAG                         TTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... tcatttccagTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
EST: gi|58695550|gb|CK084237.1|CK084237
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAG                         TTTCAGGTTGAAACATCTAAC
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... tcatttccagTTTCAGGT-GAA-CATCTAAC
EST: gi|12622914|gb|AU173127.1|AU173127
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAG                         TTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... tcatttccagTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
EST: gi|84117187|gb|CD150954.1|CD150954
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAG                         TTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... tcatttccagTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
EST: gi|58654339|gb|CK043019.1|CK043019
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAG                         TTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... tcatttccagTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
EST: gi|33677576|gb|CF305815.1|CF305815
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAG                         TTTCAGGTGAACATCTAACATGGATGATCACATGGGATGATGTACAGTTGG
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... tcatttccagTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
EST: gi|29643362|gb|CB648369.1|CB648369
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAG                         TTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... tcatttccagTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
EST: gi|427901|gb|D24044.1|D24044
EST:     CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGCAGAAGGGAGAAGGAAAG                         TTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG
genomic: CAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgct ... tcatttccagTTTCAGGTGAACATCTAACATGGATGATCACATGGGAAGACGGACAGTTGG

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGGAATGGTCTCGGAGGGTTCTTAGCTGGCTTTTCGATTGGATTAGCAGCAGCCGGGTCAGACGGAGCGGAGGCCGTGCCGGAGAAGGGAGAAGGAAAGgttggccgctgttctttcaccttgtatgtgtggattgttcagatgttacctgtgttgttgtctctgtcgtccgatggacgggtccgtgtgattgtgttcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggacggg