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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgtgcactgctcctcgtaacactttgtttttttttcttttggacgcattgacaaaaccgggagtaatctgactcgtgtcgtgttgtttgtgtacatgaaaagGCGGGGCGTGTGGGTATGGGAACCTGTACAGCACCGGGTACGGCACCAACACGGCGGCGCTGAGCACGGTGCTGTTCAACGACGGCGCGGCGTGCGGGTC

Basic information

species Oryza sativa
transcript LOC_Os01g60770.1
intron # 1
splice site 3'
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|572402|gb|D41913.1|D41913
EST:     GAGCGCCCACGCCACGTTCTACGNCGGCGGCGATGCGTCCGGCACGATGG                         GCGGGGCGTGTGGGTATGGGAACCTGTACAGCACCGGGTACGTCACCAACA
genomic: GAGCGCCCACGCCACGTTCTACGGCGGCGGCGATGCGTCCGGCACGATGGgtacgtgtgc ... acatgaaaagGCGGGGCGTGTGGGTATGGGAACCTGTACAGCACCGGGTACGGCACCAACA
EST: gi|58662059|gb|CK050739.1|CK050739
EST:     GAGCGCCCACGCCACGTTCTACGGCGGCGGCGATGCGTCCGGCACGATGG                         GCGGGGCGTGTGGGTATGGGAACCTGTACAGCACCGGGTACGGCACCAACA
genomic: GAGCGCCCACGCCACGTTCTACGGCGGCGGCGATGCGTCCGGCACGATGGgtacgtgtgc ... acatgaaaagGCGGGGCGTGTGGGTATGGGAACCTGTACAGCACCGGGTACGGCACCAACA
EST: gi|569178|gb|D40027.1|D40027
EST:     AGCGCCCACGCCACGTTCTACGGGCGGCGGCGATGCGTCCGGCACGATGG                         GCGGGGCGTGTGGGTATGGGAACCTGTACAGCACCGGGTACGNCACCAACA
genomic: AGCGCCCACGCCACGTTCTACGG-CGGCGGCGATGCGTCCGGCACGATGGgtacgtgtgc ... acatgaaaagGCGGGGCGTGTGGGTATGGGAACCTGTACAGCACCGGGTACGGCACCAACA
EST: gi|571908|gb|D41419.1|D41419
EST:     GAGCGCCCACGCCACGTTCTACGGCGGCGGCGATGCGTCCGGCACGATGG                         GCGGGGCGTGTGGGTATGGGAACCTGTACAGCACCGGGTACGGCACCAACA
genomic: GAGCGCCCACGCCACGTTCTACGGCGGCGGCGATGCGTCCGGCACGATGGgtacgtgtgc ... acatgaaaagGCGGGGCGTGTGGGTATGGGAACCTGTACAGCACCGGGTACGGCACCAACA
EST: gi|569583|gb|D40432.1|D40432
EST:     GAGCGCCCACGGCACGTTCTACGGCGGCGGCGATGCGTCCGGNACGATGG                         GCGGGGCGTGTGGGTATGGAAACCTGTACAGCACCGGGTACGGCACCAACA
genomic: GAGCGCCCACGCCACGTTCTACGGCGGCGGCGATGCGTCCGGCACGATGGgtacgtgtgc ... acatgaaaagGCGGGGCGTGTGGGTATGGGAACCTGTACAGCACCGGGTACGGCACCAACA
EST: gi|88368671|gb|CI659935.1|CI659935
EST:     GAGCGCCCACGCCACGTTCTACGGCGGCGGCGATGCGTCCGGCACGATGG                         GCGGGGCGTGTGGGTATGGGAACCTGTACAGCACCGGGTACGGCACCAACA
genomic: GAGCGCCCACGCCACGTTCTACGGCGGCGGCGATGCGTCCGGCACGATGGgtacgtgtgc ... acatgaaaagGCGGGGCGTGTGGGTATGGGAACCTGTACAGCACCGGGTACGGCACCAACA
EST: gi|58592293|gb|CF990601.1|CF990601
EST:     GAGCGCCCACGCCACGTTCTACGGCGGCGGCGATGCGTCCGGCACGATGG                         GCGGGGCGTGTGGGTATGGGAACCTGTACAGCACCGGGTACGGCACCAACA
genomic: GAGCGCCCACGCCACGTTCTACGGCGGCGGCGATGCGTCCGGCACGATGGgtacgtgtgc ... acatgaaaagGCGGGGCGTGTGGGTATGGGAACCTGTACAGCACCGGGTACGGCACCAACA
EST: gi|568574|gb|D39423.1|D39423
EST:     GAGCGCCCACGCCACGTTCTACGGCGGCGGCGATGCGTCCGGCACGATGG                         GCGGGGCGTGTGGGTATGGGAACCTGTACAGCACCGGGTACGGCACCAACA
genomic: GAGCGCCCACGCCACGTTCTACGGCGGCGGCGATGCGTCCGGCACGATGGgtacgtgtgc ... acatgaaaagGCGGGGCGTGTGGGTATGGGAACCTGTACAGCACCGGGTACGGCACCAACA
EST: gi|428052|gb|D24200.1|D24200
EST:     GAGCGCCCACGNCACGTTCTACGGCGNCGNCGATGCGTCCGGCACGATGG                         GCGGGGCGTGTGGGTATGGGAACCTGTACAGCACCGGGTACGGCACCAACA
genomic: GAGCGCCCACGCCACGTTCTACGGCGGCGGCGATGCGTCCGGCACGATGGgtacgtgtgc ... acatgaaaagGCGGGGCGTGTGGGTATGGGAACCTGTACAGCACCGGGTACGGCACCAACA
EST: gi|58588301|gb|CF986609.1|CF986609
EST:     GAGCGCCCACGCCACGTTCTACGGCGGCGGCGATGCGTCCGGCACGATGG                         GCGGGGCGTGTGGGTATGGGAACCTGTACAGCACCGGGTACGGCACCAACA
genomic: GAGCGCCCACGCCACGTTCTACGGCGGCGGCGATGCGTCCGGCACGATGGgtacgtgtgc ... acatgaaaagGCGGGGCGTGTGGGTATGGGAACCTGTACAGCACCGGGTACGGCACCAACA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 44 (upstream exon), 56 (downstream exon)
Score: 9

GCCTTCTGCTTCCTCGCCCGGCGAGCCGCCGCCGACTACGGCTCCTGGCAGAGCGCCCACGCCACGTTCTACGGCGGCGGCGATGCGTCCGGCACGATGGgtacgtgtgc ... acatgaaaagGCGGGGCGTGTGGGTATGGGAACCTGTACAGCACCGGGTACGGCACCAACACGGCGGCGCTGAGCACGGTGCTGTTCAACGACGGCGCGGCGTGCGGGTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgacaaaaccgggagtaatctgactcgtgtcgtgttgtttgtgtacatgaaaagGCGGGGCGTGTGGGTATGGGAACCTGTACAGCACCGGGTACGGCACCAACACGGCGGCGCTGAGCACGGTGCTGTTCAACGACGGCGCGGCGTGCGGGTC
                  atctgac  putative branch site (score: 9)
                                               atgaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtgtgcactgctcctcgtaacactttgtttttttttcttttggacgcattgacaaaaccgggagtaatctgactcgtgtcgtgttgtttgtgtacatgaaaagGCGGGGCGTGTGGGTATGGGAACCTGTACAGCACCGGGTACGGCACCAACACGGCGGCGCTGAGCACGGTGCTGTTCAACGACGGCGCGGCGTGCGGGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT