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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggatcaaaagaatcacatctatagagaacgagatgcccggaaaagtttgtgcttaatgtctttgtcttttgttgaaaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG

Basic information

species Oryza sativa
transcript LOC_Os01g73970.1
intron # 13
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|86841951|gb|CI338360.1|CI338360
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|86424012|gb|CI062773.1|CI062773
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|88470908|gb|CI408179.1|CI408179
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|58595145|gb|CF993453.1|CF993453
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|86536269|gb|CI176475.1|CI176475
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|88479440|gb|CI416711.1|CI416711
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|12404721|gb|AU166322.1|AU166322
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|86893421|gb|CI313341.1|CI313341
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|88522872|gb|CI450665.1|CI450665
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|1854181|gb|AA231809.1|AA231809
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|29663566|gb|CB659841.1|CB659841
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|88279267|gb|CI400267.1|CI400267
EST:     TGATTCCCAATGGATTGTACATCAAGT-GTNTCCTTCTCTTGGGAACCAG                         GGGCANTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TGATTCCCAATGGATTGTACATCAAGTGGT-TCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|88523350|gb|CI451164.1|CI451164
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|88489023|gb|CI426294.1|CI426294
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|88902346|gb|CI374954.1|CI374954
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|3760914|gb|C98168.1|C98168
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|29641985|gb|CB646992.1|CB646992
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|86526488|gb|CI166694.1|CI166694
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCGG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|5803529|gb|AI978499.1|AI978499
EST:     TTGATTCCCAATGGNNNGTACATCAAGTGGTTCCNNCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|86888761|gb|CI307819.1|CI307819
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         CGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
EST: gi|88663212|gb|CI479204.1|CI479204
EST:     TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG                         GGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
genomic: TTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG

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: 52 (upstream exon), 73 (downstream exon)
Score: 26

CCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAGgtaaggatca ... aaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatgcccggaaaagtttgtgcttaatgtctttgtcttttgttgaaaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG
                    gcttaat  putative branch site (score: 26)
                                    ttttgttgaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggatcaaaagaatcacatctatagagaacgagatgcccggaaaagtttgtgcttaatgtctttgtcttttgttgaaaattcacagGGGCAGTCAGAGCACGGGAGGGCACCGTGGGAAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA