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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacggacctgctcatcatgatcaaacagtagtatatattgtatgcttgaacagagtttgctaattgttttttgttcagGTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCAACCATTTTTACACTGGAGGCAGGCAGAATTTCACAGTTGCATCTGAGAC

Basic information

species Oryza sativa
transcript LOC_Os02g01280.1
intron # 14
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|88832900|gb|CI369790.1|CI369790
EST:     CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAG                         GTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
genomic: CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAGgtacacggac ... ttttgttcagGTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
EST: gi|6934866|gb|AU082403.1|AU082403
EST:     CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAG                         GTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
genomic: CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAGgtacacggac ... ttttgttcagGTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
EST: gi|88264131|gb|CI367905.1|CI367905
EST:     CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAG                         GTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
genomic: CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAGgtacacggac ... ttttgttcagGTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
EST: gi|88906229|gb|CI375301.1|CI375301
EST:     CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAG                         GTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
genomic: CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAGgtacacggac ... ttttgttcagGTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
EST: gi|29631899|gb|CB636908.1|CB636908
EST:     CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAG                         GTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
genomic: CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAGgtacacggac ... ttttgttcagGTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
EST: gi|88996581|gb|CI389247.1|CI389247
EST:     CAGCTGCTGCTTGGAACCCCATGGGTGGATCAG                         GTTTTGGATTTTAGTTTAGAAGAAGAAGAGTACCCTTTTTGGCAGTTGGCA
genomic: CAGCTGCTGCTGGGAACCCAATGGGTGGATCAGgtacacggac ... ttttgttcagGTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
EST: gi|88978439|gb|CI384821.1|CI384821
EST:     CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAG                         GTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAAGTTGGC
genomic: CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAGgtacacggac ... ttttgttcagGTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCA-GTTGGC
EST: gi|88270788|gb|CI386046.1|CI386046
EST:     CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAG                         GTTTTGGATTTTAGGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGC
genomic: CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAGgtacacggac ... ttttgttcagGTTTTGGATTTTA-GTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGC
EST: gi|88449887|gb|CI529866.1|CI529866
EST:     CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAG                         GTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
genomic: CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAGgtacacggac ... ttttgttcagGTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
EST: gi|88263369|gb|CI367143.1|CI367143
EST:     CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAG                         GTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
genomic: CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAGgtacacggac ... ttttgttcagGTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
EST: gi|88266148|gb|CI377050.1|CI377050
EST:     CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAG                         GTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
genomic: CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAGgtacacggac ... ttttgttcagGTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
EST: gi|88834725|gb|CI370028.1|CI370028
EST:     CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAG                         GTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGCCAGTTGGCA
genomic: CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAGgtacacggac ... ttttgttcagGTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
EST: gi|88275358|gb|CI395209.1|CI395209
EST:     CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAG                         GTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
genomic: CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAGgtacacggac ... ttttgttcagGTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
EST: gi|89185536|gb|CI052062.1|CI052062
EST:     CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAG                         GTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
genomic: CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAGgtacacggac ... ttttgttcagGTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
EST: gi|88291087|gb|CI527477.1|CI527477
EST:     CAAGGAGCCTGAGAAACCAGCTGCTGCTGGGAACCCAATGGGTGGATCAG                         GTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
genomic: CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAGgtacacggac ... ttttgttcagGTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
EST: gi|86826727|gb|CI364251.1|CI364251
EST:     CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAG                         GTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
genomic: CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAGgtacacggac ... ttttgttcagGTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
EST: gi|88464262|gb|CI532197.1|CI532197
EST:     CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAG                         GTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
genomic: CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAGgtacacggac ... ttttgttcagGTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
EST: gi|86884887|gb|CI314463.1|CI314463
EST:     CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAG                         GTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCACGTTGGC
genomic: CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAGgtacacggac ... ttttgttcagGTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCA-GTTGGC
EST: gi|86869378|gb|CI339102.1|CI339102
EST:     CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAG                         GTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
genomic: CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAGgtacacggac ... ttttgttcagGTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
EST: gi|88376066|gb|CI530570.1|CI530570
EST:     CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAG                         GTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
genomic: CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAGgtacacggac ... ttttgttcagGTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA
EST: gi|88977896|gb|CI384378.1|CI384378
EST:     CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAG                         GTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCACTTGGCA
genomic: CAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAGgtacacggac ... ttttgttcagGTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCA

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: 59 (upstream exon), 75 (downstream exon)
Score: 35

GCGTCGGTGGCGAAAACATTCATCACATCAGATGCTGTTGTGGTGGACATCAAGGAGCCTGAGAAAGCAGCTGCTGCTGGGAACCCAATGGGTGGATCAGgtacacggac ... ttttgttcagGTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCAACCATTTTTACACTGGAGGCAGGCAGAATTTCACAGTTGCATCTGAGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacagtagtatatattgtatgcttgaacagagtttgctaattgttttttgttcagGTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCAACCATTTTTACACTGGAGGCAGGCAGAATTTCACAGTTGCATCTGAGAC
                                  tgctaat  putative branch site (score: 35)
                                           ttttttgttc  putative PPT
     tagtatatattgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacggacctgctcatcatgatcaaacagtagtatatattgtatgcttgaacagagtttgctaattgttttttgttcagGTTTTGGATTTTAGTTTAGAAGAAGAGGAGTACCCTTTTTGGCAGTTGGCAACCATTTTTACACTGGAGGCAGGCAGAATTTCACAGTTGCATCTGAGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG