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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCAACATTGGATTCAGAGGAACGATCAAAAGCACCAGTTCCTATTCCTGATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAGgtatatatatttacactgctcagccgaatcacattagtggcctgatattcttccacctaaaaccccactactaacagcattacttcaagaatcatcctag...

Basic information

species Oryza sativa
transcript LOC_Os01g48190.1
intron # 4
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|86537682|gb|CI177888.1|CI177888
EST:     GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAG                         GATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGAAAACAATC
genomic: GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAGgtatatatat ... tccatggcagGATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
EST: gi|15852246|gb|BI805042.1|BI805042
EST:     CCATGGGAATCAAG                         GATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACACAG
genomic: CCATGGGAATCAAGgtatatatat ... tccatggcagGATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACA-AG
EST: gi|33690044|gb|CF318283.1|CF318283
EST:     GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAG                         GATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
genomic: GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAGgtatatatat ... tccatggcagGATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
EST: gi|41882403|gb|BX927902.1|BX927902
EST:     GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAG                         GATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
genomic: GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAGgtatatatat ... tccatggcagGATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
EST: gi|86499111|gb|CI141744.1|CI141744
EST:     GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAG                         GATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
genomic: GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAGgtatatatat ... tccatggcagGATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
EST: gi|58596919|gb|CK007447.1|CK007447
EST:     GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAG                         GATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
genomic: GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAGgtatatatat ... tccatggcagGATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
EST: gi|86536326|gb|CI176532.1|CI176532
EST:     GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAG                         GATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGAAAACAAGC
genomic: GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAGgtatatatat ... tccatggcagGATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
EST: gi|89166922|gb|CI104208.1|CI104208
EST:     GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAG                         GATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
genomic: GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAGgtatatatat ... tccatggcagGATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
EST: gi|16753330|gb|BM037709.1|BM037709
EST:     GTGATACATCAAGTTCATAAGGATACTCCTGCTCACCCATGGGAATCAAG                         GATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
genomic: -TGATACATCAA-TTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAGgtatatatat ... tccatggcagGATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
EST: gi|86479261|gb|CI121894.1|CI121894
EST:     GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAG                         GATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
genomic: GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAGgtatatatat ... tccatggcagGATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
EST: gi|88834636|gb|CI077919.1|CI077919
EST:     CATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAG                         GATCGACTCGTCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
genomic: CATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAGgtatatatat ... tccatggcagGATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
EST: gi|86887701|gb|CI311908.1|CI311908
EST:     GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAG                         GATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
genomic: GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAGgtatatatat ... tccatggcagGATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
EST: gi|86429282|gb|CI075963.1|CI075963
EST:     GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAG                         GATCGACTCGTCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
genomic: GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAGgtatatatat ... tccatggcagGATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
EST: gi|58597316|gb|CK007844.1|CK007844
EST:     GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAG                         GATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
genomic: GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAGgtatatatat ... tccatggcagGATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
EST: gi|88844223|gb|CI005596.1|CI005596
EST:     GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAG                         GATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
genomic: GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAGgtatatatat ... tccatggcagGATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
EST: gi|88834654|gb|CI077937.1|CI077937
EST:     GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAG                         GATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
genomic: GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAGgtatatatat ... tccatggcagGATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
EST: gi|14982059|gb|BI306737.1|BI306737
EST:     GCCATGGGAATCAAG                         GATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
genomic: GCCATGGGAATCAAGgtatatatat ... tccatggcagGATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
EST: gi|88985157|gb|CI006811.1|CI006811
EST:     GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAG                         GATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
genomic: GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAGgtatatatat ... tccatggcagGATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
EST: gi|88842011|gb|CI081267.1|CI081267
EST:     GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAG                         GATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
genomic: GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAGgtatatatat ... tccatggcagGATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
EST: gi|88835384|gb|CI005074.1|CI005074
EST:     GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAG                         GATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
genomic: GATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAGgtatatatat ... tccatggcagGATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
EST: gi|88993775|gb|CI112679.1|CI112679
EST:     ATAAGGATACTCCTGCTCAGCCATGGGAATCAAG                         GATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
genomic: ATAAGGATACTCCTGCTCAGCCATGGGAATCAAGgtatatatat ... tccatggcagGATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGC
EST: gi|22304857|gb|BQ906079.1|BQ906079
EST:     CCATGGGAATCAGAG                         GATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAATAGCGGAAACAAG
genomic: CCATGGGAATCA-AGgtatatatat ... tccatggcagGATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAG

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: 75 (upstream exon), 72 (downstream exon)
Score: 33

TCTCAACATTGGATTCAGAGGAACGATCAAAAGCACCAGTTCCTATTCCTGATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAGgtatatatat ... tccatggcagGATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGCCACTGACAGAGCAACCTTTGTGCAAGGCCTGGTGCTCTCCACTTTATTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTCAACATTGGATTCAGAGGAACGATCAAAAGCACCAGTTCCTATTCCTGATGATACATCAATTCATAAGGATACTCCTGCTCAGCCATGGGAATCAAGgtatatatatttacactgctcagccgaatcacattagtggcctgatattcttccacctaaaaccccactactaacagcattacttcaagaatcatcctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccact