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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcctgtctgctgctggttcttttctgttgcctgaatttctgaatgcttagcgtttttcagaggaaaatttatctaaccttgtgagcactgtgctccctgcactgcag

Basic information

species Oryza sativa
transcript LOC_Os03g38590.1
intron # 12
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|12404727|gb|AU166328.1|AU166328
EST:     GTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: GTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|88506206|gb|CI433712.1|CI433712
EST:     CGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: CGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|88475023|gb|CI412294.1|CI412294
EST:     ATTCGCAATG-TTTGCCTGGGAGTCCCTGGTCAGCATGTGGGTTATTCAG                         CGTGGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCG
genomic: ATTCGCAATGTTTTGCCT-GGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGT-GTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCG
EST: gi|88258581|gb|CI361167.1|CI361167
EST:     TGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTTTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATTAAGCGC
genomic: TGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|88476593|gb|CI413864.1|CI413864
EST:     TCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: TCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|88428152|gb|CI557046.1|CI557046
EST:     TGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: TGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|88482190|gb|CI419461.1|CI419461
EST:     GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|88511461|gb|CI438967.1|CI438967
EST:     GATTCCCAATNTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGGCAGCGGGAAAGAGGCCGAGATGAAGCG
genomic: GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCC-GGGGCAGCGGGAAAGAGGCCGAGATGAAGCG
EST: gi|29662769|gb|CB659044.1|CB659044
EST:     GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGGGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCG
genomic: GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCG
EST: gi|86884619|gb|CI312998.1|CI312998
EST:     ATTCCCAATGTTTTGCCTGGAATCGCTGCTCAGGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: ATTCGCAATGTTTTGCCTGGAGTCGCTGCTCA-GCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|88260970|gb|CI364546.1|CI364546
EST:     GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCACCGGGAAAGAGGCCGAGATGAAGCGC
genomic: GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|29662682|gb|CB658957.1|CB658957
EST:     GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|86511240|gb|CI153873.1|CI153873
EST:     GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|29662718|gb|CB658993.1|CB658993
EST:     GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|88366315|gb|CI553713.1|CI553713
EST:     GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|88485149|gb|CI422420.1|CI422420
EST:     GATTCGCAATGTTTTGCCTGGATTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCACCGGGAAAGAGGCCGAGATGAAGCCC
genomic: GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|86261561|gb|CI017303.1|CI017303
EST:     GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|88509345|gb|CI436851.1|CI436851
EST:     GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|88475024|gb|CI412295.1|CI412295
EST:     GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|88284372|gb|CI405818.1|CI405818
EST:     CGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATNTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGCCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: CGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC

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: 66 (upstream exon), 67 (downstream exon)
Score: 11

GTGTTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGCGAGGCTGCACGCAGCGCAGCGAGGGCGGCGTTTTGATGATGATGTACGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcctgtctgctgctggttcttttctgttgcctgaatttctgaatgcttagcgtttttcagaggaaaatttatctaaccttgtgagcactgtgctccctgcactgcag

- - - - - - - - - - - - - - - - - - - -  GCTGCT