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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACAAACCATCAAATGATTGGAGGGGTGGTGTTGGCTACATATCCAAGGACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTTgtgagtagtctttgtcatttctgcttatagttctgctgatattctttaagcttttgacaagagtttgtacaattttaaagctcgcttataatctccatcaacattatcttcattcatgtgtagcataaacatgattattaatgttggaatgtaagaaagcatcagtcattcaatggtttttgcttggtcag

Basic information

species Oryza sativa
transcript LOC_Os01g07910.1
intron # 11
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|88267058|gb|CI378993.1|CI378993
EST:     CATTGCCTTGAAAGGTTTGCCACGGGCCAGGGGAGGATTCTCTGATCCTT                         GTTTGTGGTCCTCCAGGTATGATGAATCAAATATCCGGTGACAAGGCAAAG
genomic: CATTGCCTTGAAAGGTTTGCCAC-GGCCAGGGGAGGATTCTCTGATCCTTgtgagtagtc ... gcttggtcagGTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
EST: gi|86866447|gb|CI343418.1|CI343418
EST:     ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTT                         GTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
genomic: ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTTgtgagtagtc ... gcttggtcagGTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
EST: gi|88238022|gb|CI237871.1|CI237871
EST:     ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTT                         GTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
genomic: ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTTgtgagtagtc ... gcttggtcagGTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
EST: gi|86420283|gb|CI056272.1|CI056272
EST:     ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTT                         GTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
genomic: ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTTgtgagtagtc ... gcttggtcagGTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
EST: gi|163927043|gb|EG715166.1|EG715166
EST:     CTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTT                         GTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
genomic: CTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTTgtgagtagtc ... gcttggtcagGTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
EST: gi|86824941|gb|CI358146.1|CI358146
EST:     GCCAGGGGAGGATTCTCTGATCCTT                         GTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGCTGAC-AGGCAAAG
genomic: GCCAGGGGAGGATTCTCTGATCCTTgtgagtagtc ... gcttggtcagGTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
EST: gi|88507988|gb|CI435494.1|CI435494
EST:     ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTT                         GTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
genomic: ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTTgtgagtagtc ... gcttggtcagGTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
EST: gi|88376370|gb|CI535474.1|CI535474
EST:     ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTT                         GTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
genomic: ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTTgtgagtagtc ... gcttggtcagGTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
EST: gi|163928246|gb|EG714638.1|EG714638
EST:     ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTT                         GTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
genomic: ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTTgtgagtagtc ... gcttggtcagGTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
EST: gi|89184292|gb|CI046857.1|CI046857
EST:     ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTT                         GTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
genomic: ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTTgtgagtagtc ... gcttggtcagGTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
EST: gi|88485015|gb|CI422286.1|CI422286
EST:     CCAGGGGAGGATTCTCTGATCCTT                         GTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
genomic: CCAGGGGAGGATTCTCTGATCCTTgtgagtagtc ... gcttggtcagGTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
EST: gi|88463003|gb|CI522114.1|CI522114
EST:     ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTT                         GTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
genomic: ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTTgtgagtagtc ... gcttggtcagGTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
EST: gi|27554208|gb|CA998108.1|CA998108
EST:     ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTT                         GTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
genomic: ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTTgtgagtagtc ... gcttggtcagGTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
EST: gi|88319567|gb|CI518411.1|CI518411
EST:     ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTT                         GTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
genomic: ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTTgtgagtagtc ... gcttggtcagGTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
EST: gi|86546020|gb|CI186226.1|CI186226
EST:     GGGAGGATTCTCTGATCCTT                         GTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
genomic: GGGAGGATTCTCTGATCCTTgtgagtagtc ... gcttggtcagGTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
EST: gi|86250752|gb|CI007615.1|CI007615
EST:     ACATTGCCTTGACAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTT                         GTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
genomic: ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTTgtgagtagtc ... gcttggtcagGTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
EST: gi|58586540|gb|CF984848.1|CF984848
EST:     ACATGGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTT                         GTTTGTGGTCCTCCAGGTATGATGAATCATATATCCG
genomic: ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTTgtgagtagtc ... gcttggtcagGTTTGTGGTCCTCCAGGTATGATGAATCATATATCCG
EST: gi|86494415|gb|CI137048.1|CI137048
EST:     ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTT                         GTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
genomic: ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTTgtgagtagtc ... gcttggtcagGTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
EST: gi|88485354|gb|CI422625.1|CI422625
EST:     ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTT                         GTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG
genomic: ACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTTgtgagtagtc ... gcttggtcagGTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAG

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: 56 (upstream exon), 43 (downstream exon)
Score: 8

GGACAAACCATCAAATGATTGGAGGGGTGGTGTTGGCTACATATCCAAGGACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTTgtgagtagtc ... gcttggtcagGTTTGTGGTCCTCCAGGTATGATGAATCATATATCCGGTGACAAGGCAAAGGATAGATCGCAGGGCGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACAAACCATCAAATGATTGGAGGGGTGGTGTTGGCTACATATCCAAGGACATTGCCTTGAAAGGTTTGCCACGGCCAGGGGAGGATTCTCTGATCCTTgtgagtagtctttgtcatttctgcttatagttctgctgatattctttaagcttttgacaagagtttgtacaattttaaagctcgcttataatctccatcaacattatcttcattcatgtgtagcataaacatgattattaatgttggaatgtaagaaagcatcagtcattcaatggtttttgcttggtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT