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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtatcagctttcagtatgaacaaaattgcaggaaaccagtacccttttctacaaggaggaaaccagcatctatgcgttgacgaataaaactgcttacattctcagctgaaccactccaacagattttatctgaattttcatcctcatgtgcttccgaatgttctgcactgcagGCCACTTCAGAGTTTGGTGCAGAGAAGCAAATACACGAACTTCTGTTTCCTAGGATACAGCAAGAGGGACAGTCACCACAAACTAGACAGAAAGAGTCTT

Basic information

species Oryza sativa
transcript LOC_Os11g34130.1
intron # 10
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|86851984|gb|CI317746.1|CI317746
EST:     TGTGCTCAGGAACACAAGTGCAGACACTGAGATTTGCGTTCCCTGCAAAG                         GCCACTTCAGAGTTTGGTGCAGAGAAGCAAATACACGAACTTCTGTTTCCT
genomic: TGTGCTCAGGAACACAAGTGCAGACACTGAGATTTGCGTTCCCTGCAAAGgtcagtatca ... tgcactgcagGCCACTTCAGAGTTTGGTGCAGAGAAGCAAATACACGAACTTCTGTTTCCT
EST: gi|27548857|gb|CA766920.2|CA766920
EST:     TGTGCTCAGGAACACAAGTGCAGACACTGAGATTTGCGTTCCCTGCAAAG                         GCCACTTCAGAGTTTGGTGCAGAGAAGCAAATACACGAACTTCTGTTTCCT
genomic: TGTGCTCAGGAACACAAGTGCAGACACTGAGATTTGCGTTCCCTGCAAAGgtcagtatca ... tgcactgcagGCCACTTCAGAGTTTGGTGCAGAGAAGCAAATACACGAACTTCTGTTTCCT
EST: gi|29628214|gb|CB633225.1|CB633225
EST:     TGTGCTCAGGAACACAAGTGCAGCCACTGAGATTTGCGTTCCCTGCAAAG                         GCCACTTCAGAGTTTGGTGCAGAGAAGCAAATACACGAACTTCTGTTTCCT
genomic: TGTGCTCAGGAACACAAGTGCAGACACTGAGATTTGCGTTCCCTGCAAAGgtcagtatca ... tgcactgcagGCCACTTCAGAGTTTGGTGCAGAGAAGCAAATACACGAACTTCTGTTTCCT
EST: gi|25806431|gb|CA762392.1|CA762392
EST:     TGTGCTCAGGAACACAAGTGCAGACACTGAGATTTGCGTTCCCTGCAAAG                         GCCACTTCAGAGTTTGGTGCAGAGAAGCAAATACACGAACTTCTGTTTCCT
genomic: TGTGCTCAGGAACACAAGTGCAGACACTGAGATTTGCGTTCCCTGCAAAGgtcagtatca ... tgcactgcagGCCACTTCAGAGTTTGGTGCAGAGAAGCAAATACACGAACTTCTGTTTCCT
EST: gi|29628175|gb|CB633186.1|CB633186
EST:     TGTGCTCAGGAACACAAGTGCAGACACTGAGATTTGCGTTCCCTGCAAAG                         GCCACTTCAGAGTTTGGTGCAGAGAAGCAAATACACGAACTTCTGTTTCCT
genomic: TGTGCTCAGGAACACAAGTGCAGACACTGAGATTTGCGTTCCCTGCAAAGgtcagtatca ... tgcactgcagGCCACTTCAGAGTTTGGTGCAGAGAAGCAAATACACGAACTTCTGTTTCCT
EST: gi|58694239|gb|CK082926.1|CK082926
EST:     TGTGCTCAGGAACACAAGTGCAGACACTGAGATTTGCGTTCCCTGCAAAG                         GCCACTTCAGAGTTTGGTGCAGAGAAGCAAATACACGAACTTCTGTTTCCT
genomic: TGTGCTCAGGAACACAAGTGCAGACACTGAGATTTGCGTTCCCTGCAAAGgtcagtatca ... tgcactgcagGCCACTTCAGAGTTTGGTGCAGAGAAGCAAATACACGAACTTCTGTTTCCT
EST: gi|88974799|gb|CI023095.1|CI023095
EST:     TGTGCTCAGGAACACAAGTGCAGACACTGAGATTTGCGTTCCCTGCAAAG                         GCCACTTCAGAGTTTGGTGCAGAGAAGCAAATACACGAACTTCTGTTTCCT
genomic: TGTGCTCAGGAACACAAGTGCAGACACTGAGATTTGCGTTCCCTGCAAAGgtcagtatca ... tgcactgcagGCCACTTCAGAGTTTGGTGCAGAGAAGCAAATACACGAACTTCTGTTTCCT
EST: gi|86600733|gb|CI356490.1|CI356490
EST:     TGTGCTCAGGAACACAAGTGCAGGCACTGAGATTTGCGTTCCCTGCAAAG                         GCCACTTCAGAGTTTGGTGCAGAGAAGCAAATACACGAACTTCTGTTTCCT
genomic: TGTGCTCAGGAACACAAGTGCAGACACTGAGATTTGCGTTCCCTGCAAAGgtcagtatca ... tgcactgcagGCCACTTCAGAGTTTGGTGCAGAGAAGCAAATACACGAACTTCTGTTTCCT
EST: gi|88844475|gb|CI020322.1|CI020322
EST:     TGTGCTCAGGAACACAAGTGCAGACACTGAGATTTGCGTTCCCTGCAAAG                         GCCACTTCAGAGTTTGGTGCAGAGAAGCAAATACACGAACTTCTGTTTCCT
genomic: TGTGCTCAGGAACACAAGTGCAGACACTGAGATTTGCGTTCCCTGCAAAGgtcagtatca ... tgcactgcagGCCACTTCAGAGTTTGGTGCAGAGAAGCAAATACACGAACTTCTGTTTCCT

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: 49 (upstream exon), 65 (downstream exon)
Score: 4

GAGGCAGCTGTCATTGGAGTGGACTGCCTTGGGTTTGACTTGAGAGTGTGCTCAGGAACACAAGTGCAGACACTGAGATTTGCGTTCCCTGCAAAGgtcagtatca ... tgcactgcagGCCACTTCAGAGTTTGGTGCAGAGAAGCAAATACACGAACTTCTGTTTCCTAGGATACAGCAAGAGGGACAGTCACCACAAACTAGACAGAAAGAGTCTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagattttatctgaattttcatcctcatgtgcttccgaatgttctgcactgcagGCCACTTCAGAGTTTGGTGCAGAGAAGCAAATACACGAACTTCTGTTTCCTAGGATACAGCAAGAGGGACAGTCACCACAAACTAGACAGAAAGAGTCTT
     ttttatctgaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtatcagctttcagtatgaacaaaattgcaggaaaccagtacccttttctacaaggaggaaaccagcatctatgcgttgacgaataaaactgcttacattctcagctgaaccactccaacagattttatctgaattttcatcctcatgtgcttccgaatgttctgcactgcagGCCACTTCAGAGTTTGGTGCAGAGAAGCAAATACACGAACTTCTGTTTCCTAGGATACAGCAAGAGGGACAGTCACCACAAACTAGACAGAAAGAGTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG