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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGGTCCCACTATAATGGGAGGAAATGATCCAGTCACAGGTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGGgtatgctattatttttggacaaagaatgtcgcatgaagtttcttaagtatggagataataatttcattctaacttgattctaactttttgtcctctag

Basic information

species Oryza sativa
transcript LOC_Os06g35530.1
intron # 2
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|58589448|gb|CF987756.1|CF987756
EST:     GTCATATAATTTCAACTACTATTGGAGGGCAGAACGATGAGCCCAAAAGG                         ACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGT
genomic: GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGGgtatgctatt ... tgtcctctagACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGT
EST: gi|66914786|gb|CX101634.1|CX101634
EST:     GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGG                         ACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
genomic: GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGGgtatgctatt ... tgtcctctagACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
EST: gi|33793859|gb|CF322817.1|CF322817
EST:     GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGG                         ACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
genomic: GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGGgtatgctatt ... tgtcctctagACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
EST: gi|58608373|gb|CK036406.1|CK036406
EST:     GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGG                         ACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
genomic: GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGGgtatgctatt ... tgtcctctagACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
EST: gi|29672896|gb|CB669171.1|CB669171
EST:     GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGG                         ACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
genomic: GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGGgtatgctatt ... tgtcctctagACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
EST: gi|33676536|gb|CF304775.1|CF304775
EST:     GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGG                         ACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
genomic: GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGGgtatgctatt ... tgtcctctagACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
EST: gi|58653237|gb|CK041917.1|CK041917
EST:     GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGG                         ACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
genomic: GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGGgtatgctatt ... tgtcctctagACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
EST: gi|29689142|gb|CB685417.1|CB685417
EST:     GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGG                         ACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
genomic: GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGGgtatgctatt ... tgtcctctagACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
EST: gi|29660849|gb|CB657124.1|CB657124
EST:     GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGG                         ACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT
genomic: GTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGGgtatgctatt ... tgtcctctagACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTT

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: 74 (upstream exon), 60 (downstream exon)
Score: 31

CATGGTCCCACTATAATGGGAGGAAATGATCCAGTCACAGGTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGGgtatgctatt ... tgtcctctagACTATTAGCTATATGGCTGAACGAGTTGTTGGAACTGGATCCTTTGGTGTTGTATTCCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGGTCCCACTATAATGGGAGGAAATGATCCAGTCACAGGTCATATAATTTCAACTACTATTGGAGGGAAGAACGATGAGCCCAAAAGGgtatgctattatttttggacaaagaatgtcgcatgaagtttcttaagtatggagataataatttcattctaacttgattctaactttttgtcctctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC