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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGCTGGTTTTTGCTAACAAGCAAGATCTTCCTAATGCAATGAATGCTGCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatggttgcttttgttgtcacttgtaggctgtctacttctcatctcatccattcctatttttgttctaagtttgatggtcttgtattctggttt...

Basic information

species Oryza sativa
transcript LOC_Os01g16030.3
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|88662499|gb|CI470127.1|CI470127
EST:     GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
genomic: GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
EST: gi|88510648|gb|CI438154.1|CI438154
EST:     GCTGAGATCACAGATAAGCTTGGTCCCCATTCCCTGCGCCAACGCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
genomic: GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
EST: gi|86870888|gb|CI326714.1|CI326714
EST:     TCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
genomic: -CTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
EST: gi|88439804|gb|CI541361.1|CI541361
EST:     TGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
genomic: TGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
EST: gi|88511231|gb|CI438737.1|CI438737
EST:     GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
genomic: GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
EST: gi|88323630|gb|CI556261.1|CI556261
EST:     GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
genomic: GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
EST: gi|88661093|gb|CI450226.1|CI450226
EST:     GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
genomic: GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
EST: gi|86526009|gb|CI166215.1|CI166215
EST:     GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
genomic: GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
EST: gi|88510108|gb|CI437614.1|CI437614
EST:     GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
genomic: GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
EST: gi|88475381|gb|CI412652.1|CI412652
EST:     GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
genomic: GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
EST: gi|396941528|gb|HO188737.1|HO188737
EST:     GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
genomic: GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
EST: gi|163929270|gb|EG711031.1|EG711031
EST:     GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGG
genomic: GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGG
EST: gi|88440306|gb|CI549187.1|CI549187
EST:     GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
genomic: GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
EST: gi|88489531|gb|CI426803.1|CI426803
EST:     GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
genomic: GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
EST: gi|86825487|gb|CI360103.1|CI360103
EST:     GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACCCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
genomic: GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
EST: gi|88284844|gb|CI406290.1|CI406290
EST:     GCTGACATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
genomic: GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
EST: gi|88661493|gb|CI455632.1|CI455632
EST:     GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
genomic: GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
EST: gi|88662713|gb|CI473255.1|CI473255
EST:     GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
genomic: GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
EST: gi|88663339|gb|CI480406.1|CI480406
EST:     GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
genomic: GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
EST: gi|88486537|gb|CI423808.1|CI423808
EST:     CCATTCCCTGCGCCAACGCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
genomic: CCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
EST: gi|88475737|gb|CI413008.1|CI413008
EST:     GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
genomic: GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
EST: gi|88289060|gb|CI520390.1|CI520390
EST:     GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
genomic: GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
EST: gi|88475917|gb|CI413188.1|CI413188
EST:     TGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
genomic: TGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
EST: gi|88518078|gb|CI445732.1|CI445732
EST:     GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
genomic: GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
EST: gi|88486800|gb|CI424071.1|CI424071
EST:     GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
genomic: GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
EST: gi|88512596|gb|CI440102.1|CI440102
EST:     GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTG                         GTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT
genomic: GCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatg ... tgtcatttagGTATATCCAGAGTACATGCGCCACAACAGGAGAGGGTTTATATGAGGGCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGCTGGTTTTTGCTAACAAGCAAGATCTTCCTAATGCAATGAATGCTGCTGAGATCACAGATAAGCTTGGTCTCCATTCCCTGCGCCAACGCCACTGgtaatatatggttgcttttgttgtcacttgtaggctgtctacttctcatctcatccattcctatttttgttctaagtttgatggtcttgtattctggttt

- - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA