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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatttcttccaggtctctttatcccagtgtgcattcgaattggatttgtacaacagttttccagctgaacaagctatatatcttatgtctatgttgtagAGGCATGAAATCGAGGTTAGCGGCAACATATCCAGATGCTTTTCCTACTGGCGCAATGGCAGAGACGATGGACCAAAGACCGGACCTTGAAAGTCCTCTT

Basic information

species Oryza sativa
transcript LOC_Os03g43900.2
intron # 6
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|88469779|gb|CI407050.1|CI407050
EST:     CTTCTCAAGTCCATGAAGGCTGATCTTGACCATATTTTCCTGAAGTTGAG                         AGGCATGAAATCGAGGTTAGCGGCAACATATCCAGATGCTTTTCCTACTGG
genomic: CTTCTCAAGTCCATGAAGGCTGATCTTGACCATATTTTCCTGAAGTTGAGgtacatttct ... tatgttgtagAGGCATGAAATCGAGGTTAGCGGCAACATATCCAGATGCTTTTCCTACTGG
EST: gi|88283343|gb|CI404789.1|CI404789
EST:     CTTCTCAAGTCCATGAAGGCTGATCTTGACCATATTTTCCTGAAGTTGAG                         AGGCATGAAATCGAGGGTTAGCGGCAACATATCCAGATGCTTTTCCTACTG
genomic: CTTCTCAAGTCCATGAAGGCTGATCTTGACCATATTTTCCTGAAGTTGAGgtacatttct ... tatgttgtagAGGCATGAAATCGA-GGTTAGCGGCAACATATCCAGATGCTTTTCCTACTG
EST: gi|88486588|gb|CI423859.1|CI423859
EST:     CTTCTCAAGTCCATGAGGGCTGATCTTNACCATATTTTCCTGAAGTTGAG                         AGGCATGAAATCGAGGTTAGCGGCAACATATCCAGATGCTTTTCGTACTGG
genomic: CTTCTCAAGTCCATGAAGGCTGATCTTGACCATATTTTCCTGAAGTTGAGgtacatttct ... tatgttgtagAGGCATGAAATCGAGGTTAGCGGCAACATATCCAGATGCTTTTCCTACTGG
EST: gi|88513213|gb|CI440719.1|CI440719
EST:     CTTCTCAAGTCCATGAAGGCTGATCTTGACCATATTTTCCTGAAGTTGAG                         AGGCATGAAATCGAGGTTAGCGGCAACATATCCAGATGCTTTTCCTACTGG
genomic: CTTCTCAAGTCCATGAAGGCTGATCTTGACCATATTTTCCTGAAGTTGAGgtacatttct ... tatgttgtagAGGCATGAAATCGAGGTTAGCGGCAACATATCCAGATGCTTTTCCTACTGG
EST: gi|89189578|gb|CI049117.1|CI049117
EST:     CTTCTCAAGTCCATGAAGGCTGATCTTGACCATATTTTCCTGAAGTTGAG                         AGGCATGAAATCGAGGTTAGCGGCAACATATCCAGATGCTTTTCCTACTGG
genomic: CTTCTCAAGTCCATGAAGGCTGATCTTGACCATATTTTCCTGAAGTTGAGgtacatttct ... tatgttgtagAGGCATGAAATCGAGGTTAGCGGCAACATATCCAGATGCTTTTCCTACTGG
EST: gi|88505132|gb|CI432638.1|CI432638
EST:     CTTCTCAAGTCCATGAAGGCTGATCTTGACCATATTTTCCTGAAGTTGAG                         AGGCATGAAATCGAGGTTAGCGGCAACATATCCAGATGCTTTTCCTACTGG
genomic: CTTCTCAAGTCCATGAAGGCTGATCTTGACCATATTTTCCTGAAGTTGAGgtacatttct ... tatgttgtagAGGCATGAAATCGAGGTTAGCGGCAACATATCCAGATGCTTTTCCTACTGG
EST: gi|86505882|gb|CI148515.1|CI148515
EST:     CTTCTCAAGTCCATGAAGGCTGATCTTGACCATATTTTCCTGAAGTTGAG                         AGGCATGAAATCGAGGTTAGCGGCAACATATCCAGATGCTTTTCCTACTGG
genomic: CTTCTCAAGTCCATGAAGGCTGATCTTGACCATATTTTCCTGAAGTTGAGgtacatttct ... tatgttgtagAGGCATGAAATCGAGGTTAGCGGCAACATATCCAGATGCTTTTCCTACTGG
EST: gi|88491988|gb|CI429260.1|CI429260
EST:     CTTCTCAAGTCCATGAAGGCTGATCTTGACCATATTTTCCTGAAGTTGAG                         AGGCATGAAATCGAGGTTAGCGGCAACATATCCAGATGCTTTTCCTACTGG
genomic: CTTCTCAAGTCCATGAAGGCTGATCTTGACCATATTTTCCTGAAGTTGAGgtacatttct ... tatgttgtagAGGCATGAAATCGAGGTTAGCGGCAACATATCCAGATGCTTTTCCTACTGG
EST: gi|88515099|gb|CI442753.1|CI442753
EST:     CTTCTCAAGTCCATGAAGGCTGATCTTGACCATATTTTCCTGAAGTTGAG                         AGGCATGAAATCGAGGTTAGCGGCAACATATCCAGATGCTTTTCCTACTGG
genomic: CTTCTCAAGTCCATGAAGGCTGATCTTGACCATATTTTCCTGAAGTTGAGgtacatttct ... tatgttgtagAGGCATGAAATCGAGGTTAGCGGCAACATATCCAGATGCTTTTCCTACTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtacaacagttttccagctgaacaagctatatatcttatgtctatgttgtagAGGCATGAAATCGAGGTTAGCGGCAACATATCCAGATGCTTTTCCTACTGGCGCAATGGCAGAGACGATGGACCAAAGACCGGACCTTGAAAGTCCTCTT
                              tatatatcttatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatttcttccaggtctctttatcccagtgtgcattcgaattggatttgtacaacagttttccagctgaacaagctatatatcttatgtctatgttgtagAGGCATGAAATCGAGGTTAGCGGCAACATATCCAGATGCTTTTCCTACTGGCGCAATGGCAGAGACGATGGACCAAAGACCGGACCTTGAAAGTCCTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA