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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTAACGACAATGCTACATTTGTGGAAGATAACTCGTTGCCATCGTTCTCAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAGgtctgcatatcatgaggaatctactgaccttgattgttgttgcagtatgtgttttgtcatttccatgaataaaccagctgattgatttccttttatactgtgtgcag

Basic information

species Oryza sativa
transcript LOC_Os01g37910.2
intron # 7
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|58692028|gb|CK080715.1|CK080715
EST:     CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAG                         TACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
genomic: CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAGgtctgcatat ... ctgtgtgcagTACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
EST: gi|51946162|gb|CV152503.1|CV152503
EST:     CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAG                         TACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
genomic: CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAGgtctgcatat ... ctgtgtgcagTACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
EST: gi|29680574|gb|CB676849.1|CB676849
EST:     CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAG                         TACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
genomic: CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAGgtctgcatat ... ctgtgtgcagTACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
EST: gi|58600998|gb|CK011526.1|CK011526
EST:     GGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCGAGGAGAG                         TACCGCAAATTGCCTGAGAGTTCTCCTAGAGAAAAACGAAGCTCGGAAGC
genomic: GGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGC-A-GA-AGgtctgcatat ... ctgtgtgcagTACCGCAAATTGCCTGAGAGTTCTCCT-GAGAAAAACGAAGCTCGGAAGC
EST: gi|29676766|gb|CB673041.1|CB673041
EST:     CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAG                         TACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
genomic: CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAGgtctgcatat ... ctgtgtgcagTACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
EST: gi|38482190|gb|CF966244.1|CF966244
EST:     CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAG                         TACCGCAAATTGCCTGAGAGTTCTCCTGAGAGGGACGAAGCTCGGAAGCAA
genomic: CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAGgtctgcatat ... ctgtgtgcagTACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
EST: gi|29641856|gb|CB646863.1|CB646863
EST:     AAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAG                         TACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
genomic: AAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAGgtctgcatat ... ctgtgtgcagTACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
EST: gi|4715982|gb|AU057098.1|AU057098
EST:     CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAG                         TACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
genomic: CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAGgtctgcatat ... ctgtgtgcagTACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
EST: gi|58592657|gb|CF990965.1|CF990965
EST:     CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAG                         TACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
genomic: CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAGgtctgcatat ... ctgtgtgcagTACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
EST: gi|58682333|gb|CK071020.1|CK071020
EST:     CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAG                         TACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
genomic: CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAGgtctgcatat ... ctgtgtgcagTACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
EST: gi|58692781|gb|CK081468.1|CK081468
EST:     CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAG                         TACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
genomic: CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAGgtctgcatat ... ctgtgtgcagTACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
EST: gi|2275793|gb|C24770.1|C24770
EST:     CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAG                         TACCGCAAATTGCCTGANAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
genomic: CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAGgtctgcatat ... ctgtgtgcagTACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
EST: gi|58686800|gb|CK075487.1|CK075487
EST:     CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAG                         TACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
genomic: CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAGgtctgcatat ... ctgtgtgcagTACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
EST: gi|58696195|gb|CK084882.1|CK084882
EST:     CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAG                         TACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
genomic: CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAGgtctgcatat ... ctgtgtgcagTACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
EST: gi|2312973|gb|C29128.1|C29128
EST:     CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAG                         TACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
genomic: CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAGgtctgcatat ... ctgtgtgcagTACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
EST: gi|29641855|gb|CB646862.1|CB646862
EST:     CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAG                         TACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA
genomic: CAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAGgtctgcatat ... ctgtgtgcagTACCGCAAATTGCCTGAGAGTTCTCCTGAGAAAAACGAAGCTCGGAAGCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTAACGACAATGCTACATTTGTGGAAGATAACTCGTTGCCATCGTTCTCAAGGGCTGTTAATCAGCGGGATGCTGACCTGGTTTACTTCTGGCAGAAGgtctgcatatcatgaggaatctactgaccttgattgttgttgcagtatgtgttttgtcatttccatgaataaaccagctgattgatttccttttatactgtgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG