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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGAAGAATTTCAGCATACAGCATATGCAACCAATGCATATGTTGCCTTGGGACCACTGTGGAAGCCAGCACTACAAGgtaaatgtttctttctcgtgaactttccatcttattttacgagcgatggatgaacatcttatgtgtaaagttcaacgcttgaacacaccactatctttgt...

Basic information

species Oryza sativa
transcript LOC_Os11g48090.4
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g48090.4 (Oryza sativa), 5'ss of exon 18
lower sequence: Vv02s0087g00070.t01 (Vitis vinifera), 5'ss of exon 18
AAAGAAGAATTTCAGCATACAGCATATGCAACCAATGCATATGTTGCCTTGGGACCACTGTGGAAGCCAGCACTACAAGgtaaatgtttctttctcgtgaactttccatcttattttacgagcgatggatgaacatcttatgtgtaaagttcaacgcttgaacacaccactatctttgt---
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AAAGAAGAATTTCAGCATACAGCTTATGCTACAAATGCTTACGTGACATTGGGACTATTGTGGAAGCAAGTATCGCATGgtaa--gctcctttgtttttaagtata-atgaaatgtaagaaagaaaagaaactgatcaaaaaaaaaaaaaagaaagaaagaaaagaactaaaaaaaaattaa
















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|87023349|gb|CI272177.1|CI272177
EST:     AACCAATGCATATGTCGCCTTGGGACCATTGTGGAAGCCAGCACTACAAG                         GGAACAGACCGTTCAAGCTTAGCGTTGCTTTTCACTCTCAGGATAAAGGTA
genomic: AACCAATGCATATGTTGCCTTGGGACCACTGTGGAAGCCAGCACTACAAGgtaaatgttt ... atatatgcagGGAACAGACCGGTCAAGCTTAGCGTTGCTTTTCACTCTCAGGATAAAGGTA
EST: gi|86903584|gb|CI300438.1|CI300438
EST:     AACCAATGCATATGTTGCCTTGGGACCACTGTGGAAGCCAGCACTACAAG                         GGAACAGACCGGTCAAGCTTAGCGTTGCTTTTCACTCTCAGGATAAAGGTA
genomic: AACCAATGCATATGTTGCCTTGGGACCACTGTGGAAGCCAGCACTACAAGgtaaatgttt ... atatatgcagGGAACAGACCGGTCAAGCTTAGCGTTGCTTTTCACTCTCAGGATAAAGGTA
EST: gi|87027466|gb|CI272231.1|CI272231
EST:     AACCAATGCATATGTTGCCTTGGGACCACTGTGGAAGCCAGCACTACAAG                         GGAACAGACCGGTCAAGCTTAGCGTTGCTTTTCACTCTCAGGATAAAGGTA
genomic: AACCAATGCATATGTTGCCTTGGGACCACTGTGGAAGCCAGCACTACAAGgtaaatgttt ... atatatgcagGGAACAGACCGGTCAAGCTTAGCGTTGCTTTTCACTCTCAGGATAAAGGTA
EST: gi|29682977|gb|CB679252.1|CB679252
EST:     AACCAATGCATATGTTGCCTTGGGACCACTGTGGAAGCCAGCACTACAAG                         GGAACAGACCGGTCAAGCTTAGCGTTGCTTTTCACTCTCAGGATAAAGGTA
genomic: AACCAATGCATATGTTGCCTTGGGACCACTGTGGAAGCCAGCACTACAAGgtaaatgttt ... atatatgcagGGAACAGACCGGTCAAGCTTAGCGTTGCTTTTCACTCTCAGGATAAAGGTA
EST: gi|86479042|gb|CI121675.1|CI121675
EST:     AACCAATGCATATGTTGCCTTGGGACCACTGTGGAAGCCAGCACTACAAG                         GGAACAGACCGGTCAAGCTTAGCGTTGCTTTTCACTCTCAGGATAAAGGTA
genomic: AACCAATGCATATGTTGCCTTGGGACCACTGTGGAAGCCAGCACTACAAGgtaaatgttt ... atatatgcagGGAACAGACCGGTCAAGCTTAGCGTTGCTTTTCACTCTCAGGATAAAGGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGAAGAATTTCAGCATACAGCATATGCAACCAATGCATATGTTGCCTTGGGACCACTGTGGAAGCCAGCACTACAAGgtaaatgtttctttctcgtgaactttccatcttattttacgagcgatggatgaacatcttatgtgtaaagttcaacgcttgaacacaccactatctttgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG