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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTTGAGCATGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTGgtaggtagtattgcactgtgaccattcgttgtcttccttgtactgttctggtgttacaaattatctcttcaaatgcagagaatcttgctcgctgctagtt...

Basic information

species Oryza sativa
transcript LOC_Os02g17320.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g17320.3 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G169462_T01 (Zea mays), 5'ss of exon 9
GTTGTTGAGCATGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTGgtaggtag-tattgcactgtgaccattcgttgtcttccttgtactgttctggtgttacaaattatctcttcaaatgca--gagaat-cttgctcgctgctagtt-------
||||| || |||||||||||||||||||| ||| |||||||||||||||| ||||| ||||||| | || |  |  | | | |   |||  ||| ||| | || |           || || || |||||||||||| |  | || | | || ||      |  |       
GTTGTCGAACATGGTCTTGGTCATCTTCCTTTCCAGGAAAAGCAGGTCATCACTCCGACTGgtaagcaggtcctctattat-atagttccctgttttcttcgtgca----------tataagttttctcttcaaatgaaatgcgagtacatgttcaagataatgtagtaaaa

upper sequence: LOC_Os02g17320.3 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G034143_T03 (Zea mays), 5'ss of exon 11
GTTGTTGAGCATGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTGgtaggtagtattgcactgtgaccattcgttgtcttccttgtactgttctggtgttacaaattatctcttcaaatgca--gagaat-cttgctcgctgctagtt---------
||||| || |||||||||||||||||||| ||  |||||||||||||||| ||||| ||||||| | ||   | | ||||    ||| | |    ||| |||  | |||  |  | | || || |||||| ||||| |  |||| | | || ||  || || |          
GTTGTGGAACATGGTCTTGGTCATCTTCCTTTTCAGGAAAAGCAGGTCATCACTCCGACTGgtaagcagg--tcctctgt----atttggt----tccctgttttcttcgtgcat-ataagttttctcttaaaatgaaatgagagtacatgttca-tgataatgtggctaaat

upper sequence: LOC_Os02g17320.3 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 5'ss of exon 10
GTTGTTGAGCATGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTGgtagg-tagtattgcactgtgaccattcg-ttgtcttccttgtactgttctggtgttacaaattatctcttcaaatgcagagaatcttgctcgctgctagtt---
|||||||| ||||| || ||||||||||||||||  ||||||||||| || ||||||||||||| | |  |||| | |  ||||||   | ||||    ||  | |||||   |||||    ||| ||  |   | |||  ||  |       ||   | | |   
GTTGTTGAACATGGCCTAGGTCATCTTCCATTCACAGAAAAGCAGGTGATCACTCCAACTGgtaagctgatattactcaatgaccacctgattgtacaactcttgctgttt--gtgttg-gcattttcattggtagtgccaag--ttagatgggccatttgctctc

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|86902718|gb|CI306521.1|CI306521
EST:     TGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTG                         GATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAG
genomic: TGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTGgtaggtagta ... atgcgtgcagGATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAG
EST: gi|33675270|gb|CF303509.1|CF303509
EST:     TGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTG                         GATCGGTTTACA
genomic: TGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTGgtaggtagta ... atgcgtgcagGATCGGTTTACA
EST: gi|29643325|gb|CB648332.1|CB648332
EST:     GGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCNCA-CTG                         GATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCT
genomic: GGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTC-CAACTGgtaggtagta ... atgcgtgcagGATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCT
EST: gi|12623049|gb|AU173262.1|AU173262
EST:     TGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTG                         GATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGGGTGGTATCTCAG
genomic: TGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTGgtaggtagta ... atgcgtgcagGATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAG
EST: gi|29675373|gb|CB671648.1|CB671648
EST:     CATTCAAGGAAAAGCAGGTCATAACTCCAACTG                         GATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAG
genomic: CATTCAAGGAAAAGCAGGTCATAACTCCAACTGgtaggtagta ... atgcgtgcagGATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAG
EST: gi|29627016|gb|CB632027.1|CB632027
EST:     TGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTG                         GATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAG
genomic: TGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTGgtaggtagta ... atgcgtgcagGATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAG
EST: gi|66922909|gb|CX109757.1|CX109757
EST:     TGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTG                         GCTCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAG
genomic: TGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTGgtaggtagta ... atgcgtgcagGATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGTTGAGCATGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTGgtaggtagtattgcactgtgaccattcgttgtcttccttgtactgttctggtgttacaaattatctcttcaaatgcagagaatcttgctcgctgctagtt

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