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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAATCGCTTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtatccttgtgtcattttgcacattcgaaagggttatcttgtcaaatgctgaccaatgtcctattaatttttgcag

Basic information

species Oryza sativa
transcript LOC_Os12g13590.2
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g13590.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM5G823484_T01 (Zea mays), 5'ss of exon 7
GGAAATCGCTTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtatccttgtgtcatttt-gcacattcgaaagggttatcttgtcaaatgctgaccaatgtcc--tattaatttttgcag----------------------
||||||||||||||||||||||| || |||||||||||||||||||||||||||||||||||  ||| || |||||  | |||    |    ||  | || |    | |||    ||| |     | ||||   |                         
GGAAATCGCTTGCATAAGGGGCTGCTTAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtactcttctgccatttcagaacaaataactctgtcctttt-ttggcttctggttcatggctgtcttcaattcacgtttttctggtggattaatttgttac

upper sequence: LOC_Os12g13590.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA16G01660.1 (Glycine max), 5'ss of exon 21
GGAAATCGCTTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtatccttgtgtcattttgcacattcgaaagggt-tatcttgtcaa-atgctgaccaatgtcctattaatttttgcag----------------------
|||||||||||||| |||| |||||| || |||||||||||||  || |||| ||| |||||           |  ||||      |     | |||||||| |  || |  |  | |||  ||   | || |                          
GGAAATCGCTTGCACAAGGTGCTACTAAACCATTGGCAGAAGTATACTTTTAATCCAAGgtaatagacctgggtcctgcattccttactttatctatcttgttaccatacatattactgtaatacatacttctttgacttggaaaaaatgttcataagc

upper sequence: LOC_Os12g13590.2 (Oryza sativa), 5'ss of exon 18
lower sequence: Vv15s0046g02200.t01 (Vitis vinifera), 5'ss of exon 21
GGAAATCGCTTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtatccttgtgtcattttg---cacattcgaaagggttatcttgtcaaatgctgaccaatgtcctattaatttttgcag
||||| | ||||||||| ||||| || |||||||||||||||||||| || |  || ||||| | |    ||  ||     ||||||        |  |||  | |  | || |   | ||     |  |  | ||||
GGAAACCACTTGCATAAAGGGCTGCTTAATCATTGGCAGAAGTTCACTTTCAACCCTAGgtaacatgacttctcttctgctcacatttttctcactgttctgttgatttactcattcacgtttctcttgtcgt-gcag

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|33689209|gb|CF317448.1|CF317448
EST:     TTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTAGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
genomic: TTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtatccttgt ... atttttgcagTGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
EST: gi|87029720|gb|CI274401.1|CI274401
EST:     TTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
genomic: TTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtatccttgt ... atttttgcagTGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
EST: gi|66920327|gb|CX107175.1|CX107175
EST:     TTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
genomic: TTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtatccttgt ... atttttgcagTGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
EST: gi|88974506|gb|CI022047.1|CI022047
EST:     TTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
genomic: TTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtatccttgt ... atttttgcagTGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
EST: gi|58666677|gb|CK055363.1|CK055363
EST:     GGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
genomic: GGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtatccttgt ... atttttgcagTGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
EST: gi|33689213|gb|CF317452.1|CF317452
EST:     TTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTAGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
genomic: TTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtatccttgt ... atttttgcagTGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
EST: gi|87029773|gb|CI274454.1|CI274454
EST:     TTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAG                         TGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG
genomic: TTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtatccttgt ... atttttgcagTGGTGGGTTACGGCTGAAACGTGATATCACTGAGTACGGGGAATTCGTTCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAATCGCTTGCATAAGGGGCTACTCAATCATTGGCAGAAGTTCACATTTAGTCCCAGgtatccttgtgtcattttgcacattcgaaagggttatcttgtcaaatgctgaccaatgtcctattaatttttgcag

- - - - - - - - - - - - - - - - - -  AGAAGT