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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactttcatcattgattcactgtgctcctttcaactttgaaaaaacaaattactatgcaggcccgaatgacacaacttcaagatgcccaaaagggtgcagAAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAG

Basic information

species Oryza sativa
transcript LOC_Os08g14460.3
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g14460.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G147500_T02 (Zea mays), 3'ss of exon 11
------------------------------------aactttcatcattgattcactgtgctcctttca--actttgaaaaaacaaattactatg-----caggcccgaatgacacaacttcaagatgcccaaaagggtgcagAAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAG
                                    || |   ||   |     ||     |  |||||  || |    | ||  | ||   |||     ||||| ||||||||||||||||||||||| || || |||||||||||||| || || || || || ||||| ||||| |||||||||||||| |||||||| |                    
gtaggagccactggattgagactataagcatcgtacaattgctatttctcccatacacacttgttttcattacatgatgataattatttctgatgacaaccagGCACGAATGACACAACTTCAAGATGCTCAGAAAGGTGCAGAAGTGACTTCTGAGGCAACTGACCGGGAGCTTGAGCTTGAAGCTCAACTGGTTGAAGCAA--------------------

upper sequence: LOC_Os08g14460.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA17G07040.1 (Glycine max), 3'ss of exon 12
----------------------------------------aactttcatcattgattcactgtgctcctttcaactttgaaaaaac--aaatt--actatgcaggcccgaatgacacaacttcaagatgcccaaaagggtgcagAAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAG
                                        || | |   ||   ||  |||||    ||||     || |        |||||  | |||| |||  || |||   ||| | |||||||| ||||| |  |||||||| || ||||| ||||| ||| |||||||||| |||||||||||||| || ||||| |                    
gtaattacttattagtatcactttccaatttgtatcttttaagtatttgcagatatgaactgtttgtctttggttgttaactgcttgaaaattgaaatatgaagGAGCGTATGGTTCAATTGCAAGATGCTCAAAAAGAAGCAGAAGTTACTTCAGAGGCTACTGAGAGGGAACTTGAGCTTGAAGCTCAACTTGTCGAAGCAA--------------------

upper sequence: LOC_Os08g14460.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA13G00980.1 (Glycine max), 3'ss of exon 12
-----------------------------------------------aactttcatcattga-ttcactgtgctc--ctttcaactttgaaaaaacaaattactatgcaggcccgaatgacacaacttcaagatgcccaaaagggtgcagAAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAG
                                                 | |  || | ||| || | |||  |    | | ||||     ||||   |  | |||| |||  || |||   ||| | |||||||| |||||||  |||||||| || || || ||||| ||| |||||||||| |||||||||||||| || ||||| |                    
gtaattacttattagtatcactttccaatttttatcttttaagtatttgcatatatgaatgaattgattgtctttggttgttaactgcttgaaaattga--aatatgaagGAGCGCATGGTTCAATTGCAAGATGCTCAAAAGGAAGCAGAAGTTACTTCTGAGGCTACTGAGAGGGAACTTGAGCTTGAAGCTCAACTTGTCGAAGCAA--------------------

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|88968346|gb|CI098588.1|CI098588
EST:     GTTCGATGCAG                         AAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTGAACTAG
genomic: GTTCGATGCAGgtaaaaccat ... aagggtgcagAAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTCAACTAG
EST: gi|88958312|gb|CI095831.1|CI095831
EST:     AGTTGATGCAAGAAAATGCTGATTTGCGAGCACTATTGCGTTCGATGCAG                         AAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTCAACTAG
genomic: AGTTGATGCAAGAAAATGCTGATTTGCGAGCACTATTGCGTTCGATGCAGgtaaaaccat ... aagggtgcagAAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTCAACTAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactttcatcattgattcactgtgctcctttcaactttgaaaaaacaaattactatgcaggcccgaatgacacaacttcaagatgcccaaaagggtgcagAAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- ctttcat
- - - - - - tgattca
- - - - - - - - - - -gtgctcc
- - - - - - - - - - - - - - - - - - - - - aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcaggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acacaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgccc