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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAGgtatgttgtctattaatctttccttgcattttctgaacggcaatgatgctgaacatggtaatcagtttatcacagttccagtttatagttgacatgcataaatggtagctgccttgactaacctacacttgggaaatgaatatgcag

Basic information

species Oryza sativa
transcript LOC_Os08g14460.3
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g14460.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G147500_T02 (Zea mays), 5'ss of exon 12
--------------------AAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAGgtatgttgtctattaatctttccttgcattttctgaacggcaatgatgctgaacatggtaatcagtttatcacagttccagtttatagttgacatgcataaatggtagctgccttgactaacctacacttgggaaatgaatatgcag
                    ||||||| || || || || || ||||| ||||| |||||||||||||| |||||||| |||||||| ||||| |||||||| ||| |  | ||| | |||  ||    |||||||| || | |  | |    |||   || | ||   |     ||    ||| |||      |  ||| |  ||                                         
AGATGCTCAGAAAGGTGCAGAAGTGACTTCTGAGGCAACTGACCGGGAGCTTGAGCTTGAAGCTCAACTGGTTGAAGCAAGAAGCATCATCCAAGAGCAGgtttgt-gcatctta-tatttgtttatcatttctgaatggaagtactccctc-catatgaaacggtaagttgt--tttggatttttag--agtttctatagacagtg----------------------------------------

upper sequence: LOC_Os08g14460.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA17G07040.2 (Glycine max), 5'ss of exon 13
--------------------AAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAGgta-tgttgtctattaatctttccttgcattttctgaacggcaatgatgctgaacatggtaatcagtttatcacagttccagtttatagttgacatgcataaatggtagctgccttgactaacctacacttgggaaatgaatatgcag
                    |||| || ||||| ||||| ||| |||||||||| |||||||||||||| || ||||| || ||||| || |||||||||||| |||| | | || ||      ||| | |  |      |     | ||   |  | | |  | ||||   | | ||  | | |   ||  |     || ||    ||||||                                   
AGATGCTCAAAAAGAAGCAGAAGTTACTTCAGAGGCTACTGAGAGGGAACTTGAGCTTGAAGCTCAACTTGTCGAAGCAAGGAGCATCATACAGGAGCAGgtaatgttttttgttcatgcag--ttgaaatcacaagttaggtccaaggc---atttag-agcctgtttg--atacttttattgtgatgtaaa-----atcaacaaaagctgc-----------------------------------

upper sequence: LOC_Os08g14460.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA13G00980.1 (Glycine max), 5'ss of exon 13
--------------------AAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAGgtatgttgtctattaatctttccttgcattttctgaacggcaatgatgctgaacatggtaatcagtttatcacagttccagtttatagttgacatgcataaatggtagctgccttgactaacctacacttgggaaatgaatatgcag
                    |||| || || || ||||| ||| |||||||||| |||||||||||||| || ||||| || ||||| || ||||||||||||   ||| |       | | | |||| ||    | |   | | | |   ||     | |  ||  | |   |      | || |  |  | |  ||  ||  || ||                                      
AGATGCTCAAAAGGAAGCAGAAGTTACTTCTGAGGCTACTGAGAGGGAACTTGAGCTTGAAGCTCAACTTGTCGAAGCAAGGAGCATCATACAGGAGCAGgtaatgtgttt-------tgttcatgcaattga-aatcacaagttaggtccaaggcatttag-agcctgtttgatgctttgattgtgatgtaaaatcaacaaaagttgc--------------------------------------

upper sequence: LOC_Os08g14460.3 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv11s0052g00890.t01 (Vitis vinifera), 5'ss of exon 13
--------------------AAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAGgtatgttgtctattaatctttccttgcattttctgaacggcaat--gatgctgaacatggtaatcagtttatcacagttccagtttatagttgacatgcataaatggtagctgccttgactaacctacacttgggaaatgaatatgcag
                    | || || || ||||| || ||| |||| ||||| |||||||||||||| ||||| ||  | ||||| ||||||||||||||  | |||        |||| | ||  | | |  |  |   ||   |  ||| |  | |  ||  || |||     || || ||   | |  | ||| || ||||  || |                                     
AGATGCACAGAAAGGGGCAGAGGTTACTTCTGAAGCAACTGAGAGGGAGCTTGAGCTTGAAGCTCAACTTGTTGAGGCACGGAGCATAATCCAGGAGCAGgt--gctgta-------cttttcctggttatgcaaattgctgattcaaaactggatcttg-gattcgtctattttcatttcaattctaattctaaatggatgaatg--agtt-------------------------------------

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|88964540|gb|CI069888.1|CI069888
EST:     TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAG                         GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
genomic: TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAGgtatgttgtc ... gaatatgcagGCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
EST: gi|88969032|gb|CI099023.1|CI099023
EST:     TTGAACTTGAAGCTCGACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAG                         GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
genomic: TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAGgtatgttgtc ... gaatatgcagGCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
EST: gi|86425309|gb|CI070406.1|CI070406
EST:     TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAG                         GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
genomic: TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAGgtatgttgtc ... gaatatgcagGCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
EST: gi|88968346|gb|CI098588.1|CI098588
EST:     TTGAACTTGAAGCTGAACTAGTTGAAGGTAGAAGCATTATCCAGGAGCAG                         GCATCCCTCATGTCCAAGCACTTTACGAAGTGTGATAAACCAAG
genomic: TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAGgtatgttgtc ... gaatatgcagGCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
EST: gi|87019008|gb|CI259064.1|CI259064
EST:     TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAG                         GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
genomic: TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAGgtatgttgtc ... gaatatgcagGCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
EST: gi|88958312|gb|CI095831.1|CI095831
EST:     TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAG                         GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
genomic: TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAGgtatgttgtc ... gaatatgcagGCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
EST: gi|86413437|gb|CI067842.1|CI067842
EST:     TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAG                         GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
genomic: TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAGgtatgttgtc ... gaatatgcagGCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
EST: gi|86497077|gb|CI139710.1|CI139710
EST:     TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAG                         GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
genomic: TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAGgtatgttgtc ... gaatatgcagGCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
EST: gi|58675270|gb|CK063957.1|CK063957
EST:     TAGAAGCATTATCCAGGAGCAG                         GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
genomic: TAGAAGCATTATCCAGGAGCAGgtatgttgtc ... gaatatgcagGCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
EST: gi|88957287|gb|CI095263.1|CI095263
EST:     TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAG                         GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
genomic: TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAGgtatgttgtc ... gaatatgcagGCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
EST: gi|33798029|gb|CF324874.1|CF324874
EST:     TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAG                         GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
genomic: TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAGgtatgttgtc ... gaatatgcagGCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
EST: gi|86433159|gb|CI093502.1|CI093502
EST:     TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAG                         GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
genomic: TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAGgtatgttgtc ... gaatatgcagGCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
EST: gi|286887|gb|D15694.1|D15694
EST:     TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAG                         GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
genomic: TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAGgtatgttgtc ... gaatatgcagGCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
EST: gi|89189153|gb|CI048692.1|CI048692
EST:     AACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAG                         GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
genomic: AACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAGgtatgttgtc ... gaatatgcagGCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
EST: gi|58587881|gb|CF986189.1|CF986189
EST:     TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAG                         GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
genomic: TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAGgtatgttgtc ... gaatatgcagGCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
EST: gi|86484540|gb|CI127173.1|CI127173
EST:     TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAG                         GCATCCCTCATGTCCAAGCACTGTACGAAGTCTGATAAACCAAG
genomic: TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAGgtatgttgtc ... gaatatgcagGCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
EST: gi|88902915|gb|CI088453.1|CI088453
EST:     TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAG                         GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG
genomic: TTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAGgtatgttgtc ... gaatatgcagGCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTCAACTAGTTGAAGCTAGAAGCATTATCCAGGAGCAGgtatgttgtctattaatctttccttgcattttctgaacggcaatgatgctgaacatggtaatcagtttatcacagttccagtttatagttgacatgcataaatggtagctgccttgactaacctacacttgggaaatgaatatgcag

- - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG