Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGCATCGTGTTGGAAGTGCTGGTAACACGGCAGGTTCAAGTCGACCGAGAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttccacttccagaactagctatcctcagaatcgcggatgcatccagttgattcaaaagaattcattttcagtgcaaatgtctcatcatgcattccattgtgtctatttttcag

Basic information

species Oryza sativa
transcript LOC_Os12g06810.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g06810.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G167999_T02 (Zea mays), 5'ss of exon 2
AATGCATCGTGTTGGAAGTGCTGGTAACACGGCAGGTTCAAGTCGACCGAGAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttccacttccagaa-ctagctat------------cctcagaa--------tcgcggatgcatccagttgattcaaaagaattcattttcagtgcaaatgtc-tcatcatgcattccattgtgtctatttttcag
||||||||||||||| |||||||||||||| || || || | |||||||||||| ||||||||||| |||||||| || ||||| |||||| | ||||||||  |||    ||  | || |||||| |            | | |||         ||   | | |      |  |||| ||| ||||||| |||    |||  |   | || ||||||||  || ||| | ||||||||
AATGCATCGTGTTGGGAGTGCTGGTAACACAGCTGGCTCGACTCGACCGAGAAAAGAGAAGCGCTTCACATATGTACTCAATGATGCTGATGATAAAAAGgtatgtttatattaaataagctagctctttcagtttttccctttagatctagcttttcctaggtactctatatacattcgaaacaattcatattccactcaatggcgatgataatgcattcatttctgtttgtttttcag
















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|88357841|gb|CI625092.1|CI625092
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88423157|gb|CI613458.1|CI613458
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88398573|gb|CI598538.1|CI598538
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88299650|gb|CI574763.1|CI574763
EST:     GAAAGGAGAGGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88731171|gb|CI754784.1|CI754784
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88392717|gb|CI623948.1|CI623948
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88333238|gb|CI641081.1|CI641081
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88427243|gb|CI586791.1|CI586791
EST:     GAAAAGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88720333|gb|CI743632.1|CI743632
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88299299|gb|CI572251.1|CI572251
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88385685|gb|CI566547.1|CI566547
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88575849|gb|CI669994.1|CI669994
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|58659315|gb|CK047995.1|CK047995
EST:     AAAGGAGAAGCGCTTTACATATGTGCTGAATGAGGGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: AAAGGAGAAGCGCTTTACATATGTGCTGAATGACG-CTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88357189|gb|CI616076.1|CI616076
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88360459|gb|CI608461.1|CI608461
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88350674|gb|CI617529.1|CI617529
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATAACTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88730866|gb|CI754479.1|CI754479
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATGGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88352046|gb|CI626046.1|CI626046
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88372748|gb|CI612676.1|CI612676
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88725276|gb|CI748535.1|CI748535
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88392951|gb|CI614833.1|CI614833
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88351371|gb|CI627387.1|CI627387
EST:     GAAAGGAGGAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88581848|gb|CI699062.1|CI699062
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGGTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88411008|gb|CI606227.1|CI606227
EST:     AAAGGAGAAGCGCTTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: AAAGGAGAAGCGC-TTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88315130|gb|CI611794.1|CI611794
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88356655|gb|CI617738.1|CI617738
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88405503|gb|CI588709.1|CI588709
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|117217320|gb|CT852008.1|CT852008
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88311817|gb|CI577423.1|CI577423
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|29666968|gb|CB663243.1|CB663243
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88729484|gb|CI752994.1|CI752994
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88351353|gb|CI627369.1|CI627369
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88431514|gb|CI579631.1|CI579631
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|29678629|gb|CB674904.1|CB674904
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
EST: gi|88299553|gb|CI574666.1|CI574666
EST:     GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAG                         CATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT
genomic: GAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 68 (upstream exon), 39 (downstream exon)
Score: 31

AATGCATCGTGTTGGAAGTGCTGGTAACACGGCAGGTTCAAGTCGACCGAGAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttcca ... tatttttcagCATTGTGCTGGGATCAACTGCTTGTCATACCTAAATGCCTCTACTTCTGGTACGAGTGATTATCTTTTTACCGGGAGTCGGGATGGTACCTTGAAGAGGT




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGCATCGTGTTGGAAGTGCTGGTAACACGGCAGGTTCAAGTCGACCGAGAAAGGAGAAGCGCTTTACATATGTGCTGAATGACGCTGATAACAAAAAGgtcagttccacttccagaactagctatcctcagaatcgcggatgcatccagttgattcaaaagaattcattttcagtgcaaatgtctcatcatgcattccattgtgtctatttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT