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'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGATGCGCTTGAATCTGATTTGTCCAAAACTTTTGGAGGAATGAATAGACTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatcactaatatccaataaactcttttggtagcaattctccagtgctgcttaccttttttttttgtgctttatgtgggttaaaatagtctctcta...

Basic information

species Oryza sativa
transcript LOC_Os06g47350.2
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g47350.2 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G415846_T02 (Zea mays), 5'ss of exon 13
AAGATGCGCTTGAATCTGATTTGTCCAAAACTTTTGGAGGAATGAATAGACTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatcactaatatccaataaactcttttggtagcaattctccagtgctgct-taccttttttttttgtgctttatgtgggttaaaatagtctctcta-
|||||||  ||||||| ||| | || ||  | ||||||||| | ||||| ||||||||||||||||||||||| || ||||| || ||||| || ||||||| || |  |  ||||   | ||  |  ||| |  ||  ||  ||   |  || | ||   | |  | |||     ||  |   |  |  |  |      | 
AAGATGCAGTTGAATCCGATCTATCGAAGGCATTTGGAGGACTTAATAGGCTTGACATGTTCTTCCCATTTGACCCGTATCTACTTAAAGAGTCTGACAGgtttg-actatcaataag-agtacccattttagccagttatagtctcattatgttctagtgtgtgctcttggaggatagttatttgcatgttattcaataag

upper sequence: LOC_Os06g47350.2 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA16G21590.2 (Glycine max), 5'ss of exon 15
AAGATGCGCTTGAATCTGATTTGTCCAAAACTTTTGGAGGAATGAATAGACTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatcactaatatccaataaactcttttggtagcaattctccagtgctgcttaccttttttttttgt-gctttatgtgggttaaaatagtctctcta----------------
| |||  |||||| |||||| | |||||  ||||||| || ||  |||||||||||||||| |||||||||||||| | | || | ||  ||   || |||   |  | | | |  |  | |    |  ||||  |  ||   |  | ||      |  || |  || ||| ||||| |||     | || |  ||||| |                
ATGATATGCTTGAGTCTGATCTTTCCAAGGCTTTTGGCGGGATTGATAGACTTGACATGTTTTTCCCATTTGATCCATGTTTGTTGAAGAAAAGTGAAAGgcaagtgttattcaactaaatttgtttgatttgacattaacattttattgaattaaattttatgcttatgttgctttttgttcaccacaacaa-ctctcaatgtggactgtcttcag

upper sequence: LOC_Os06g47350.2 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA09G32870.2 (Glycine max), 5'ss of exon 17
AAGATGCGCTTGAATCTGATTTGTCCAAAACTTTTGGAGGAATGAATAGACTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatcactaatatccaataaactcttttggtagcaattctccagtgc-----------tgcttacctt--ttttttttgtgctttatgtgggttaaaatagtctctcta---
| |||  |||||| |||||| | |||||  ||||||| || ||| |||||||||||||||| |||||||||||||| | | || | ||   |   || ||||  | || | | |       | | ||  |||| ||  ||   |  | ||            ||||||| ||  ||||| || | |  |  |    | ||  | | || |||    
ATGATATGCTTGAGTCTGATCTTTCCAAGGCTTTTGGCGGGATGGATAGACTTGACATGTTTTTCCCATTTGATCCATGTTTGTTGAAGAGAAGTGAAAGgttagtattattgaaccaagtttatctgatttgatattaacattttattgagttaaattttatgcttacgttgctttttgttctccactccgactctcaatgtggactgtctccag

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|27334393|gb|CA882844.1|CA882844
EST:     CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAG                         ATATATGCGTCCAAATTTTGAGT
genomic: CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatca ... tgccctgcagATATATGCGTCCAAATTTTGAGT
EST: gi|29678965|gb|CB675240.1|CB675240
EST:     CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAG                         ATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
genomic: CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatca ... tgccctgcagATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
EST: gi|29639209|gb|CB644218.1|CB644218
EST:     CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAG                         ATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
genomic: CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatca ... tgccctgcagATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
EST: gi|2799623|gb|AA752612.1|AA752612
EST:     CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACTG                         ATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
genomic: CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatca ... tgccctgcagATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
EST: gi|58668152|gb|CK056838.1|CK056838
EST:     CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAG                         ATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
genomic: CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatca ... tgccctgcagATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
EST: gi|29624119|gb|CB629130.1|CB629130
EST:     CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAG                         ATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
genomic: CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatca ... tgccctgcagATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
EST: gi|29681087|gb|CB677362.1|CB677362
EST:     CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAG                         ATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
genomic: CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatca ... tgccctgcagATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
EST: gi|218504600|gb|FG967431.1|FG967431
EST:     CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAG                         ATATATGCGTCCAAATTTTGAGTACTGGTCCAT
genomic: CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatca ... tgccctgcagATATATGCGTCCAAATTTTGAGTACTGGTCCAT
EST: gi|86899426|gb|CI298203.1|CI298203
EST:     CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAG                         ATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
genomic: CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatca ... tgccctgcagATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
EST: gi|66922574|gb|CX109422.1|CX109422
EST:     CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAG                         ATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
genomic: CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatca ... tgccctgcagATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
EST: gi|287055|gb|D15860.1|D15860
EST:     CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAG                         ATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
genomic: CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatca ... tgccctgcagATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
EST: gi|218500322|gb|FG953822.1|FG953822
EST:     CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAG                         ATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
genomic: CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatca ... tgccctgcagATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
EST: gi|29685787|gb|CB682062.1|CB682062
EST:     CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAG                         ATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
genomic: CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatca ... tgccctgcagATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
EST: gi|218504331|gb|FG952706.1|FG952706
EST:     CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAG                         ATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
genomic: CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatca ... tgccctgcagATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
EST: gi|218503709|gb|FG953299.1|FG953299
EST:     CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAG                         ATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
genomic: CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatca ... tgccctgcagATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
EST: gi|218499202|gb|FG956934.1|FG956934
EST:     CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAG                         ATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
genomic: CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatca ... tgccctgcagATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
EST: gi|29676282|gb|CB672557.1|CB672557
EST:     CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAG                         ATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
genomic: CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatca ... tgccctgcagATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
EST: gi|38480245|gb|CF964334.1|CF964334
EST:     CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAG                         ATATATGCGTCCAAATTTTGAGTACTGGTCCGGGGTCAAGACGACATACAA
genomic: CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatca ... tgccctgcagATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
EST: gi|568168|gb|D39003.1|D39003
EST:     GTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAG                         ATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
genomic: GTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatca ... tgccctgcagATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
EST: gi|58680790|gb|CK069477.1|CK069477
EST:     CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAG                         ATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
genomic: CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatca ... tgccctgcagATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
EST: gi|56158395|gb|AU075492.2|AU075492
EST:     CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAG                         ATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
genomic: CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatca ... tgccctgcagATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAA
EST: gi|218492292|gb|FG954140.1|FG954140
EST:     CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAG                         ATATATGCGTCCAAATTTTGAGTACTGGTCCATGGT
genomic: CTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatca ... tgccctgcagATATATGCGTCCAAATTTTGAGTACTGGTCCATGGT

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: 75 (upstream exon), 74 (downstream exon)
Score: 283

AAGATGCGCTTGAATCTGATTTGTCCAAAACTTTTGGAGGAATGAATAGACTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatca ... tgccctgcagATATATGCGTCCAAATTTTGAGTACTGGTCCATGGTCAAGACGACATACAACAATTATAACAGTGATGTTGATGATGAGCTAGTGGACCTCGATGCACCT




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGATGCGCTTGAATCTGATTTGTCCAAAACTTTTGGAGGAATGAATAGACTTGACATGTTCTTCCCATTTGATCCTTATCTGCTAAAAGAATCCGACAGgtgtgcatcactaatatccaataaactcttttggtagcaattctccagtgctgcttaccttttttttttgtgctttatgtgggttaaaatagtctctcta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA