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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAATTGCTGCTGCTACCGAGAAAGCAGTGGGCATAAAAGTACAAAAGTTACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGATgtaagctcttgcctatttgttaagatcaaatctgaaactgtagctctagaattactgccttcagggaactttatgacttacgtactcataattattttgatatattttag

Basic information

species Oryza sativa
transcript LOC_Os02g09060.1
intron # 9
splice site 5'
intron type U2

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|58680116|gb|CK068803.1|CK068803
EST:     TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGAT                         ATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
genomic: TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGATgtaagctctt ... tatattttagATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
EST: gi|88838045|gb|CI372613.1|CI372613
EST:     GCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGAT                         ATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
genomic: GCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGATgtaagctctt ... tatattttagATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
EST: gi|86483356|gb|CI125989.1|CI125989
EST:     TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGAT                         ATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAAAGAATTCAA
genomic: TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGATgtaagctctt ... tatattttagATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
EST: gi|88218548|gb|CI218397.1|CI218397
EST:     GCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGAT                         ATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
genomic: GCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGATgtaagctctt ... tatattttagATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
EST: gi|86500028|gb|CI142661.1|CI142661
EST:     TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGAT                         ATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
genomic: TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGATgtaagctctt ... tatattttagATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
EST: gi|88259444|gb|CI363737.1|CI363737
EST:     GACCGGGTTTCTTAATGAT                         ATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
genomic: GACCGGGTTTCTTAATGATgtaagctctt ... tatattttagATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
EST: gi|29678198|gb|CB674473.1|CB674473
EST:     TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGAT                         ATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
genomic: TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGATgtaagctctt ... tatattttagATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
EST: gi|40492104|gb|BX900098.1|BX900098
EST:     TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGAT                         ATTCATGAAAATCTTGTTAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
genomic: TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGATgtaagctctt ... tatattttagATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
EST: gi|86881135|gb|CI339296.1|CI339296
EST:     GTGCATGGAAGAGACCGGGTTTCTTAATGAT                         ATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
genomic: GTGCATGGAAGAGACCGGGTTTCTTAATGATgtaagctctt ... tatattttagATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
EST: gi|86426354|gb|CI071451.1|CI071451
EST:     TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGAT                         ATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
genomic: TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGATgtaagctctt ... tatattttagATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
EST: gi|86412826|gb|CI067231.1|CI067231
EST:     TACAGGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGAT                         ATTCATGAAAATCTTGNNNNNNNNNCATGGAGATGTGGAGGGAGAGAATTC
genomic: TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGATgtaagctctt ... tatattttagATTCATGAAAATCTTG--TAAAAAACATGGAGATGTGGAGGGAGAGAATTC
EST: gi|88275435|gb|CI395286.1|CI395286
EST:     GGGTTTCTTAATGAT                         ATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
genomic: GGGTTTCTTAATGATgtaagctctt ... tatattttagATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
EST: gi|89175817|gb|CI042838.1|CI042838
EST:     TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGAT                         ATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
genomic: TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGATgtaagctctt ... tatattttagATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
EST: gi|88218295|gb|CI218144.1|CI218144
EST:     GCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGAT                         ATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
genomic: GCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGATgtaagctctt ... tatattttagATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
EST: gi|86543524|gb|CI183730.1|CI183730
EST:     TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGAT                         ATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
genomic: TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGATgtaagctctt ... tatattttagATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
EST: gi|86495057|gb|CI137690.1|CI137690
EST:     TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGAT                         ATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
genomic: TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGATgtaagctctt ... tatattttagATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
EST: gi|87014873|gb|CI271472.1|CI271472
EST:     TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGAT                         ATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
genomic: TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGATgtaagctctt ... tatattttagATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
EST: gi|218484344|gb|FG954469.1|FG954469
EST:     TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGAT                         ATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
genomic: TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGATgtaagctctt ... tatattttagATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
EST: gi|86490088|gb|CI132721.1|CI132721
EST:     TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGAT                         ATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
genomic: TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGATgtaagctctt ... tatattttagATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
EST: gi|89164799|gb|CI101887.1|CI101887
EST:     TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGAT                         ATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
genomic: TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGATgtaagctctt ... tatattttagATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
EST: gi|86492775|gb|CI135408.1|CI135408
EST:     TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGAT                         ATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
genomic: TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGATgtaagctctt ... tatattttagATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
EST: gi|86529860|gb|CI170066.1|CI170066
EST:     TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGAT                         ATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA
genomic: TACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGATgtaagctctt ... tatattttagATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAA

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), 70 (downstream exon)
Score: 13

AGAAATTGCTGCTGCTACCGAGAAAGCAGTGGGCATAAAAGTACAAAAGTTACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGATgtaagctctt ... tatattttagATTCATGAAAATCTTGTAAAAAACATGGAGATGTGGAGGGAGAGAATTCAAAAAGTAAAAGAAAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAATTGCTGCTGCTACCGAGAAAGCAGTGGGCATAAAAGTACAAAAGTTACAAGCAAAGCTTGATAAGTGCATGGAAGAGACCGGGTTTCTTAATGATgtaagctcttgcctatttgttaagatcaaatctgaaactgtagctctagaattactgccttcagggaactttatgacttacgtactcataattattttgatatattttag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA