Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCACATCTTACATTTACAAGTAGGAATGAAATGATGGCCGACTACCTTCTTGATCACTGCGATGTGCCCCTTCGCTTCAAGGATATGCATAAATCCAAGgtgattctcatcttccaaatctttatctcgatatttcccctaggaataaaagattccaaacccatattcacactatttacagtgagcattaggatcattt...

Basic information

species Oryza sativa
transcript LOC_Os01g50849.2
intron # 3
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|58677235|gb|CK065922.1|CK065922
EST:     TGGATCACTGCGATGTGCCCCTTCGCTTCAAGGATATGCATAAATCCAAG                         GTTGACATTGTGGCCAACTGGAGATTTTGGTAAA-TCCTATCATGTTTCAC
genomic: TTGATCACTGCGATGTGCCCCTTCGCTTCAAGGATATGCATAAATCCAAGgtgattctca ... tataatacagGTTGACATTGTGGCCAACTGGAGATTTTGGTAAAATCCTATCATGTTTCAC
EST: gi|38480545|gb|CF964634.1|CF964634
EST:     TGGATCAGTGCGATGTGCCCCTTCGCTTCAAGGATATGCATAAATCCAAG                         GTTGACATTGTGGCCAACTGGAGATTTTGGT-AAATCCTATCATGTTTCAC
genomic: TTGATCACTGCGATGTGCCCCTTCGCTTCAAGGATATGCATAAATCCAAGgtgattctca ... tataatacagGTTGACATTGTGGCCAACTGGAGATTTTGGTAAAATCCTATCATGTTTCAC
EST: gi|86494051|gb|CI136684.1|CI136684
EST:     TTGATCACTGCGATGTGCCCCTTCGCTTCAAGGATATGCATAAATCCAAG                         GTTGACATTGTGGCCAACTGGAGATTTTGGTAAAATCCTATCATGTTTCAC
genomic: TTGATCACTGCGATGTGCCCCTTCGCTTCAAGGATATGCATAAATCCAAGgtgattctca ... tataatacagGTTGACATTGTGGCCAACTGGAGATTTTGGTAAAATCCTATCATGTTTCAC
EST: gi|38475149|gb|CF959282.1|CF959282
EST:     TTGATCACTGCGATGTGCCCCTTCGCTTCAAGGATATGCATAAATCCAAG                         GTTGACATTGTGGCCAACTGGAGATTTTGGTAAAATCCTATCATGTTTCAC
genomic: TTGATCACTGCGATGTGCCCCTTCGCTTCAAGGATATGCATAAATCCAAGgtgattctca ... tataatacagGTTGACATTGTGGCCAACTGGAGATTTTGGTAAAATCCTATCATGTTTCAC
EST: gi|88581587|gb|CI698784.1|CI698784
EST:     TTGATCACTGCGATGTGCCCCTTCGCTTCAAGGATATGCATAAATCCAAG                         GTTGACATTGTGGCCAACTGGAGATTTTGGTAAAATCCTATCATGT
genomic: TTGATCACTGCGATGTGCCCCTTCGCTTCAAGGATATGCATAAATCCAAGgtgattctca ... tataatacagGTTGACATTGTGGCCAACTGGAGATTTTGGTAAAATCCTATCATGT
EST: gi|58690931|gb|CK079618.1|CK079618
EST:     TGGATCACTGCGATGTGCCCCTTCGCTTCAAGGATATGCATAAATCCAAG                         GTTGACATTGTGGCCAACTGGAGATTTTGGTAAA-TCCTATCATGTTTCAC
genomic: TTGATCACTGCGATGTGCCCCTTCGCTTCAAGGATATGCATAAATCCAAGgtgattctca ... tataatacagGTTGACATTGTGGCCAACTGGAGATTTTGGTAAAATCCTATCATGTTTCAC
EST: gi|38476695|gb|CF960828.1|CF960828
EST:     TGGATCACTGCGATGTGCCCCTTCGCTTCAAGGATATGCATAAATCCAAG                         GTTGACATTGTGGCCAACTGGAGATTTTGGTAAA-TCCTATCATGTTTCAC
genomic: TTGATCACTGCGATGTGCCCCTTCGCTTCAAGGATATGCATAAATCCAAGgtgattctca ... tataatacagGTTGACATTGTGGCCAACTGGAGATTTTGGTAAAATCCTATCATGTTTCAC
EST: gi|58602249|gb|CK012777.1|CK012777
EST:     TTGATCACTGCGATGTGCCCCTTCGCTTCAAGGATATGCATAAATCCAAG                         GTTGACATTGTGGCCAACTGGAGATTTTGGTAAAATCCTATCATGTTTCAC
genomic: TTGATCACTGCGATGTGCCCCTTCGCTTCAAGGATATGCATAAATCCAAGgtgattctca ... tataatacagGTTGACATTGTGGCCAACTGGAGATTTTGGTAAAATCCTATCATGTTTCAC

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: 49 (upstream exon), 74 (downstream exon)
Score: 11

ATCACATCTTACATTTACAAGTAGGAATGAAATGATGGCCGACTACCTTCTTGATCACTGCGATGTGCCCCTTCGCTTCAAGGATATGCATAAATCCAAGgtgattctca ... tataatacagGTTGACATTGTGGCCAACTGGAGATTTTGGTAAAATCCTATCATGTTTCACCATGGCATTTCACTGTTTGGCGCACGGTATTTAGGAGCTATTTGTATAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCACATCTTACATTTACAAGTAGGAATGAAATGATGGCCGACTACCTTCTTGATCACTGCGATGTGCCCCTTCGCTTCAAGGATATGCATAAATCCAAGgtgattctcatcttccaaatctttatctcgatatttcccctaggaataaaagattccaaacccatattcacactatttacagtgagcattaggatcattt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataaaa