Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acccccacccccaccccaaaaaaaaattgggggatccgccccagttatacatgaaaaatgttttgagcttttgagttgataagttgagaacattgaacagGGCCACTGTATTACAAGGGATGGTACCACCTATTCTACCAGTACAACCCCAAGGGAGCTGTGTGGGGCAATATCGTGTGGGCTCACTCGGTATCACAGGA

Basic information

species Oryza sativa
transcript LOC_Os02g33110.3
intron # 2
splice site 3'
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|29631187|gb|CB636196.1|CB636196
EST:     TGAACTGGATCAACGATCCGAACG                         GGCCACTGTATTACAAGGGATGGTACCACCTATTCTACCAGTACAACCCCAA
genomic: TGAACTGGATCAACGATCCGAACG
EST: gi|88743914|gb|CI765350.1|CI765350
EST:     TGAACTGGATCAACGATCCGAACG                         GGCCACTGTATTACAAGGGATGGTACCACCTATTCTACCAGTACAACCCCAA
genomic: TGAACTGGATCAACGATCCGAACG
EST: gi|88744618|gb|CI767978.1|CI767978
EST:     TGAACTGGATCAACGATCCGAACG                         GGCCACTGTATTACAAGGGATGGTACCACCTATTCTACCAGTACAACCCCAA
genomic: TGAACTGGATCAACGATCCGAACG
EST: gi|88377617|gb|CI605452.1|CI605452
EST:     TGAACTGGATCAACGATCCGAACG                         GGCCACTGTATTACAAGGGATGGTACCACCTATTCTACCAGTACAACCCCAA
genomic: TGAACTGGATCAACGATCCGAACG
EST: gi|88739913|gb|CI761423.1|CI761423
EST:     TGAACTGGATCAACGATCCGAACG                         GGCCACTGTATTACAAGGGATGGTACCACCTATTCTACCAGTACAACCCCCA
genomic: TGAACTGGATCAACGATCCGAACG
EST: gi|29634866|gb|CB639875.1|CB639875
EST:     TGAACTGGATCAACGATCCGAACG                         GGCCACTGTATTACAAGGGATGGTACCACCTATTCTACCAGTACAACCCCAA
genomic: TGAACTGGATCAACGATCCGAACG
EST: gi|88431051|gb|CI574222.1|CI574222
EST:     TGAACTGGATCAACGATCCGAACG                         GGCCACTGTATTACAAGGGATGGTACCACCTATTCTACCAGTACAACCCCAA
genomic: TGAACTGGATCAACGATCCGAACG
EST: gi|29663240|gb|CB659515.1|CB659515
EST:     TGAACTGGATCAACGATCCGAACG                         GGCCACTGTATTACAAGGGATGGTACCACCTATTCTACCAGTACAACCCCAA
genomic: TGAACTGGATCAACGATCCGAACG
EST: gi|88371527|gb|CI602705.1|CI602705
EST:     TGAACTGGATCAACGATCCGAACG                         GGCCACTGTATTACAAGGGATGGTACCACCTATTCTACCAGTACAACCCCAA
genomic: TGAACTGGATCAACGATCCGAACG
EST: gi|58666318|gb|CK055004.1|CK055004
EST:     TGAACTGGATCAACGATCCGAACG                         GGCCACTGTATTACAAGGGATGGTACCACCTATTCTACCAGTACAACCCCAA
genomic: TGAACTGGATCAACGATCCGAACG
EST: gi|29635781|gb|CB640790.1|CB640790
EST:     TGAACTGGATCAACGATCCGAACG                         GGCCACTGTATTACAAGGGATGGTACCACCTATTCTACCAGTACAACCCCAA
genomic: TGAACTGGATCAACGATCCGAACG
EST: gi|88763844|gb|CI773260.1|CI773260
EST:     TGAACTGGATCAACGATCCGAACG                         GGCCACTGTATTACAAGGGATGGTACCACCTATTCTACCAGTACAACCCCAA
genomic: TGAACTGGATCAACGATCCGAACG
EST: gi|88371360|gb|CI600208.1|CI600208
EST:     TGAACTGGATCAACGATCCGAACG                         GGCCACTGTATTACAAGGGATGGTACCACCTATTCTACCAGTACAACCCCAA
genomic: TGAACTGGATCAACGATCCGAACG
EST: gi|29635736|gb|CB640745.1|CB640745
EST:     TGAACTGGATCAACGATCCGAACG                         GGCCACTGTATTACAAGGGATGGTACCACCTATTCTACCAGTACAACCCCAA
genomic: TGAACTGGATCAACGATCCGAACG

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: 9 (upstream exon), 72 (downstream exon)
Score: 16

ATCCGAACGgtacgaattt ... cattgaacagGGCCACTGTATTACAAGGGATGGTACCACCTATTCTACCAGTACAACCCCAAGGGAGCTGTGTGGGGCAATATCGTGTGGGCTCACTCGGTATCACAGGA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatacatgaaaaatgttttgagcttttgagttgataagttgagaacattgaacagGGCCACTGTATTACAAGGGATGGTACCACCTATTCTACCAGTACAACCCCAAGGGAGCTGTGTGGGGCAATATCGTGTGGGCTCACTCGGTATCACAGGA
                            agttgat  putative branch site (score: 16)
     atgaaaaatgtttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acccccacccccaccccaaaaaaaaattgggggatccgccccagttatacatgaaaaatgttttgagcttttgagttgataagttgagaacattgaacagGGCCACTGTATTACAAGGGATGGTACCACCTATTCTACCAGTACAACCCCAAGGGAGCTGTGTGGGGCAATATCGTGTGGGCTCACTCGGTATCACAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT