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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtttgttttatttcaatgattatctgaacttttgtgcttgcacatttataaatttgctaatttgtgtatctttggttagTTGAACTATTTGAGGCGGTTCCTTGGGCGAGGATTTCTGAAGCATGCACAA

Basic information

species Oryza sativa
transcript LOC_Os03g33590.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g33590.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G057412_T02 (Zea mays), 3'ss of exon 9
gtgtttgttttatt--tcaatgattatct----gaacttttgtgcttgcacatttataaatttgctaa--tttgtgtatctttggttagTTGAACTATTTGAGGCGGTTCCTTGGGCGAGGATTTCTGAAGCATGCACAA
|||| |||| | | || | || | || | |||||| | |||| | ||| || | ||||| || || ||||||||||||| |||||||||| |||||||| ||||| ||||||||| ||||
gtgtccgtttcttgaattgattttcatttcctcaaaatgctgtgctc-cgaatttgaagtttttctgagatttgttgttcatttcttagTTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG
















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|86480343|gb|CI122976.1|CI122976
EST:     CAGGCAAGCATGGTATTTTAAGAGTTACATCATGGCGTGAATCAATACAG                         TTGAACTATTTGAGGCGGTTCCTTGGGCGAGGATTTCTGAAGCATGCACAA
genomic: CAGGCAAGCATGGTATTTTAAGAGTTACATCATGGCGTGAATCAATACAGgtgtttgttt ... ctttggttagTTGAACTATTTGAGGCGGTTCCTTGGGCGAGGATTTCTGAAGCATGCACAA
EST: gi|29682391|gb|CB678666.1|CB678666
EST:     CAGGCAAGCATGGTATTTTAAGAGTTACATCATGGCGTGAATCAATACAG                         TTGAACTATTTGAGGCGGTTCCTTGGGCGAGGATTTCTGAAGCATGCACAA
genomic: CAGGCAAGCATGGTATTTTAAGAGTTACATCATGGCGTGAATCAATACAGgtgtttgttt ... ctttggttagTTGAACTATTTGAGGCGGTTCCTTGGGCGAGGATTTCTGAAGCATGCACAA
EST: gi|29671504|gb|CB667779.1|CB667779
EST:     CAGGCAAGCATGGTATTTTAAGAGTTACATCATGGCGTGAATCAATACAG                         TTGAACTATTTGAGGCGGTTCCTTGGGCGAGGATTTCTGAAGCATGCACAA
genomic: CAGGCAAGCATGGTATTTTAAGAGTTACATCATGGCGTGAATCAATACAGgtgtttgttt ... ctttggttagTTGAACTATTTGAGGCGGTTCCTTGGGCGAGGATTTCTGAAGCATGCACAA
EST: gi|29671594|gb|CB667869.1|CB667869
EST:     CAGGCAAGCATGGTATTTTAAGAGTTACATCATGGCGTGAATCAATACAG                         TTGAACTATTTGAGGCGGTTCCTTGGGCGAGGATTTCTGAAGCATGCACAA
genomic: CAGGCAAGCATGGTATTTTAAGAGTTACATCATGGCGTGAATCAATACAGgtgtttgttt ... ctttggttagTTGAACTATTTGAGGCGGTTCCTTGGGCGAGGATTTCTGAAGCATGCACAA
EST: gi|29671505|gb|CB667780.1|CB667780
EST:     CAGGCAAGCATGGTATTTTAAGAGTTACATCATGGCGTGAATCAATACAG                         TTGAACTATTTGAGGCGGTTCCTTGGGCGAGGATTTTTGAAGCATGCACAA
genomic: CAGGCAAGCATGGTATTTTAAGAGTTACATCATGGCGTGAATCAATACAGgtgtttgttt ... ctttggttagTTGAACTATTTGAGGCGGTTCCTTGGGCGAGGATTTCTGAAGCATGCACAA
EST: gi|88222629|gb|CI222585.1|CI222585
EST:     CAGGCAAGCATGGTATTTTAAGAGTTACATCATGGCGTGAATCAATACAG                         TTGAACTATTTGAGGCGGTTCCTTGGGCGAGGATTTCTGAAGCATGCACAA
genomic: CAGGCAAGCATGGTATTTTAAGAGTTACATCATGGCGTGAATCAATACAGgtgtttgttt ... ctttggttagTTGAACTATTTGAGGCGGTTCCTTGGGCGAGGATTTCTGAAGCATGCACAA
EST: gi|29666042|gb|CB662317.1|CB662317
EST:     CAGGCAAGCATGGTATTTTAAGAGTTACATCATGGCGTGAATCAATACAG                         TTGAACTATTTGAGGCGGTTCCTTGGGCGAGGATTTCTGAAGCATGCACAA
genomic: CAGGCAAGCATGGTATTTTAAGAGTTACATCATGGCGTGAATCAATACAGgtgtttgttt ... ctttggttagTTGAACTATTTGAGGCGGTTCCTTGGGCGAGGATTTCTGAAGCATGCACAA
EST: gi|89183748|gb|CI046313.1|CI046313
EST:     CAGGCAAGCATGGTATTTTAAGAGTTACATCATGGCGTGAATCAATACAG                         TTGAACTATTTGAGGCGGTTCCTTGGGCGAGGATTTCTGAAGCATGCACAA
genomic: CAGGCAAGCATGGTATTTTAAGAGTTACATCATGGCGTGAATCAATACAGgtgtttgttt ... ctttggttagTTGAACTATTTGAGGCGGTTCCTTGGGCGAGGATTTCTGAAGCATGCACAA
EST: gi|29671595|gb|CB667870.1|CB667870
EST:     CAGGCAAGCATGGTATTTTAAGAGTTACATCATGGCGTGAATCAATACAG                         TTGAACTATTTGAGGCGGTTCCTTGGGCGAGGATTTTTGAAGCATGCACAA
genomic: CAGGCAAGCATGGTATTTTAAGAGTTACATCATGGCGTGAATCAATACAGgtgtttgttt ... ctttggttagTTGAACTATTTGAGGCGGTTCCTTGGGCGAGGATTTCTGAAGCATGCACAA

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: 60 (upstream exon), 68 (downstream exon)
Score: 3

ACTGGTGAGTGCCTTGAAGAATCACTTAGAATTGCAGGCAAGCATGGTATTTTAAGAGTTACATCATGGCGTGAATCAATACAGgtgtttgttt ... ctttggttagTTGAACTATTTGAGGCGGTTCCTTGGGCGAGGATTTCTGAAGCATGCACAA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaacttttgtgcttgcacatttataaatttgctaatttgtgtatctttggttagTTGAACTATTTGAGGCGGTTCCTTGGGCGAGGATTTCTGAAGCATGCACAA
                              tgctaat  putative branch site (score: 3)
 tatcttt  putative PPT
 acatttataaatttgc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtttgttttatttcaatgattatctgaacttttgtgcttgcacatttataaatttgctaatttgtgtatctttggttagTTGAACTATTTGAGGCGGTTCCTTGGGCGAGGATTTCTGAAGCATGCACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC