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

...ccagttataacaggaaaagaaagttgcctctgatttctgtcatctctgaaatattaatgcccctcttctttcattgtctttattttctcatcatatgcagCCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG

Basic information

species Oryza sativa
transcript LOC_Os05g36070.2
intron # 10
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|88838811|gb|CI376349.1|CI376349
EST:     T-GGTCTGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAG                         CCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTCTGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAGgtgagttctg ... tcatatgcagCCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|88244093|gb|CI243215.1|CI243215
EST:     TGGGTCTGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAG                         CCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTCTGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAGgtgagttctg ... tcatatgcagCCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|88249358|gb|CI249207.1|CI249207
EST:     TGGGTCTGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAG                         CCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTCTGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAGgtgagttctg ... tcatatgcagCCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|86539354|gb|CI179560.1|CI179560
EST:     TGGGTCTGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAG                         CCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTCTGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAGgtgagttctg ... tcatatgcagCCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|88841700|gb|CI080956.1|CI080956
EST:     TGGGTCTGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAG                         CCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTCTGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAGgtgagttctg ... tcatatgcagCCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|86538870|gb|CI179076.1|CI179076
EST:     TGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAG                         CCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAGgtgagttctg ... tcatatgcagCCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|8859158|gb|AU096476.1|AU096476
EST:     TGGGTCTGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAG                         CCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCNC
genomic: TGGGTCTGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAGgtgagttctg ... tcatatgcagCCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|86431507|gb|CI085118.1|CI085118
EST:     TGGGTCTGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAG                         CCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTCTGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAGgtgagttctg ... tcatatgcagCCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|89174130|gb|CI042023.1|CI042023
EST:     TGGGTCTGACTGTGACGATAATAGTGATGAACTGGTTCCAAGCTGCACAG                         CCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTCTGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAGgtgagttctg ... tcatatgcagCCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|29628338|gb|CB633349.1|CB633349
EST:     TGGGTCTGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAG                         CCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTCTGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAGgtgagttctg ... tcatatgcagCCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|86600029|gb|CI258369.1|CI258369
EST:     AGTGATGAACTGGTTCCAAGCTGCACAG                         CCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: AGTGATGAACTGGTTCCAAGCTGCACAGgtgagttctg ... tcatatgcagCCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|86435528|gb|CI106761.1|CI106761
EST:     TGACTGTGACCATAATAGTGATGAACTGGTTCCAAGCTGCACAG                         CCTGCTCTGTTGTACATTTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCA
genomic: TGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAGgtgagttctg ... tcatatgcagCCTGCTCTGTTGTACA-TTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCA
EST: gi|29628337|gb|CB633348.1|CB633348
EST:     TGGGTCTGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAG                         CCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTCTGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAGgtgagttctg ... tcatatgcagCCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|86431057|gb|CI083480.1|CI083480
EST:     AATAATAGTGATGAACTGGTTCCAAGCTGCACAG                         CCTGCTCTGTTGTACATTGTTCCTGGTGTGATCGGTTTTGTTGCTGTTCAC
genomic: AATAATAGTGATGAACTGGTTCCAAGCTGCACAGgtgagttctg ... tcatatgcagCCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|86880509|gb|CI320999.1|CI320999
EST:     TGGGTCTGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAG                         CCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTCTGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAGgtgagttctg ... tcatatgcagCCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|86413082|gb|CI067487.1|CI067487
EST:     TCTGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAG                         CCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TCTGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAGgtgagttctg ... tcatatgcagCCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
EST: gi|88840958|gb|CI000920.1|CI000920
EST:     TGGGTCTGACTGTGACAATAATAGTGGTGAACTGGTTCCAAGCTGCACAG                         CCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC
genomic: TGGGTCTGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAGgtgagttctg ... tcatatgcagCCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCAC

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), 75 (downstream exon)
Score: 20

AAGAGGAATTAAGAACCGCTATTTTAATAGTGCATTTTTGGGTTATACCGTGGGTCTGACTGTGACAATAATAGTGATGAACTGGTTCCAAGCTGCACAGgtgagttctg ... tcatatgcagCCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaaatattaatgcccctcttctttcattgtctttattttctcatcatatgcagCCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG
      tattaat  putative branch site (score: 20)
            tgcccctcttctttca  CT-rich tract
                           attgtctttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccagttataacaggaaaagaaagttgcctctgatttctgtcatctctgaaatattaatgcccctcttctttcattgtctttattttctcatcatatgcagCCTGCTCTGTTGTACATTGTTCCTGGTGTGATTGGTTTTGTTGCTGTTCACTGTTTGTGGAATGGTGAAGTAAAGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT