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'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagtctgagtttggttacttggctctgttgttttcctttgtactatgaaaggactcatttgttgagtttgtttttttgtgattcttgccatgtttgcagAGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAGTTGGGAAATCATCTGATGACAAAGTGAAGAAAGATATCTCCAAAAAGGATGTTGATGATC

Basic information

species Oryza sativa
transcript LOC_Os06g03770.1
intron # 1
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|117230036|gb|CT846408.1|CT846408
EST:     TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTG                         AGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAGTTGGGAAATCA
genomic: TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTGgtaacttgtg ... atgtttgcagAGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAGTTGGGAAATCA
EST: gi|88744575|gb|CI767935.1|CI767935
EST:     TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTG                         AGAGGACATGCATTTTCCACATCTGCCAATG
genomic: TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTGgtaacttgtg ... atgtttgcagAGAGGACATGCATTTTCCACATCTGCCAATG
EST: gi|88352649|gb|CI624588.1|CI624588
EST:     TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTG                         AGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAGTTGGGAAATCA
genomic: TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTGgtaacttgtg ... atgtttgcagAGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAGTTGGGAAATCA
EST: gi|88440731|gb|CI693293.1|CI693293
EST:     TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTG                         AGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAGTTGGGAAATCA
genomic: TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTGgtaacttgtg ... atgtttgcagAGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAGTTGGGAAATCA
EST: gi|88350446|gb|CI654071.1|CI654071
EST:     TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTG                         AGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAGTTGGGAAATCA
genomic: TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTGgtaacttgtg ... atgtttgcagAGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAGTTGGGAAATCA
EST: gi|88742695|gb|CI766203.1|CI766203
EST:     TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTG                         AGAGGACATGCATTTTCCACATCTGCC
genomic: TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTGgtaacttgtg ... atgtttgcagAGAGGACATGCATTTTCCACATCTGCC
EST: gi|29646655|gb|CB651662.1|CB651662
EST:     TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTG                         AGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAGTTGGGAAATCA
genomic: TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTGgtaacttgtg ... atgtttgcagAGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAGTTGGGAAATCA
EST: gi|88827640|gb|CI778205.1|CI778205
EST:     TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTG                         AGAGGACATGCATTTTCCACATCTGCCAATGCTGTG
genomic: TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTGgtaacttgtg ... atgtttgcagAGAGGACATGCATTTTCCACATCTGCCAATGCTGTG
EST: gi|5004334|gb|AU069483.1|AU069483
EST:     TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTG                         AGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAGTTGGGAAATCA
genomic: TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTGgtaacttgtg ... atgtttgcagAGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAGTTGGGAAATCA
EST: gi|88357953|gb|CI650689.1|CI650689
EST:     TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTG                         AGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAGTTGGGAAATCA
genomic: TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTGgtaacttgtg ... atgtttgcagAGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAGTTGGGAAATCA
EST: gi|88827458|gb|CI778023.1|CI778023
EST:     TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTG                         AGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAG
genomic: TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTGgtaacttgtg ... atgtttgcagAGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAG
EST: gi|86885643|gb|CI309770.1|CI309770
EST:     TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTG                         AGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAGTTGGGAAATCA
genomic: TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTGgtaacttgtg ... atgtttgcagAGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAGTTGGGAAATCA
EST: gi|5667164|gb|AU077424.1|AU077424
EST:     TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTG                         AGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAGTTGGGAAATCA
genomic: TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTGgtaacttgtg ... atgtttgcagAGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAGTTGGGAAATCA
EST: gi|88726046|gb|CI749701.1|CI749701
EST:     TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTG                         AGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGC
genomic: TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTGgtaacttgtg ... atgtttgcagAGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGC
EST: gi|95101355|gb|CI693103.1|CI693103
EST:     TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTG                         AGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAGTTGGGAAATCA
genomic: TCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTGgtaacttgtg ... atgtttgcagAGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAGTTGGGAAATCA

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: 72 (upstream exon), 72 (downstream exon)
Score: 32

GAATTGTTGGGTTTATCCCGGCGACGGGAAGTATGCCCCCTTTGGTCGCCTCAGCTGCTTCATGTCGGACTCCACCTACCCGCCGCCTCCCCGCGATGTGgtaacttgtg ... atgtttgcagAGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAGTTGGGAAATCATCTGATGACAAAGTGAAGAAAGATATCTCCAAAAAGGATGTTGATGATC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaaaggactcatttgttgagtttgtttttttgtgattcttgccatgtttgcagAGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAGTTGGGAAATCATCTGATGACAAAGTGAAGAAAGATATCTCCAAAAAGGATGTTGATGATC
                      tttgttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagtctgagtttggttacttggctctgttgttttcctttgtactatgaaaggactcatttgttgagtttgtttttttgtgattcttgccatgtttgcagAGAGGACATGCATTTTCCACATCTGCCAATGCTGTGGCAGTTGGGAAATCATCTGATGACAAAGTGAAGAAAGATATCTCCAAAAAGGATGTTGATGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - -ctgttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcttgc