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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAGgtaaggaatgcctgggtttctttctgttgttctgagtacaaatgtttaatgactgttagtacaaacttgtaattaatatttgtagagtctactgattaat...

Basic information

species Oryza sativa
transcript LOC_Os03g36750.1
intron # 6
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|12405331|gb|AU166932.1|AU166932
EST:     CAGCAACCACACTTGGAGTCGATCCATCTAG                         TTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGC
genomic: CAGCAACCACACTTGGAGTCGATCCATCTAGgtaaggaatg ... ggatatttagTTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGC
EST: gi|33684374|gb|CF312613.1|CF312613
EST:     GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG                         TTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGC
genomic: GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAGgtaaggaatg ... ggatatttagTTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGC
EST: gi|86862357|gb|CI345350.1|CI345350
EST:     CAGCAATCTAC-TACTTGCAGCAACCACAC-TGGAGTCGATCCATCTAC                         TTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGC
genomic: CAGCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAGgtaaggaatg ... ggatatttagTTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGC
EST: gi|88258818|gb|CI359208.1|CI359208
EST:     CACTTGGAGTCGATCCATCTAG                         TTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGC
genomic: CACTTGGAGTCGATCCATCTAGgtaaggaatg ... ggatatttagTTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGC
EST: gi|38472504|gb|CF956636.1|CF956636
EST:     GGAGTCGATCCATCTAG                         TAGTAGTAGTTGTTGAAGACAGTACTATAGGGCTAGCAGCAGCCAAAGCTG
genomic: GGAGTCGATCCATCTAGgtaaggaatg ... ggatatttagTTGT-GTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTG
EST: gi|29625469|gb|CB630480.1|CB630480
EST:     GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG                         TTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGC
genomic: GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAGgtaaggaatg ... ggatatttagTTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGC
EST: gi|38473540|gb|CF957672.1|CF957672
EST:     GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG                         TTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGC
genomic: GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAGgtaaggaatg ... ggatatttagTTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGC
EST: gi|33797557|gb|CF324638.1|CF324638
EST:     GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG                         TTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGC
genomic: GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAGgtaaggaatg ... ggatatttagTTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGC
EST: gi|117242305|gb|CT842941.1|CT842941
EST:     GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG                         TTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGC
genomic: GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAGgtaaggaatg ... ggatatttagTTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGC
EST: gi|29657434|gb|CB653709.1|CB653709
EST:     GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG                         TTGTGTTGTTGT
genomic: GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAGgtaaggaatg ... ggatatttagTTGTGTTGTTGT
EST: gi|29657435|gb|CB653710.1|CB653710
EST:     GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG                         TTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGC
genomic: GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAGgtaaggaatg ... ggatatttagTTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGC
EST: gi|38475316|gb|CF959449.1|CF959449
EST:     GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG                         TTGTGTTGTTGTTGAAGACAGTACTATAGGGGTTGCAGCAGCCAAAGCTGC
genomic: GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAGgtaaggaatg ... ggatatttagTTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGC
EST: gi|58586453|gb|CF984761.1|CF984761
EST:     GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG                         TTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGC
genomic: GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAGgtaaggaatg ... ggatatttagTTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGC
EST: gi|88257860|gb|CI360446.1|CI360446
EST:     GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATGCTAG                         TTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTG
genomic: GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCAT-CTAGgtaaggaatg ... ggatatttagTTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTG
EST: gi|38478320|gb|CF962453.1|CF962453
EST:     GCAAGCTGACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG                         TTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGC
genomic: GCAATCT-ACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAGgtaaggaatg ... ggatatttagTTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGC
EST: gi|29687538|gb|CB683813.1|CB683813
EST:     GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG                         TTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGC
genomic: GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAGgtaaggaatg ... ggatatttagTTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGC

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: 47 (upstream exon), 67 (downstream exon)
Score: 47

GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAGgtaaggaatg ... ggatatttagTTGTGTTGTTGTTGAAGACAGTACTATAGGGCTTGCAGCAGCCAAAGCTGCTGGTATGAAGTGTATCGTAACAAAAAGCGG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAGgtaaggaatgcctgggtttctttctgttgttctgagtacaaatgtttaatgactgttagtacaaacttgtaattaatatttgtagagtctactgattaat

- - - - - - - - - - - - - - TTGGAG