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'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   		32  
 5'  3'   		33  
 5'  3'   		34  
 5'  3'   		35  
 5'  3'   		36  
 5'  3'   		37  
 5'  3'   		38  
 5'  3'   		39  
 5'  3'   		40  
 5'  3'   
41  
 5'  3'   		42  
 5'  3'   		43  
 5'  3'   		44  
 5'  3'   		45  
 5'  3'   		46  
 5'  3'   		47  
 5'  3'   		48  
 5'  3'   		49  
 5'  3'   		50  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcggatgattacttactatgtggtctcctttttttgtttgtatgcaaatatacaccctttctgatgggaactaaatctgaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTTAACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAA

Basic information

species Oryza sativa
transcript LOC_Os10g40780.1
intron # 49
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|29644838|gb|CB649845.1|CB649845
EST:     CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAG                         GAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
genomic: CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAGgtatcggatg ... gaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
EST: gi|29686205|gb|CB682480.1|CB682480
EST:     CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAG                         GAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGTTAATAGTT
genomic: CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAGgtatcggatg ... gaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
EST: gi|9886370|gb|BE607462.1|BE607462
EST:     CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAG                         GAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGACTAATAGTT
genomic: CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAGgtatcggatg ... gaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
EST: gi|29686204|gb|CB682479.1|CB682479
EST:     CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAG                         GAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
genomic: CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAGgtatcggatg ... gaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
EST: gi|29616068|gb|CB621080.1|CB621080
EST:     CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAG                         GAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
genomic: CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAGgtatcggatg ... gaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
EST: gi|58670528|gb|CK059214.1|CK059214
EST:     CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAG                         GAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
genomic: CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAGgtatcggatg ... gaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
EST: gi|29674319|gb|CB670594.1|CB670594
EST:     CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAG                         GAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
genomic: CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAGgtatcggatg ... gaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
EST: gi|89198422|gb|CI007482.1|CI007482
EST:     CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAG                         GAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
genomic: CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAGgtatcggatg ... gaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
EST: gi|29629738|gb|CB634747.1|CB634747
EST:     CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAG                         GAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
genomic: CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAGgtatcggatg ... gaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
EST: gi|29629914|gb|CB634923.1|CB634923
EST:     CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAG                         GAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
genomic: CACACTATTTTTCCTTCATAATTCTTTACTTGTTTTCTGAGGCAAACCAGgtatcggatg ... gaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
EST: gi|88220672|gb|CI220232.1|CI220232
EST:     TTTCTGAGGCAAACCAG                         GAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT
genomic: TTTCTGAGGCAAACCAGgtatcggatg ... gaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttgtatgcaaatatacaccctttctgatgggaactaaatctgaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTTAACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAA
                                   aactaaa  putative branch site (score: 2)
            aaatataca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcggatgattacttactatgtggtctcctttttttgtttgtatgcaaatatacaccctttctgatgggaactaaatctgaaatcgcagGAAATAGTCCAGGAGCAAATAACTAGGGTACTTCTGGAACGGCTAATAGTTAACCGCCCTCACCCGTGGGGGCTACTAATTACTTTCATTGAGCTTATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT