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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtcttgtcagttaaacggacgccttgatattttctctgctttgactgatggattcttggtgtacatgtagGTCTCTATGTGGGAGCATTTAGTCCATATGGACCAGAAGTTGTGCAGCTCCGTCGAAAGTTCGGCCATTGGAACAGCACAGATGAAGTGGAGTTTTTCGA

Basic information

species Oryza sativa
transcript LOC_Os01g01790.1
intron # 7
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|29623733|gb|CB628744.1|CB628744
EST:     GATCCATTTAGTG                         GTCTCTATGTGGGAGCATTTAGTCCATATGGACCAGAAGTTGTGCAGCTCC
genomic: GATCCATTTAGTGgtaatgtctt ... gtacatgtagGTCTCTATGTGGGAGCATTTAGTCCATATGGACCAGAAGTTGTGCAGCTCC
EST: gi|25802741|gb|CA758702.1|CA758702
EST:     GGCTCAGATCCATTTAGTG                         GTCTCTATGTGGGAGCATTTAGTCCATATGGACCAGAAGTTGTGCAGCTCC
genomic: GGCTCAGATCCATTTAGTGgtaatgtctt ... gtacatgtagGTCTCTATGTGGGAGCATTTAGTCCATATGGACCAGAAGTTGTGCAGCTCC
EST: gi|29624183|gb|CB629194.1|CB629194
EST:     GATCCATTTAGTG                         GTCTCTATGTGGGAGCATTTAGTCCATATGGACCAGAAGTTGTGCAGCTCC
genomic: GATCCATTTAGTGgtaatgtctt ... gtacatgtagGTCTCTATGTGGGAGCATTTAGTCCATATGGACCAGAAGTTGTGCAGCTCC
EST: gi|29630522|gb|CB635531.1|CB635531
EST:     CAATAGGATCATTACTGACAGTAACGGCTCAGATCCATTTAGTG                         GTCTCTATGTGGGAGCATTTAGTCCATATGGACCAGAAGTTGTGCAGCTCC
genomic: CAATAGGATCATTACTGACAGTAACGGCTCAGATCCATTTAGTGgtaatgtctt ... gtacatgtagGTCTCTATGTGGGAGCATTTAGTCCATATGGACCAGAAGTTGTGCAGCTCC
EST: gi|58690330|gb|CK079017.1|CK079017
EST:     AATTTTCAATAGGATCATTACTGACAGTAACGGCTCAGATCCATTTAGTG                         GTCTCTATGTGGGAGCATTTAGTCCATATGGACCAGAAGTTGTGCAGCTCC
genomic: AATTTTCAATAGGATCATTACTGACAGTAACGGCTCAGATCCATTTAGTGgtaatgtctt ... gtacatgtagGTCTCTATGTGGGAGCATTTAGTCCATATGGACCAGAAGTTGTGCAGCTCC
EST: gi|218496693|gb|FG970613.1|FG970613
EST:     AATTTTCAATAGGATCATTACTGACAGTAACGGCTCAGATCCATTTAGTG                         GTCTCTATGTGAGGAGCATTTAGTCCATAT
genomic: AATTTTCAATAGGATCATTACTGACAGTAACGGCTCAGATCCATTTAGTGgtaatgtctt ... gtacatgtagGTCTCTATGTG-GGAGCATTTAGTCCATAT
EST: gi|29624598|gb|CB629609.1|CB629609
EST:     GATCCATTTAGTG                         GTCTCTATGTGGGAGCATTTAGTCCATATGGACCAGAAGTTGTGCAGCTCC
genomic: GATCCATTTAGTGgtaatgtctt ... gtacatgtagGTCTCTATGTGGGAGCATTTAGTCCATATGGACCAGAAGTTGTGCAGCTCC
EST: gi|29669220|gb|CB665495.1|CB665495
EST:     CAGATCCATTTAGTG                         GTCTCTATGTGGGAGCATTTAGTCCATATGGACCAGAAGTTGTGCAGCTCC
genomic: CAGATCCATTTAGTGgtaatgtctt ... gtacatgtagGTCTCTATGTGGGAGCATTTAGTCCATATGGACCAGAAGTTGTGCAGCTCC
EST: gi|29621884|gb|CB626895.1|CB626895
EST:     GATCCATTTAGTG                         GTCTCTATGTGGGAGCATTTAGTCCATATGGACCAGAAGTTGTGCAGCTCC
genomic: GATCCATTTAGTGgtaatgtctt ... gtacatgtagGTCTCTATGTGGGAGCATTTAGTCCATATGGACCAGAAGTTGTGCAGCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggacgccttgatattttctctgctttgactgatggattcttggtgtacatgtagGTCTCTATGTGGGAGCATTTAGTCCATATGGACCAGAAGTTGTGCAGCTCCGTCGAAAGTTCGGCCATTGGAACAGCACAGATGAAGTGGAGTTTTTCGA
                           gactgat  putative branch site (score: 3)
        ttgatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgtcttgtcagttaaacggacgccttgatattttctctgctttgactgatggattcttggtgtacatgtagGTCTCTATGTGGGAGCATTTAGTCCATATGGACCAGAAGTTGTGCAGCTCCGTCGAAAGTTCGGCCATTGGAACAGCACAGATGAAGTGGAGTTTTTCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG