Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccctcttggaacctccctgtagaattgtcctctatttctactgttaattgtctaatttcttcatactggaattgtgctagATGGGAGTGAAATGGATTTTTCTACTCTCCCTCGCACTTCTGCAAGCTGCATATTACCGGCGCATGAAGTGGTCCGTCTACAAGTCGCGCAAGCTGGTCC

Basic information

species Oryza sativa
transcript LOC_Os01g70960.2
intron # 6
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|86486845|gb|CI129478.1|CI129478
EST:     TCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATGGAAGAGAGAAAACTG                         ATGGGAGTGAAATGGATTTTTCTACTCTCCCTCGCACTTCTGCAAGCTGCA
genomic: TCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATGGAAGAGAGAAAACTGgtaaccctct ... attgtgctagATGGGAGTGAAATGGATTTTTCTACTCTCCCTCGCACTTCTGCAAGCTGCA
EST: gi|89168991|gb|CI020531.1|CI020531
EST:     TCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATGGAAGAGAGAAAACTG                         ATGGGAGTGAAATGGATTTTTCTACTCTCCCTCGCACTTTTGCAAGCTGCA
genomic: TCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATGGAAGAGAGAAAACTGgtaaccctct ... attgtgctagATGGGAGTGAAATGGATTTTTCTACTCTCCCTCGCACTTCTGCAAGCTGCA
EST: gi|89164688|gb|CI101776.1|CI101776
EST:     TCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATGGAAGAGAGAAAACTG                         ATGGGAGTGAAATGGATTTTTCTACTCTCCCTCGCACTTCTGCAAGCTGCA
genomic: TCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATGGAAGAGAGAAAACTGgtaaccctct ... attgtgctagATGGGAGTGAAATGGATTTTTCTACTCTCCCTCGCACTTCTGCAAGCTGCA
EST: gi|27920999|gb|CB096807.1|CB096807
EST:     TCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATGGAAGAGAGAAAACTG                         ATGGGAGTGAAATGGATTTTTCTACTCTCCCTCGCACTTCTGCAAGCTGCA
genomic: TCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATGGAAGAGAGAAAACTGgtaaccctct ... attgtgctagATGGGAGTGAAATGGATTTTTCTACTCTCCCTCGCACTTCTGCAAGCTGCA
EST: gi|88222829|gb|CI220894.1|CI220894
EST:     TCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATGGAAGAGAGAAAACTG                         ATGGGAGTGAAATGGATTTTTCTACTCTCCCTCGCACTTCTGCAAGCTGCA
genomic: TCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATGGAAGAGAGAAAACTGgtaaccctct ... attgtgctagATGGGAGTGAAATGGATTTTTCTACTCTCCCTCGCACTTCTGCAAGCTGCA
EST: gi|86502387|gb|CI145020.1|CI145020
EST:     TCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATGGAAGAGAGAAAACTG                         ATGGGAGTGAAATGGATTTTTCTACTCTCCCTCGCACTTCTGCAAGCTGCA
genomic: TCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATGGAAGAGAGAAAACTGgtaaccctct ... attgtgctagATGGGAGTGAAATGGATTTTTCTACTCTCCCTCGCACTTCTGCAAGCTGCA
EST: gi|86433950|gb|CI094293.1|CI094293
EST:     TCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATGGAAGAGAGAAAACTG                         ATGGGAGTGAAATGGATTTTTCTACTCTCCCTCGCACTTCTGCAAGCTGCA
genomic: TCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATGGAAGAGAGAAAACTGgtaaccctct ... attgtgctagATGGGAGTGAAATGGATTTTTCTACTCTCCCTCGCACTTCTGCAAGCTGCA
EST: gi|86508914|gb|CI151547.1|CI151547
EST:     TCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATGGAAGAGAGAAAACTG                         ATGGGAGTGAAATGGATTTTTCTACTCTCCCTCGCACTTCTGCAAGCTGCA
genomic: TCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATGGAAGAGAGAAAACTGgtaaccctct ... attgtgctagATGGGAGTGAAATGGATTTTTCTACTCTCCCTCGCACTTCTGCAAGCTGCA
EST: gi|88993878|gb|CI114168.1|CI114168
EST:     GGAGCCTGAGATGGAAGAGAGAAAACTG                         ATGGGAGTGAAATGGATTTTTCTACTCTCCCTCGCACTTCTGCAAGCTGCA
genomic: GGAGCCTGAGATGGAAGAGAGAAAACTGgtaaccctct ... attgtgctagATGGGAGTGAAATGGATTTTTCTACTCTCCCTCGCACTTCTGCAAGCTGCA
EST: gi|86418967|gb|CI053768.1|CI053768
EST:     TCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATGGAAGAGAGAAAACTG                         ATGGGAGTGAAATGGATTTTTCTACTCTCCCTCGCACTTCTGCAAGCTGCA
genomic: TCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATGGAAGAGAGAAAACTGgtaaccctct ... attgtgctagATGGGAGTGAAATGGATTTTTCTACTCTCCCTCGCACTTCTGCAAGCTGCA
EST: gi|87029581|gb|CI257376.1|CI257376
EST:     TCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATGGAAGAGAGAAAACTG                         ATGGGAGTGAAATGGATTTTTCTACTCTCCCTCGCACTTCTGCAAGCTGCA
genomic: TCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATGGAAGAGAGAAAACTGgtaaccctct ... attgtgctagATGGGAGTGAAATGGATTTTTCTACTCTCCCTCGCACTTCTGCAAGCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcctctatttctactgttaattgtctaatttcttcatactggaattgtgctagATGGGAGTGAAATGGATTTTTCTACTCTCCCTCGCACTTCTGCAAGCTGCATATTACCGGCGCATGAAGTGGTCCGTCTACAAGTCGCGCAAGCTGGTCC
                        gtctaat  putative branch site (score: 3)
                  ttaattgtctaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaccctcttggaacctccctgtagaattgtcctctatttctactgttaattgtctaatttcttcatactggaattgtgctagATGGGAGTGAAATGGATTTTTCTACTCTCCCTCGCACTTCTGCAAGCTGCATATTACCGGCGCATGAAGTGGTCCGTCTACAAGTCGCGCAAGCTGGTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG