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

gtataacctctttatcccttttttgtcttcctacgtttacttcttatacattagtggtttattgtttacatatatcttctctttaaccagATATTATGGGTGTCATAACTGAAATTGGTGCAACAGACACTCTACGCCCAAAATCAAGAAACACAGAAACTTTGAAAAGAACAATGCAGATTTGGGATGC

Basic information

species Oryza sativa
transcript LOC_Os01g29390.1
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|88487288|gb|CI424559.1|CI424559
EST:     ACCTTTTCAAGACGCCCCGTCTCTTGTGGACAGAAATGCTTTCTATGTTG                         ATATTATGGGTGTCATAACTGAAATTGGTGCAACAGACACTCTACGCCCAA
genomic: ACCTTTTCAAGACGCCCCGTCTCTTGTGGACAGAAATGCTTTCTATGTTGgtataacctc ... ctttaaccagATATTATGGGTGTCATAACTGAAATTGGTGCAACAGACACTCTACGCCCAA
EST: gi|38478879|gb|CF963012.1|CF963012
EST:     ACCTTTTCAAGACGCCCCGTCTCTTGTGGACAGAAATGCTTTCTATGTTG                         ATATTATGGGTGTCATAACTGAAATTGGTGCAACAGACACTCTACGCCCAA
genomic: ACCTTTTCAAGACGCCCCGTCTCTTGTGGACAGAAATGCTTTCTATGTTGgtataacctc ... ctttaaccagATATTATGGGTGTCATAACTGAAATTGGTGCAACAGACACTCTACGCCCAA
EST: gi|89190931|gb|CI392784.1|CI392784
EST:     ACCTTTTCAAGACGCCCCGTCTCTTGTGGACAGAAATGCTTTCTA---T-                         ATATTATGGGTGTCATAACT-AAATTGGTGCAACAGACACTCTACGCCCAA
genomic: ACCTTTTCAAGACGCCCCGTCTCTTGTGGACAGAAATGCTTTCTATGTTGgtataacctc ... ctttaaccagATATTATGGGTGTCATAACTGAAATTGGTGCAACAGACACTCTACGCCCAA
EST: gi|88275732|gb|CI396336.1|CI396336
EST:     AGACGCCCCGTCTCTTGTGGACAGAAATGCTTTCTATGTTG                         ATATTATGGGTGTCATAACTGAAATTGGTGCAACAGACACTCTACGCCCAA
genomic: AGACGCCCCGTCTCTTGTGGACAGAAATGCTTTCTATGTTGgtataacctc ... ctttaaccagATATTATGGGTGTCATAACTGAAATTGGTGCAACAGACACTCTACGCCCAA
EST: gi|86868722|gb|CI333099.1|CI333099
EST:     ACCTTTTCAAGACGCCCCGTCTCTTGTGGACAGAAATGCTTTCTATGTTG                         ATATTATGGGTGTCATAACTGAAATTGGTGCAACAGACACTCTACGCCCAA
genomic: ACCTTTTCAAGACGCCCCGTCTCTTGTGGACAGAAATGCTTTCTATGTTGgtataacctc ... ctttaaccagATATTATGGGTGTCATAACTGAAATTGGTGCAACAGACACTCTACGCCCAA
EST: gi|157650503|gb|EX450137.1|EX450137
EST:     ACCTTTTCAAGACGCCCCGTCTCTTGTGGACAGAAATGCTTTCTATGTTG                         ATATTATGGGTGTCATAACTGAAATTGGTGCAACAGACACTCTACGCCCAA
genomic: ACCTTTTCAAGACGCCCCGTCTCTTGTGGACAGAAATGCTTTCTATGTTGgtataacctc ... ctttaaccagATATTATGGGTGTCATAACTGAAATTGGTGCAACAGACACTCTACGCCCAA
EST: gi|86844233|gb|CI337612.1|CI337612
EST:     ACCTTTTCAAGACGCCCCGTCTCTTGTGGACAGAAATGCTTTCTATGTTG                         ATATTATGGGTGTCATAACTGAAATTGGTGCAACAGACACTCTACGCCCAA
genomic: ACCTTTTCAAGACGCCCCGTCTCTTGTGGACAGAAATGCTTTCTATGTTGgtataacctc ... ctttaaccagATATTATGGGTGTCATAACTGAAATTGGTGCAACAGACACTCTACGCCCAA
EST: gi|88559283|gb|CI489848.1|CI489848
EST:     ACCTTTTCAAGACGCCCCGTCTCTTGTGGACAGAAATGCTTTCTATGTTG                         ATATTATGGGTGTCATAACTGAAATTGGTGCAACAGACACTCTACGCCCAA
genomic: ACCTTTTCAAGACGCCCCGTCTCTTGTGGACAGAAATGCTTTCTATGTTGgtataacctc ... ctttaaccagATATTATGGGTGTCATAACTGAAATTGGTGCAACAGACACTCTACGCCCAA
EST: gi|88547021|gb|CI477289.1|CI477289
EST:     ACCTTTTCAAGACGCCCCGTCTCTTGTGGACAGAAATGCTTTCTATGTTG                         ATATTATGGGTGTCATAACTGAAATTGGTGCAACAGACACTCTACGCCCAA
genomic: ACCTTTTCAAGACGCCCCGTCTCTTGTGGACAGAAATGCTTTCTATGTTGgtataacctc ... ctttaaccagATATTATGGGTGTCATAACTGAAATTGGTGCAACAGACACTCTACGCCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttacttcttatacattagtggtttattgtttacatatatcttctctttaaccagATATTATGGGTGTCATAACTGAAATTGGTGCAACAGACACTCTACGCCCAAAATCAAGAAACACAGAAACTTTGAAAAGAACAATGCAGATTTGGGATGC
                                   tatatcttctcttt  CT-rich tract
                      tttattgtttacatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataacctctttatcccttttttgtcttcctacgtttacttcttatacattagtggtttattgtttacatatatcttctctttaaccagATATTATGGGTGTCATAACTGAAATTGGTGCAACAGACACTCTACGCCCAAAATCAAGAAACACAGAAACTTTGAAAAGAACAATGCAGATTTGGGATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT