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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttttctgcaacctctgagacgatatgtctgctactctgctcttcaatttgtattgacctcactatgataaactttttgtgttgattctgatatctttctcttttgtattaacttcagCAAATTCAGTCCTGTACCCTTTCGTTTGGCTTCTTGGAGAAATTCTAGCTGCACCTTTCCGGCTTGTTGTTGCGATAGCAAGTTTTGTGGCAGACTCTTT

Basic information

species Oryza sativa
transcript LOC_Os02g53210.3
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|58600474|gb|CK011002.1|CK011002
EST:     GATGATTATATGGCCTTTTTGGCTGGTCTTCAGTGTTGTGCTTAATGTTG                         CAAATTCAGTCCTGTACCCTTTCGTTTGGCTTCTTGGAGAAATTCTAGCTG
genomic: GATGATTATATGGCCTTTTTGGCTGGTCTTCAGTGTTGTGCTTAATGTTGgtatgttttc ... ttaacttcagCAAATTCAGTCCTGTACCCTTTCGTTTGGCTTCTTGGAGAAATTCTAGCTG
EST: gi|33692950|gb|CF321189.1|CF321189
EST:     GATGATTATATGGCCTTTTTGGCTGGTCTTCAGTGTTGTGCTTAATGTTG                         CAAATTCAGTCCTGTACCCTTTCGTTTGGCTTCTTGGAGAAATTCTAGCTG
genomic: GATGATTATATGGCCTTTTTGGCTGGTCTTCAGTGTTGTGCTTAATGTTGgtatgttttc ... ttaacttcagCAAATTCAGTCCTGTACCCTTTCGTTTGGCTTCTTGGAGAAATTCTAGCTG
EST: gi|33683910|gb|CF312149.1|CF312149
EST:     ATGATTATATGGCCTTTTTGGCTGGTCTTCNAGTGTTGTGCTTAATGTTG                         CAAATTCAGTCCTGTACCCTNTCGTTTGGCTTCTTGGAGAAATTCTAGCTG
genomic: ATGATTATATGGCCTTTTTGGCTGGTCTTC-AGTGTTGTGCTTAATGTTGgtatgttttc ... ttaacttcagCAAATTCAGTCCTGTACCCTTTCGTTTGGCTTCTTGGAGAAATTCTAGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgataaactttttgtgttgattctgatatctttctcttttgtattaacttcagCAAATTCAGTCCTGTACCCTTTCGTTTGGCTTCTTGGAGAAATTCTAGCTGCACCTTTCCGGCTTGTTGTTGCGATAGCAAGTTTTGTGGCAGACTCTTT
                                           tattaac  putative branch site (score: 1)
                              tctttctcttttgtat  CT-rich tract
                                      ttttgtattaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttttctgcaacctctgagacgatatgtctgctactctgctcttcaatttgtattgacctcactatgataaactttttgtgttgattctgatatctttctcttttgtattaacttcagCAAATTCAGTCCTGTACCCTTTCGTTTGGCTTCTTGGAGAAATTCTAGCTGCACCTTTCCGGCTTGTTGTTGCGATAGCAAGTTTTGTGGCAGACTCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG