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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgataatgatttgattgaattttgttctatataaatcacctgttgtgcaatttgctgaatcatttgcactcccactttcagAATGATGGATTGCTGCACACAACATGTGGCAGCCCCAATTATATTGCTCCTGAG

Basic information

species Oryza sativa
transcript LOC_Os01g18800.4
intron # 4
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|58691843|gb|CK080530.1|CK080530
EST:     ATATCAAGATCTCTGACTTTGGCCTAAGTGCTTTGCCTCAACATCTTGGG                         AATGATGGATTGCTGCACACAACATGTGGCAGCCCCAATTATATTGCTCCT
genomic: ATATCAAGATCTCTGACTTTGGCCTAAGTGCTTTGCCTCAACATCTTGGGgtatgataat ... ccactttcagAATGATGGATTGCTGCACACAACATGTGGCAGCCCCAATTATATTGCTCCT
EST: gi|86596798|gb|CI286711.1|CI286711
EST:     ATATCAAGATCTCTGACTTTGGCCTAAGTGCTTTGCCTCAACATCTTGGG                         AATGATGGATTGCTGCACACAACATGTGGCAGCCCCAATTATATTGCTCCT
genomic: ATATCAAGATCTCTGACTTTGGCCTAAGTGCTTTGCCTCAACATCTTGGGgtatgataat ... ccactttcagAATGATGGATTGCTGCACACAACATGTGGCAGCCCCAATTATATTGCTCCT
EST: gi|58590709|gb|CF989017.1|CF989017
EST:     ATATCAAGATCTCTGACTTTGGCCTAAGTGCTGTGCCTCAACATCTTGGG                         AATGATGGATTGCTGCACACAACATGTGGCAGCCCCAATTATATTGCTCCT
genomic: ATATCAAGATCTCTGACTTTGGCCTAAGTGCTTTGCCTCAACATCTTGGGgtatgataat ... ccactttcagAATGATGGATTGCTGCACACAACATGTGGCAGCCCCAATTATATTGCTCCT
EST: gi|29682962|gb|CB679237.1|CB679237
EST:     TATCA-GATCTCTGACTTTGGCCTAAGTGCTTTGCCCTCA-CATCTTGGG                         AATGATGGGAT-GCTGCACACAAC
genomic: TATCAAGATCTCTGACTTTGGCCTAAGTGCTTTGCC-TCAACATCTTGGGgtatgataat ... ccactttcagAATGATGG-ATTGCTGCACACAAC
EST: gi|24468762|gb|CA305711.1|CA305711
EST:     ATATCAAGATCTCTGACTTTGGCCTAAGTGCTTTGCCTCAACATCTTGGG                         AATGATGGATTGCTGCACACAACATGTGGCAGCCCCAATTATATTGCTCCT
genomic: ATATCAAGATCTCTGACTTTGGCCTAAGTGCTTTGCCTCAACATCTTGGGgtatgataat ... ccactttcagAATGATGGATTGCTGCACACAACATGTGGCAGCCCCAATTATATTGCTCCT
EST: gi|29624069|gb|CB629080.1|CB629080
EST:     ATATCAAGATCTCTGACTTTGGCCTAAGTGCTTTGCCTCAACATCTTGGG                         AATGATGGATTGCTGCACACAACATGTGGCAGCCCCAATTATATTGCTCCT
genomic: ATATCAAGATCTCTGACTTTGGCCTAAGTGCTTTGCCTCAACATCTTGGGgtatgataat ... ccactttcagAATGATGGATTGCTGCACACAACATGTGGCAGCCCCAATTATATTGCTCCT
EST: gi|4714882|gb|AU055999.1|AU055999
EST:     ATATCAAGATCTCTGACTTTGGCCTAAGTGCTTTGCCTCAACATCTTGGG                         AATGATGGATTGCTGCACACAACATGTGGCAGCCCCAATTATATTGCTCCT
genomic: ATATCAAGATCTCTGACTTTGGCCTAAGTGCTTTGCCTCAACATCTTGGGgtatgataat ... ccactttcagAATGATGGATTGCTGCACACAACATGTGGCAGCCCCAATTATATTGCTCCT
EST: gi|38476067|gb|CF960200.1|CF960200
EST:     CTGACTTTGGCCTAAGTGCTTTGCCTCAACATCTTGGG                         AATGATGGATTGCGTGCACACAACATGTGGCAGCCCCAATTATATTGCTCC
genomic: CTGACTTTGGCCTAAGTGCTTTGCCTCAACATCTTGGGgtatgataat ... ccactttcagAATGATGGATTGC-TGCACACAACATGTGGCAGCCCCAATTATATTGCTCC
EST: gi|58659268|gb|CK047948.1|CK047948
EST:     ATATCAAGATCTCTGACTTTGGCCTAAGTGCTTTGCCTCAACATCTTGGG                         AATGATGGATTGCTGCACACAACATGTGGCAGCCCCAATTATATTGCTCCT
genomic: ATATCAAGATCTCTGACTTTGGCCTAAGTGCTTTGCCTCAACATCTTGGGgtatgataat ... ccactttcagAATGATGGATTGCTGCACACAACATGTGGCAGCCCCAATTATATTGCTCCT
EST: gi|58664713|gb|CK053399.1|CK053399
EST:     ATATCAAGATCTCTGACTTTGGCCTAAGTGCTTTGCCTCAACATCTTGGG                         AATGATGGATTGCTGCACACAACATGTGGCAGCCCCAATTATATTGCTCCT
genomic: ATATCAAGATCTCTGACTTTGGCCTAAGTGCTTTGCCTCAACATCTTGGGgtatgataat ... ccactttcagAATGATGGATTGCTGCACACAACATGTGGCAGCCCCAATTATATTGCTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatataaatcacctgttgtgcaatttgctgaatcatttgcactcccactttcagAATGATGGATTGCTGCACACAACATGTGGCAGCCCCAATTATATTGCTCCTGAG
                                          ctcccactttc  CT-rich tract
                               aatcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgataatgatttgattgaattttgttctatataaatcacctgttgtgcaatttgctgaatcatttgcactcccactttcagAATGATGGATTGCTGCACACAACATGTGGCAGCCCCAATTATATTGCTCCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC