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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgtgtttgaattttgaaccaacttatgctatttgggaagcactgatttgttgttatcttgcttcgttgtgactgtggtttgtgaatcgacagctgcagCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGGGGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG

Basic information

species Oryza sativa
transcript LOC_Os02g19510.2
intron # 1
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|29641723|gb|CB646730.1|CB646730
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGCTGCAG                    
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTT-C--CG-T-C-Ggtacgatttc ... acagc
EST: gi|58659150|gb|CK047830.1|CK047830
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGCTGCAG                    
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTT-C--CG-T-C-Ggtacgatttc ... acagc
EST: gi|29676038|gb|CB672313.1|CB672313
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGCTGCAG                    
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTT-C--CG-T-C-Ggtacgatttc ... acagc
EST: gi|58687148|gb|CK075835.1|CK075835
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGCTGCAG                    
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTT-C--CG-T-C-Ggtacgatttc ... acagc
EST: gi|58670226|gb|CK058912.1|CK058912
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGGGGAAGA
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... acagctgcagCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGGGGAAGA
EST: gi|58666569|gb|CK055255.1|CK055255
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGCTGCAG                    
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTT-C--CG-T-C-Ggtacgatttc ... acagc
EST: gi|58691339|gb|CK080026.1|CK080026
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGCTGCAG                    
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTT-C--CG-T-C-Ggtacgatttc ... acagc
EST: gi|29640936|gb|CB645943.1|CB645943
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGCTGCAG                    
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTT-C--CG-T-C-Ggtacgatttc ... acagc
EST: gi|29624841|gb|CB629852.1|CB629852
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGCTGCAG                    
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTT-C--CG-T-C-Ggtacgatttc ... acagc
EST: gi|88696183|gb|CI739758.1|CI739758
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGCTGCAG                    
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTT-C--CG-T-C-Ggtacgatttc ... acagc
EST: gi|58601351|gb|CK011879.1|CK011879
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGCTGCAG                    
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTT-C--CG-T-C-Ggtacgatttc ... acagc
EST: gi|66913022|gb|CX099870.1|CX099870
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGCTGCAG                    
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTT-C--CG-T-C-Ggtacgatttc ... acagc
EST: gi|88356602|gb|CI626217.1|CI626217
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGCTGCAG                    
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTT-C--CG-T-C-Ggtacgatttc ... acagc
EST: gi|88396973|gb|CI578122.1|CI578122
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGCTGCAG                    
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTT-C--CG-T-C-Ggtacgatttc ... acagc


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttgttgttatcttgcttcgttgtgactgtggtttgtgaatcgacagctgcagCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGGGGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG
 cactgat  putative branch site (score: 3)
      ttgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgtgtttgaattttgaaccaacttatgctatttgggaagcactgatttgttgttatcttgcttcgttgtgactgtggtttgtgaatcgacagctgcagCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGGGGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - tgtttga
- - - - - - - - gaaccaa
- - - - - - - - - - - -cttatgc
- - - - - - - - - - - - - - - - - - - - gcactga
- - - - - - - - - - - - - - - - - - - - - - - - ttgttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgaatc