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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcacctgcttgtttgtttagtcactctgagcctgtttgagcttccccgttcctttgtctccgcacccgaagtgaacttaatttttgatttgtttatgtagGTGATGGATTCAGTGTCATTGTCACTACTCGATAGTATTTCAAATTTCCGGGTGCTGTCTTCAAGCAATGCCTCGAAAACAGAGCTAGTTAAGAAATATT

Basic information

species Oryza sativa
transcript LOC_Os01g66130.1
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|88310874|gb|CI659477.1|CI659477
EST:     ACACGGGAGTCCGAATCCTCCTCCTCCCCCCTCCATTGGAGGCCTCCGAG                         GTGATGGATTCAGTGTCATTGTCACTACTCGATAGTATTTCAAATTTCCGG
genomic: ACACGGGAGTCCGAATCCTCCTCCTCCCCCCTCCATTGGAGGCCTCCGAGgtaacggggc ... gtttatgtagGTGATGGATTCAGTGTCATTGTCACTACTCGATAGTATTTCAAATTTCCGG
EST: gi|88326550|gb|CI658260.1|CI658260
EST:     ACACGGGAGTCCGAATCCTCCTCCTCCCCCCTCCATTGGAGGCCTCCGAG                         GTGATGGATTCAGTGTCATTGTCACTACTCGATAGTATTTCAAATTTCCGG
genomic: ACACGGGAGTCCGAATCCTCCTCCTCCCCCCTCCATTGGAGGCCTCCGAGgtaacggggc ... gtttatgtagGTGATGGATTCAGTGTCATTGTCACTACTCGATAGTATTTCAAATTTCCGG
EST: gi|88355124|gb|CI651827.1|CI651827
EST:     ACACGGGAGTCCGAATCCTCCTCCTCCCCCCTCCATTGGAGGCCTCCGAG                         GTGATGGATTCAGTGTCATTGTCACTACTCGATAGTATTTCAAATTTCCGG
genomic: ACACGGGAGTCCGAATCCTCCTCCTCCCCCCTCCATTGGAGGCCTCCGAGgtaacggggc ... gtttatgtagGTGATGGATTCAGTGTCATTGTCACTACTCGATAGTATTTCAAATTTCCGG
EST: gi|88445428|gb|CI584541.1|CI584541
EST:     ACACGGGAGTCCGAATCCTCCTCCTCCCCCCTCCATTGGAGGCCTCCGAG                         GTGATGGATTCAGTGTCATTGTCACTACTCGATAGTATTTCAAATTTCCGG
genomic: ACACGGGAGTCCGAATCCTCCTCCTCCCCCCTCCATTGGAGGCCTCCGAGgtaacggggc ... gtttatgtagGTGATGGATTCAGTGTCATTGTCACTACTCGATAGTATTTCAAATTTCCGG
EST: gi|88407009|gb|CI578537.1|CI578537
EST:     ACACGGGAGTCCGAATCCTCCTCCTCCCCCCTCCATTGGAGGCCTCCGAG                         GTGATGGATTCAGTGTCATTGTCACTACTCGATAGTATTTCAAATTTCCGG
genomic: ACACGGGAGTCCGAATCCTCCTCCTCCCCCCTCCATTGGAGGCCTCCGAGgtaacggggc ... gtttatgtagGTGATGGATTCAGTGTCATTGTCACTACTCGATAGTATTTCAAATTTCCGG
EST: gi|88569640|gb|CI660815.1|CI660815
EST:     ACACGGGAGTCCGAATCCTCCTCCTCCCCCCTCCATTGGAGGCCTCCGAG                         GTGATGGATTCAGTGTCATTGTCACTACTCGATAGTATTTCAAATTTCCGG
genomic: ACACGGGAGTCCGAATCCTCCTCCTCCCCCCTCCATTGGAGGCCTCCGAGgtaacggggc ... gtttatgtagGTGATGGATTCAGTGTCATTGTCACTACTCGATAGTATTTCAAATTTCCGG
EST: gi|88332681|gb|CI660199.1|CI660199
EST:     ACACGGGAGTCCGAATCCTCCTCCTCCCCCCTCCATTGGAGGCCTCCGAG                         GTGATGGATTCAGTGTCATTGTCACTACTCGATAGTATTTCAAATTTCCGG
genomic: ACACGGGAGTCCGAATCCTCCTCCTCCCCCCTCCATTGGAGGCCTCCGAGgtaacggggc ... gtttatgtagGTGATGGATTCAGTGTCATTGTCACTACTCGATAGTATTTCAAATTTCCGG
EST: gi|88340406|gb|CI659612.1|CI659612
EST:     ACACGGGAGTCCGAATCCTCCTCCTCCCCCCTCCATTGGAGGCCTCCGAG                         GTGATGGATTCAGTGTCATTGTCACTACTCGATAGTATTTCAAATTTCCGG
genomic: ACACGGGAGTCCGAATCCTCCTCCTCCCCCCTCCATTGGAGGCCTCCGAGgtaacggggc ... gtttatgtagGTGATGGATTCAGTGTCATTGTCACTACTCGATAGTATTTCAAATTTCCGG
EST: gi|88389697|gb|CI603196.1|CI603196
EST:     ACACGGGAGTCCGAATCCTCCTCCTCCCCCCTCCATTGGAGGCCTCCGAG                         GTGATGGATTCAGTGTCATTGTCACTACTCGATAGTATTTCAAATTTCCGG
genomic: ACACGGGAGTCCGAATCCTCCTCCTCCCCCCTCCATTGGAGGCCTCCGAGgtaacggggc ... gtttatgtagGTGATGGATTCAGTGTCATTGTCACTACTCGATAGTATTTCAAATTTCCGG
EST: gi|58665740|gb|CK054426.1|CK054426
EST:     ACGCGGGAGTCCGAATCCTCCTCCTCCCCCCTCCATTGGAGGCCTCCGAG                         GTGATGGATTCAGTGTCATTGTCACTACTCGATAGTATTTCAAATTTCCGG
genomic: ACACGGGAGTCCGAATCCTCCTCCTCCCCCCTCCATTGGAGGCCTCCGAGgtaacggggc ... gtttatgtagGTGATGGATTCAGTGTCATTGTCACTACTCGATAGTATTTCAAATTTCCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgttcctttgtctccgcacccgaagtgaacttaatttttgatttgtttatgtagGTGATGGATTCAGTGTCATTGTCACTACTCGATAGTATTTCAAATTTCCGGGTGCTGTCTTCAAGCAATGCCTCGAAAACAGAGCTAGTTAAGAAATATT
                                    ttttgat  putative branch site (score: 4)
                                          tttgttt  CT-rich tract
                            aacttaatttttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcacctgcttgtttgtttagtcactctgagcctgtttgagcttccccgttcctttgtctccgcacccgaagtgaacttaatttttgatttgtttatgtagGTGATGGATTCAGTGTCATTGTCACTACTCGATAGTATTTCAAATTTCCGGGTGCTGTCTTCAAGCAATGCCTCGAAAACAGAGCTAGTTAAGAAATATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- -cctgctt
- - - - - - - - - - - - - - - -ctgtttg