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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcttctcaagcatctgaatttcctttcttctttcacctgtaatgctttctgattcgaatatggtgtaaaactaagaaaggatctaattctcacattctcaatctgtaccattatatgccaatggctattacagTTATGTGCTGCTCACAAGCTATCATCAAAACTGAAGAGAGAAATTATCCTTGGCTCCTCTAGTCTTGATGATCCACCCCAGTTCATCACT

Basic information

species Oryza sativa
transcript LOC_Os04g18030.3
intron # 21
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|88541073|gb|CI469165.1|CI469165
EST:     TGGGTCAGCGATTATTTGTTTTTGTTATTGGTGGTGCTACTCGATCTGAG                         TTATNTGCTGCTCACAAGCTATCATCAAAACTGAAGAGAGAAATTATCCTT
genomic: TGGGTCAGCGATTATTTGTTTTTGTTATTGGTGGTGCTACTCGATCTGAGgtatcttctc ... gctattacagTTATGTGCTGCTCACAAGCTATCATCAAAACTGAAGAGAGAAATTATCCTT
EST: gi|88521877|gb|CI449597.1|CI449597
EST:     TGGGTCAGCGATTATTTGTTTTTGTTATTGGTGGTGCTACTCGATCTGAG                         TTATGTGCTGCTCACAAGCTATCATCAAAACTGAAGAGAGAAATTATCCTT
genomic: TGGGTCAGCGATTATTTGTTTTTGTTATTGGTGGTGCTACTCGATCTGAGgtatcttctc ... gctattacagTTATGTGCTGCTCACAAGCTATCATCAAAACTGAAGAGAGAAATTATCCTT
EST: gi|88835711|gb|CI370816.1|CI370816
EST:     GTTATTGGT-GTGCTACTCGATCTGAG                         TTATGTGCTGCTCACAAGCTATCATCAAAACTGAAGAGAGAAATTATCCTT
genomic: GTTATTGGTGGTGCTACTCGATCTGAGgtatcttctc ... gctattacagTTATGTGCTGCTCACAAGCTATCATCAAAACTGAAGAGAGAAATTATCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatctaattctcacattctcaatctgtaccattatatgccaatggctattacagTTATGTGCTGCTCACAAGCTATCATCAAAACTGAAGAGAGAAATTATCCTTGGCTCCTCTAGTCTTGATGATCCACCCCAGTTCATCACT
        ttctcac  putative branch site (score: 2)
                               attatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcttctcaagcatctgaatttcctttcttctttcacctgtaatgctttctgattcgaatatggtgtaaaactaagaaaggatctaattctcacattctcaatctgtaccattatatgccaatggctattacagTTATGTGCTGCTCACAAGCTATCATCAAAACTGAAGAGAGAAATTATCCTTGGCTCCTCTAGTCTTGATGATCCACCCCAGTTCATCACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC