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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttgagctgaaatttgtttatgtttgtgattgttgtgcctgctgtggtttccttcatcagtgatttattcttgttggatgtttttttttcatgcggagATTGGAAGGAGCACCGAAGGGTGTAGCACAAGGCCGAGTTGCATGGGGCGATAATGCCAGAGTTGCGGGGTGGTGTTTGGAGAGCTCGTCTGAGGTCCAA

Basic information

species Oryza sativa
transcript LOC_Os03g57940.4
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|58612234|gb|CK039946.1|CK039946
EST:     TCCCGAGGCGCCGCCCTCCGCCGCCGCGGGCATCCGCTTCCGACGACGAT                         ATTGGAAGGAGCACCGAAGGGTGTAGCACAAGGCCGAGTTGCATGGGGCGA
genomic: TCCCGAGGCGCCGCCCTCCGCCGCCGCGGGCATCCGCTTCCGACGACGATgtaagccgct ... tcatgcggagATTGGAAGGAGCACCGAAGGGTGTAGCACAAGGCCGAGTTGCATGGGGCGA
EST: gi|58607670|gb|CK035703.1|CK035703
EST:     CCGCCGCCGCGGGCATACGCTTCCGACGACGAT                         ATTGGAAGGAGCACCGAAGGGTGTAGCACAAGGCCGAGTTGCATGGGGCGA
genomic: CCGCCGCCGCGGGCATCCGCTTCCGACGACGATgtaagccgct ... tcatgcggagATTGGAAGGAGCACCGAAGGGTGTAGCACAAGGCCGAGTTGCATGGGGCGA
EST: gi|88325947|gb|CI649798.1|CI649798
EST:     TCCCGAGGCGCCGCCCTCCGCCGCCGCGGGCATCCGCTTCCGACGACGAT                         ATTGGAAGGAGCACCGAAGGGTGTAGCACAAGGCCGAGTTGCATGGGGCGA
genomic: TCCCGAGGCGCCGCCCTCCGCCGCCGCGGGCATCCGCTTCCGACGACGATgtaagccgct ... tcatgcggagATTGGAAGGAGCACCGAAGGGTGTAGCACAAGGCCGAGTTGCATGGGGCGA
EST: gi|117246415|gb|CT843264.1|CT843264
EST:     TCCCGAGGCGCCGCCCTCCGCCGCCGCGGGCATCCGCTTCCGACGACGAT                         ATTGGAAGGAGCACCGAAGGGTGTAGCACAAGGCCGAGTTGCATGGGGCGA
genomic: TCCCGAGGCGCCGCCCTCCGCCGCCGCGGGCATCCGCTTCCGACGACGATgtaagccgct ... tcatgcggagATTGGAAGGAGCACCGAAGGGTGTAGCACAAGGCCGAGTTGCATGGGGCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggtttccttcatcagtgatttattcttgttggatgtttttttttcatgcggagATTGGAAGGAGCACCGAAGGGTGTAGCACAAGGCCGAGTTGCATGGGGCGATAATGCCAGAGTTGCGGGGTGGTGTTTGGAGAGCTCGTCTGAGGTCCAA
                                   tgtttttttttcat  CT-rich tract
                                  atgtttttttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttgagctgaaatttgtttatgtttgtgattgttgtgcctgctgtggtttccttcatcagtgatttattcttgttggatgtttttttttcatgcggagATTGGAAGGAGCACCGAAGGGTGTAGCACAAGGCCGAGTTGCATGGGGCGATAATGCCAGAGTTGCGGGGTGGTGTTTGGAGAGCTCGTCTGAGGTCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT