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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactcctcccccatcggaatgcccgagaaaattgctgaaattttaccgcgttcccgtgctcccagttgtcatgggtgctgagtatttttttattttgatttgtgtttggtgcgtgcgcagAAGGTGTTTGCTGGATTGCCTCACCGGAGAAGGGTGCTGTTTTCTGGTGTGTCGAGCAGAACGCGAAGAGGCAGGATCAGGAGCGTCAAGGACGACTCGC

Basic information

species Oryza sativa
transcript LOC_Os01g56350.3
intron # 2
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|29667324|gb|CB663599.1|CB663599
EST:     TGGCGCCGCAGGCCACCGCCCAGACTGTTCCTCGCCCCCTCCAGTCCTTG                         AAGGTGTTTGCTGGATTGCCTCACCGGAGAAGGGTGCTGTTTTCTGGTGTG
genomic: TGGCGCCGCAGGCCACCGCCCAGACTGTTCCTCGCCCCCTCCAGTCCTTGgtaactcctc ... gcgtgcgcagAAGGTGTTTGCTGGATTGCCTCACCGGAGAAGGGTGCTGTTTTCTGGTGTG
EST: gi|25798528|gb|CA754489.1|CA754489
EST:     TGGCACCGCAGGCCACCGCCCAGACTGTTCCTCGCCCCCTCCAGTCCTTG                         AAGGTGTTTGCTGGATTGCCTCACCGGAGAAGGGTGCTGTTTTCTGGTGTG
genomic: TGGCGCCGCAGGCCACCGCCCAGACTGTTCCTCGCCCCCTCCAGTCCTTGgtaactcctc ... gcgtgcgcagAAGGTGTTTGCTGGATTGCCTCACCGGAGAAGGGTGCTGTTTTCTGGTGTG
EST: gi|88324314|gb|CI566127.1|CI566127
EST:     TGGCGCCGCAGGCCACCGCCCAGACTGTTCCTCGCCCCCTCCAGTCCTTG                         AAGGTGTTTGCTGGATTGCCTCACCGGAGAAGGGTGCTGTTTTCTGGTGTG
genomic: TGGCGCCGCAGGCCACCGCCCAGACTGTTCCTCGCCCCCTCCAGTCCTTGgtaactcctc ... gcgtgcgcagAAGGTGTTTGCTGGATTGCCTCACCGGAGAAGGGTGCTGTTTTCTGGTGTG
EST: gi|88300573|gb|CI587377.1|CI587377
EST:     TGGCGCCGCAGGCCACCGCCCAGACTGTTCCTCGCCCCCTCCAGTCCTTG                         AAGGTGTTTGCTGGATTGCCTCACCGGAGAAGGGTGCTGTTTTCTGGTGTG
genomic: TGGCGCCGCAGGCCACCGCCCAGACTGTTCCTCGCCCCCTCCAGTCCTTGgtaactcctc ... gcgtgcgcagAAGGTGTTTGCTGGATTGCCTCACCGGAGAAGGGTGCTGTTTTCTGGTGTG
EST: gi|88358075|gb|CI605000.1|CI605000
EST:     TGGCGCCGCAGGCCACCGCCCAGACTGTTCCTCGCCCCCTCCAGTCCTTG                         AAGGTGTTTGCTGGATTGCCTCACCGGAGAAGGGTGCTGTTTTCTGGTGTG
genomic: TGGCGCCGCAGGCCACCGCCCAGACTGTTCCTCGCCCCCTCCAGTCCTTGgtaactcctc ... gcgtgcgcagAAGGTGTTTGCTGGATTGCCTCACCGGAGAAGGGTGCTGTTTTCTGGTGTG
EST: gi|88370900|gb|CI595012.1|CI595012
EST:     TGGCGCCGCAGGCCACCGCCCAGACTGTTCCTCGCCCCCTCCAGTCCTTG                         AAGGTGTTTGCTGGATTGCCTCACCGGAGAAGGGTGCTGTTTTCTGGTGTG
genomic: TGGCGCCGCAGGCCACCGCCCAGACTGTTCCTCGCCCCCTCCAGTCCTTGgtaactcctc ... gcgtgcgcagAAGGTGTTTGCTGGATTGCCTCACCGGAGAAGGGTGCTGTTTTCTGGTGTG
EST: gi|66921825|gb|CX108673.1|CX108673
EST:     TGGCGCCGCAGGCCACCGCCCAGACTGTTCCTCGCCCCCTCCAGTCCTTG                         AAGGTGTTTGCTGGATTGCCTCACCGGAGAAGGGTGCTGTTTTCTGGTGTG
genomic: TGGCGCCGCAGGCCACCGCCCAGACTGTTCCTCGCCCCCTCCAGTCCTTGgtaactcctc ... gcgtgcgcagAAGGTGTTTGCTGGATTGCCTCACCGGAGAAGGGTGCTGTTTTCTGGTGTG
EST: gi|88729927|gb|CI753148.1|CI753148
EST:     TGGCGCCGCAGGCCACCGCCCAGACTGTTCCTCGCCCCCTCCAGTCCTTG                         AAGGTGTTTGCTGGATTGCCTCNAC-GGAGAAGGGTGCTGTTTTCTGGTGT
genomic: TGGCGCCGCAGGCCACCGCCCAGACTGTTCCTCGCCCCCTCCAGTCCTTGgtaactcctc ... gcgtgcgcagAAGGTGTTTGCTGGATTGCCTC-ACCGGAGAAGGGTGCTGTTTTCTGGTGT
EST: gi|88696544|gb|CI740119.1|CI740119
EST:     TGGCGCCGCAGGCCACCGCCCAGACTGTTCCTCGCCCCCTCCAGTCCTTG                         AAGGTGTTTGCTGGATTGCCTCACCGGAGAAGGGTGCTGTTTTCTGGTGTG
genomic: TGGCGCCGCAGGCCACCGCCCAGACTGTTCCTCGCCCCCTCCAGTCCTTGgtaactcctc ... gcgtgcgcagAAGGTGTTTGCTGGATTGCCTCACCGGAGAAGGGTGCTGTTTTCTGGTGTG
EST: gi|66918856|gb|CX105704.1|CX105704
EST:     TGGCGCCGCAGGCCACCGCCCAGACTGTTCCTCGCCCCCTCCAGTCCTTG                         AAGGTGTTTGCTGGATTGCCTCACCGGAGAAGGGTGCTGTTTTCTGGTGTG
genomic: TGGCGCCGCAGGCCACCGCCCAGACTGTTCCTCGCCCCCTCCAGTCCTTGgtaactcctc ... gcgtgcgcagAAGGTGTTTGCTGGATTGCCTCACCGGAGAAGGGTGCTGTTTTCTGGTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtcatgggtgctgagtatttttttattttgatttgtgtttggtgcgtgcgcagAAGGTGTTTGCTGGATTGCCTCACCGGAGAAGGGTGCTGTTTTCTGGTGTGTCGAGCAGAACGCGAAGAGGCAGGATCAGGAGCGTCAAGGACGACTCGC
                           ttttgat  putative branch site (score: 4)
               agtatttttttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactcctcccccatcggaatgcccgagaaaattgctgaaattttaccgcgttcccgtgctcccagttgtcatgggtgctgagtatttttttattttgatttgtgtttggtgcgtgcgcagAAGGTGTTTGCTGGATTGCCTCACCGGAGAAGGGTGCTGTTTTCTGGTGTGTCGAGCAGAACGCGAAGAGGCAGGATCAGGAGCGTCAAGGACGACTCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG