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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtacccgcacgcacatcctcaaccgtagcttctcttgtagatccgaaagctcccctctttcccttcaatcttagtactaacagcagcttgtttgtttcaaacaaatttgggggtttcagCAGCTGAACCCCTCCCATCCCATGCCCTACGCTATGTCCGCCCCTGATATTGCGAGGATGCCGCTGGTTCTGTTTAGGCAGGGGACAACGGATTCCCGTG

Basic information

species Oryza sativa
transcript LOC_Os11g36830.1
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|88356471|gb|CI624891.1|CI624891
EST:     CGCCGAGCGGCTCCGCCGTCGTTCCTGCAGCTTCCGCCGCATCCTCGCCG                         CAGCTGAACCCCTCCCATCCCATGCCCTACGCTATGTCCGCCCCTGATATT
genomic: CGCCGAGCGGCTCCGCCGTCGTTCCTGCAGCTTCCGCCGCATCCTCGCCGgtgagtaccc ... ggggtttcagCAGCTGAACCCCTCCCATCCCATGCCCTACGCTATGTCCGCCCCTGATATT
EST: gi|88718025|gb|CI741535.1|CI741535
EST:     CGCCGAGCGGCTCCGCCGTCGTTCCTGCAGCTTCCGCCGCATCCTCGCCG                         CAGCTGAACCCCTCCCATCCCATGCCCTACGCTATGTCCGCCCCTGATATT
genomic: CGCCGAGCGGCTCCGCCGTCGTTCCTGCAGCTTCCGCCGCATCCTCGCCGgtgagtaccc ... ggggtttcagCAGCTGAACCCCTCCCATCCCATGCCCTACGCTATGTCCGCCCCTGATATT
EST: gi|88723300|gb|CI746810.1|CI746810
EST:     CGCCGAGCGGCTCCGCCGTCGTTCCTGCAGCTTCCGCCGCATCCTCGCCG                         CAGCTGAACCCCTCCCATCCCATGCCCTACGCTATGTCCGCCCCTGATATT
genomic: CGCCGAGCGGCTCCGCCGTCGTTCCTGCAGCTTCCGCCGCATCCTCGCCGgtgagtaccc ... ggggtttcagCAGCTGAACCCCTCCCATCCCATGCCCTACGCTATGTCCGCCCCTGATATT
EST: gi|88294723|gb|CI604595.1|CI604595
EST:     CGCCGAGCGGCTCCGCCGTCGTTCCTGCAGCTTCCGCCGCATCCTCGCCG                         CAGCTGAACCCCTCCCATCCCATGCCCTACGCTATGTCCGCCCCTGATATT
genomic: CGCCGAGCGGCTCCGCCGTCGTTCCTGCAGCTTCCGCCGCATCCTCGCCGgtgagtaccc ... ggggtttcagCAGCTGAACCCCTCCCATCCCATGCCCTACGCTATGTCCGCCCCTGATATT
EST: gi|163921235|gb|EG710463.1|EG710463
EST:     CGCCGAGCGGCTCCGCCGTCGTTCCTGCAGCTTCCGCCGCATCCTCGCCG                         CAGCTGAACCCCTCCCATCCCATGCCCTACGCTATGTCCGCCCCTGATATT
genomic: CGCCGAGCGGCTCCGCCGTCGTTCCTGCAGCTTCCGCCGCATCCTCGCCGgtgagtaccc ... ggggtttcagCAGCTGAACCCCTCCCATCCCATGCCCTACGCTATGTCCGCCCCTGATATT
EST: gi|88720585|gb|CI743884.1|CI743884
EST:     CGCCGAGCGGCTCCGCCGTCGTTCCTGCAGCTTCCGCCGCATCCTCGCCG                         CAGCTGAACCCCTCCCATCCCATGCCCTACGCTATGTCCGCCCCTGATATT
genomic: CGCCGAGCGGCTCCGCCGTCGTTCCTGCAGCTTCCGCCGCATCCTCGCCGgtgagtaccc ... ggggtttcagCAGCTGAACCCCTCCCATCCCATGCCCTACGCTATGTCCGCCCCTGATATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatcttagtactaacagcagcttgtttgtttcaaacaaatttgggggtttcagCAGCTGAACCCCTCCCATCCCATGCCCTACGCTATGTCCGCCCCTGATATTGCGAGGATGCCGCTGGTTCTGTTTAGGCAGGGGACAACGGATTCCCGTG
          tactaac  putative branch site (score: 0)
                              tttcaaacaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtacccgcacgcacatcctcaaccgtagcttctcttgtagatccgaaagctcccctctttcccttcaatcttagtactaacagcagcttgtttgtttcaaacaaatttgggggtttcagCAGCTGAACCCCTCCCATCCCATGCCCTACGCTATGTCCGCCCCTGATATTGCGAGGATGCCGCTGGTTCTGTTTAGGCAGGGGACAACGGATTCCCGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG