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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataatctctaccattaatttctttattattagaaccttcattaaaaatgtatataatttaaaatctctcgtgcgtattaatctccgttttttctaactgaaatatgaacaattgttttttcagTTGCCATGCATTATGTGGCTGTCGATCATGAAGCCAAAGAGGTTTGGCTTGTCCTGGTGCATCAACTGG

Basic information

species Oryza sativa
transcript LOC_Os12g14100.1
intron # 3
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|87011477|gb|CI279386.1|CI279386
EST:     GACTGCTAGGCTTCTTTGGTGGCTTTGCGTTTGCTCCAACGACCTACTTC                         TTGCCATGCATTATGTGGCTGTCGATCATGAAGCCAAAGAGGTTTGGCTTG
genomic: GACTGCTAGGCTTCTTTGGTGGCTTTGCGTTTGCTCCAACGACCTACTTCgtaataatct ... gttttttcagTTGCCATGCATTATGTGGCTGTCGATCATGAAGCCAAAGAGGTTTGGCTTG
EST: gi|88259822|gb|CI364313.1|CI364313
EST:     GACTGCTAGGCTTCTTTGGTGGCTTTGCGTTTGCTCCAACGACCTACTTC                         TTGCCATGCATTATGTGGCTGTCGATCATGAAGCCAAAGAGGTTTGGCTTG
genomic: GACTGCTAGGCTTCTTTGGTGGCTTTGCGTTTGCTCCAACGACCTACTTCgtaataatct ... gttttttcagTTGCCATGCATTATGTGGCTGTCGATCATGAAGCCAAAGAGGTTTGGCTTG
EST: gi|86864894|gb|CI343939.1|CI343939
EST:     GACTGCTAGGTTTCTTTGGTGGCTTTGCGTTTGCTCCAACGACCTACTTC                         TTGCCATGCATTATGTGGCTGTCGATCATGAAGCCAAAGAGGTTTGGCTTG
genomic: GACTGCTAGGCTTCTTTGGTGGCTTTGCGTTTGCTCCAACGACCTACTTCgtaataatct ... gttttttcagTTGCCATGCATTATGTGGCTGTCGATCATGAAGCCAAAGAGGTTTGGCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtgcgtattaatctccgttttttctaactgaaatatgaacaattgttttttcagTTGCCATGCATTATGTGGCTGTCGATCATGAAGCCAAAGAGGTTTGGCTTGTCCTGGTGCATCAACTGG
                      ttctaac  putative branch site (score: 1)
                                           ttgttttttc  putative PPT
                               aaatatgaacaattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataatctctaccattaatttctttattattagaaccttcattaaaaatgtatataatttaaaatctctcgtgcgtattaatctccgttttttctaactgaaatatgaacaattgttttttcagTTGCCATGCATTATGTGGCTGTCGATCATGAAGCCAAAGAGGTTTGGCTTGTCCTGGTGCATCAACTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG