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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggcaaacctatgcacaaacaaataggcaactatcttgaatcagattcagactgatttccttcagaattaagccaagcaatcaagcaccattgatttttcttcttgttttctccgactctgagaatagTTTTTCGTGCGCCATCTTATCGAGGAAAATGACGGCACCTGGTTTTGCTTCCCCGCGACGTGCAGCAGTGGATGGAGAA

Basic information

species Oryza sativa
transcript LOC_Os07g48750.1
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|88360411|gb|CI612130.1|CI612130
EST:     GGTTGGCCGGCTGCTCCC-ACCCGCCATCGTGGCGGAAATTCCAGTATAG                         TTTTTCGTGCGCCATCTTATCGAGGAAAATGACGGCACCTGGTTTTGCTTC
genomic: GGTTGGCCGGCTGCTCCCCACCCGCCATCGTGGCGGACATTCCAGTATAGgtacggcaaa ... ctgagaatagTTTTTCGTGCGCCATCTTATCGAGGAAAATGACGGCACCTGGTTTTGCTTC
EST: gi|88695934|gb|CI739509.1|CI739509
EST:     GGTTGGCCGGCTGCTCCCCACCCGCCATCGTGGCGGACATTCCAGTATAG                         TTTTTCGTGCGCCATCTTATCGAGGAAAATGACGGCACCTGGTTTTGCTTC
genomic: GGTTGGCCGGCTGCTCCCCACCCGCCATCGTGGCGGACATTCCAGTATAGgtacggcaaa ... ctgagaatagTTTTTCGTGCGCCATCTTATCGAGGAAAATGACGGCACCTGGTTTTGCTTC
EST: gi|88454324|gb|CI569896.1|CI569896
EST:     GGTTGGCAGGCTGCTCCCCACCCGCCATCGTGGCGGACATTCCAGTATAG                         TTTTTCGTGCGCCATCTTATCGAGGAAAATGACGGCACCTGGTTTTGGTTC
genomic: GGTTGGCCGGCTGCTCCCCACCCGCCATCGTGGCGGACATTCCAGTATAGgtacggcaaa ... ctgagaatagTTTTTCGTGCGCCATCTTATCGAGGAAAATGACGGCACCTGGTTTTGCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagcaatcaagcaccattgatttttcttcttgttttctccgactctgagaatagTTTTTCGTGCGCCATCTTATCGAGGAAAATGACGGCACCTGGTTTTGCTTCCCCGCGACGTGCAGCAGTGGATGGAGAA
               cattgat  putative branch site (score: 4)
                     tttttcttcttgtttt  CT-rich tract
                attgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacggcaaacctatgcacaaacaaataggcaactatcttgaatcagattcagactgatttccttcagaattaagccaagcaatcaagcaccattgatttttcttcttgttttctccgactctgagaatagTTTTTCGTGCGCCATCTTATCGAGGAAAATGACGGCACCTGGTTTTGCTTCCCCGCGACGTGCAGCAGTGGATGGAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA