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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacttcacagctcatgagccaacattcagtttttccttttcgtttctgaattctgatgtcccattttgcttgtttattttttatttttaccatctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCATTTGAACGGTGCAACGTTGTGGTGGATGAAGTGCCCTGCTGTCCGTGAG

Basic information

species Oryza sativa
transcript LOC_Os01g51840.1
intron # 6
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|88993517|gb|CI110338.1|CI110338
EST:     AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|86881817|gb|CI324104.1|CI324104
EST:     AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|86864482|gb|CI334759.1|CI334759
EST:     AGACATGAATGGCTTCACACCCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|86884489|gb|CI337057.1|CI337057
EST:     AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|86868088|gb|CI331855.1|CI331855
EST:     AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|89168353|gb|CI109557.1|CI109557
EST:     AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|88987370|gb|CI034334.1|CI034334
EST:     AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|86592238|gb|CI272584.1|CI272584
EST:     AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|86833517|gb|CI336306.1|CI336306
EST:     AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGTTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|86887777|gb|CI319727.1|CI319727
EST:     AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|88983121|gb|CI020685.1|CI020685
EST:     AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|86868827|gb|CI334199.1|CI334199
EST:     AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|38477194|gb|CF961327.1|CF961327
EST:     AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|86833337|gb|CI334932.1|CI334932
EST:     AGACATGAATGGCTTCACACCCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaattctgatgtcccattttgcttgtttattttttatttttaccatctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCATTTGAACGGTGCAACGTTGTGGTGGATGAAGTGCCCTGCTGTCCGTGAG
     ttctgat  putative branch site (score: 3)
 ttttttatttttacc  putative PPT
 attttgcttgtttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacttcacagctcatgagccaacattcagtttttccttttcgtttctgaattctgatgtcccattttgcttgtttattttttatttttaccatctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCATTTGAACGGTGCAACGTTGTGGTGGATGAAGTGCCCTGCTGTCCGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- cttcaca
- - - - - - catgagc
- - - - - - - - - - - cattcag
- - - - - - - - - - - - - - - - - - - - - tttctga
- - - - - - - - - - - - - - - - - - - - - - - - - - ctgatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgcttg