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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcgaattttgtgccagctttttttatttcacatcctatactcttagaaaagaaagtgtgattccaatggtcatggcattttgttttatatttgttacagTGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAGATCTTTGGGCTACGGAGTTATTGATTCATGGAGACCGTGGCACCTGAAT

Basic information

species Oryza sativa
transcript LOC_Os12g15470.1
intron # 11
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|86537567|gb|CI177773.1|CI177773
EST:     AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAG                         TGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
genomic: AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAGgtccgacatg ... tttgttacagTGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
EST: gi|58609188|gb|CK037221.1|CK037221
EST:     GTTATCACAAAGAACCTCACAGGCCAGGGTTATCGTGCTTGCATATACAG                         TGGTGATCATGATATGTGTGTACC
genomic: GTTATCACAA-GAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAGgtccgacatg ... tttgttacagTGGTGATCATGATATGTGTGTACC
EST: gi|29638179|gb|CB643188.1|CB643188
EST:     AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAG                         TGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
genomic: AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAGgtccgacatg ... tttgttacagTGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
EST: gi|86501069|gb|CI143702.1|CI143702
EST:     GTTATCACCAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAG                         TGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
genomic: GTTATCA-CAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAGgtccgacatg ... tttgttacagTGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
EST: gi|33684071|gb|CF312310.1|CF312310
EST:     AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAG                         TGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
genomic: AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAGgtccgacatg ... tttgttacagTGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
EST: gi|88903221|gb|CI088759.1|CI088759
EST:     AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTTATATACAG                         TGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
genomic: AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAGgtccgacatg ... tttgttacagTGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
EST: gi|86537559|gb|CI177765.1|CI177765
EST:     AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAG                         TGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
genomic: AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAGgtccgacatg ... tttgttacagTGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
EST: gi|29644492|gb|CB649499.1|CB649499
EST:     AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAG                         TGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
genomic: AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAGgtccgacatg ... tttgttacagTGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
EST: gi|29668082|gb|CB664357.1|CB664357
EST:     AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAG                         TGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
genomic: AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAGgtccgacatg ... tttgttacagTGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
EST: gi|29661783|gb|CB658058.1|CB658058
EST:     AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAG                         TGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
genomic: AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAGgtccgacatg ... tttgttacagTGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
EST: gi|88245431|gb|CI245280.1|CI245280
EST:     AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAG                         TGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
genomic: AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAGgtccgacatg ... tttgttacagTGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
EST: gi|29659837|gb|CB656112.1|CB656112
EST:     AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAG                         TGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
genomic: AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAGgtccgacatg ... tttgttacagTGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
EST: gi|88957594|gb|CI011523.1|CI011523
EST:     CACAGGCCAGGGTTATCGTGCTTTCATATACAG                         TGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
genomic: CACAGGCCAGGGTTATCGTGCTTTCATATACAGgtccgacatg ... tttgttacagTGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
EST: gi|86594292|gb|CI251164.1|CI251164
EST:     AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTAATATACAG                         TGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
genomic: AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAGgtccgacatg ... tttgttacagTGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
EST: gi|86259349|gb|CI008026.1|CI008026
EST:     AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAG                         TGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
genomic: AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAGgtccgacatg ... tttgttacagTGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
EST: gi|29661784|gb|CB658059.1|CB658059
EST:     AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAG                         TGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
genomic: AGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAGgtccgacatg ... tttgttacagTGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
EST: gi|33684072|gb|CF312311.1|CF312311
EST:     TCACAGGCCAGGGTTATCGTGCTTTCATATACAG                         TGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG
genomic: TCACAGGCCAGGGTTATCGTGCTTTCATATACAGgtccgacatg ... tttgttacagTGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 58 (upstream exon), 73 (downstream exon)
Score: 10

TTATATGCACCAACGTGTTGGATTTCATCCATGATGCTGGAAGTATGATCAGTTATCACAAGAACCTCACAGGCCAGGGTTATCGTGCTTTCATATACAGgtccgacatg ... tttgttacagTGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAGATCTTTGGGCTACGGAGTTATTGATTCATGGAGACCGTGGCACCTGAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaaagaaagtgtgattccaatggtcatggcattttgttttatatttgttacagTGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAGATCTTTGGGCTACGGAGTTATTGATTCATGGAGACCGTGGCACCTGAAT
                                attttgttttatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcgaattttgtgccagctttttttatttcacatcctatactcttagaaaagaaagtgtgattccaatggtcatggcattttgttttatatttgttacagTGGTGATCATGATATGTGTGTACCTTATACCGGGACTGAAGCATGGACCAGATCTTTGGGCTACGGAGTTATTGATTCATGGAGACCGTGGCACCTGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - gtgccag
- - - - - - - - - - - - - - -cacatcc
- - - - - - - - - - - - - - - - - - - - - - - - aaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catggca