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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaggagaccgataattggtcataccttccattgttccaatagtaaatgttatgctgactccacaaattacacctaactggtttcagGTTTTATCCGGTCGTCCTTTGGTGAATAAAGAGGAAAATAATGCTAATGATGTTGCGTTCACTGATGCTGTTGGTTTTCAGGAGAAG

Basic information

species Oryza sativa
transcript LOC_Os10g40780.3
intron # 37
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|58666011|gb|CK054697.1|CK054697
EST:     GTTTTGCTTCCGTGAAGGATGAAAATATTAGACAGTCAAGGGATAAAAAG                         GTTTTATCCGGTCGTCCTTTGGTGAATAAAGAGGAAAATAATGCTAATGA
genomic: GTTTTGCTTCCGTGAAGGATGAAAATATTAGACAGTCAAGGGATAAAAAGgtcaggagac ... ctggtttcagGTTTTATCCGGTCGTCCTTTGGTGAATAAAGAGGAAAATAATGCTAATGA
EST: gi|58612277|gb|CK039989.1|CK039989
EST:     TTGCTTCCGTGAAGGATGAAAATATTAGACATGTCAATGGGATAACAAAG                         GTTTTATCCGGTCTTCCTTTGGTGAATAACAGAGGAAAATAATGCTAATG
genomic: TTGCTTCCGTGAAGGATGAAAATATTAGACA-GTCAA-GGGATAA-AAAGgtcaggagac ... ctggtttcagGTTTTATCCGGTCGTCCTTTGGTGAATAA-AGAGGAAAATAATGCTAATG
EST: gi|29615806|gb|CB620818.1|CB620818
EST:     GTTTTGCTTCCGTGAAGGATGAAAATATTAGACAGTCAAGGGATAAAAAG                         GTTTTATCCGGTCGTCCTTTGGTGAATAAAGAGGAAAATAATGCTAATGAT
genomic: GTTTTGCTTCCGTGAAGGATGAAAATATTAGACAGTCAAGGGATAAAAAGgtcaggagac ... ctggtttcagGTTTTATCCGGTCGTCCTTTGGTGAATAAAGAGGAAAATAATGCTAATGAT
EST: gi|29629737|gb|CB634746.1|CB634746
EST:     GTTTTGCTTCCGTGAAGGATGAAAATATTAGACAGTCAAGGGATAAAAAG                         GTTTTATCCGGTCGTCCTTTGGTGAATAAAGAGGAAAATAATGCTAATGAT
genomic: GTTTTGCTTCCGTGAAGGATGAAAATATTAGACAGTCAAGGGATAAAAAGgtcaggagac ... ctggtttcagGTTTTATCCGGTCGTCCTTTGGTGAATAAAGAGGAAAATAATGCTAATGAT
EST: gi|58604721|gb|CK015249.1|CK015249
EST:     GTTTTGCTTCCGTGAAGGATGAAAATATTAGACAGTCAAGGGATAAAAAG                         GTTTTATCCGGTCGTCCTTTGGTGAATAAAGAGGAAAATAATGCTAATGAT
genomic: GTTTTGCTTCCGTGAAGGATGAAAATATTAGACAGTCAAGGGATAAAAAGgtcaggagac ... ctggtttcagGTTTTATCCGGTCGTCCTTTGGTGAATAAAGAGGAAAATAATGCTAATGAT
EST: gi|58672055|gb|CK060741.1|CK060741
EST:     GTTTTGCTTCCGTGAAGGATGAAAATATTAGACAGTCAAGGGATAAAAAG                         GTTTTATCCGGTCGTCCTTTGGTGAATAAAGAGGAAAATAATGCTAATGAT
genomic: GTTTTGCTTCCGTGAAGGATGAAAATATTAGACAGTCAAGGGATAAAAAGgtcaggagac ... ctggtttcagGTTTTATCCGGTCGTCCTTTGGTGAATAAAGAGGAAAATAATGCTAATGAT

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: 64 (upstream exon), 70 (downstream exon)
Score: 16

CAGGCCCAGTTCTCCTGAATCGCTGCAGCAGTTGATTGAAATCGCTAGAAGTTTTGCTTCCGTGAAGGATGAAAATATTAGACAGTCAAGGGATAAAAAGgtcaggagac ... ctggtttcagGTTTTATCCGGTCGTCCTTTGGTGAATAAAGAGGAAAATAATGCTAATGATGTTGCGTTCACTGATGCTGTTGGTTTTCAGGAGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttccaatagtaaatgttatgctgactccacaaattacacctaactggtttcagGTTTTATCCGGTCGTCCTTTGGTGAATAAAGAGGAAAATAATGCTAATGATGTTGCGTTCACTGATGCTGTTGGTTTTCAGGAGAAG
                                       acctaac  putative branch site (score: 16)
      aatagtaaatgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaggagaccgataattggtcataccttccattgttccaatagtaaatgttatgctgactccacaaattacacctaactggtttcagGTTTTATCCGGTCGTCCTTTGGTGAATAAAGAGGAAAATAATGCTAATGATGTTGCGTTCACTGATGCTGTTGGTTTTCAGGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA