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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcggtcttactgacaagaatcaacaactatcaattcttaatttcgaagatagttcctttgccggtgatgcttatgcagataatgccatcgatcttgcagGCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAGACCAAGGATAACTGGAAAAGTTAATACCGATGCAACTGTTACTCTTCGT

Basic information

species Oryza sativa
transcript LOC_Os03g21460.1
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|33659110|gb|CF281723.1|CF281723
EST:     AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAG                         GCAAAGTTTGGTGCCAAGTCGCCAGTTGGGGCCCTGCGAGAAGTTAGGAAG
genomic: AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAGgttctaatcc ... gatcttgcagGCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
EST: gi|33661943|gb|CF292910.1|CF292910
EST:     AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAG                         GCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
genomic: AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAGgttctaatcc ... gatcttgcagGCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
EST: gi|87022853|gb|CI269789.1|CI269789
EST:     AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAG                         GCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
genomic: AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAGgttctaatcc ... gatcttgcagGCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
EST: gi|86523306|gb|CI163512.1|CI163512
EST:     AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAG                         GCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
genomic: AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAGgttctaatcc ... gatcttgcagGCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
EST: gi|218494169|gb|FG952751.1|FG952751
EST:     AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAG                         GCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
genomic: AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAGgttctaatcc ... gatcttgcagGCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
EST: gi|33687223|gb|CF315462.1|CF315462
EST:     GGAATTTGAGACAAACCACCTTCATGCGTGTTGATCTGCCAGAAATACAG                         GCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
genomic: GGAATTTGAGACAAA-CACCTTCATGCGTGTTGATCTGCCAGAAATACAGgttctaatcc ... gatcttgcagGCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
EST: gi|89196526|gb|CI399112.1|CI399112
EST:     AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAG                         GCAAAGTTTGGTGCCAAGTCGCCANTTGAGGGCCCTGCGAGAAGTTAGGAA
genomic: AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAGgttctaatcc ... gatcttgcagGCAAAGTTTGGTGCCAAGTCGCCAGTTGA-GGCCCTGCGAGAAGTTAGGAA
EST: gi|33808258|gb|CF330018.1|CF330018
EST:     AGGAATTTGAGTCAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAG                         GCAAAGTTTGGTGCCAAGTCGCCAGTTGATGCCCTGCGAGAAGTTAGGAAG
genomic: AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAGgttctaatcc ... gatcttgcagGCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
EST: gi|86836168|gb|CI346183.1|CI346183
EST:     AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAG                         GCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
genomic: AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAGgttctaatcc ... gatcttgcagGCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
EST: gi|86599871|gb|CI256033.1|CI256033
EST:     AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAG                         GCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
genomic: AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAGgttctaatcc ... gatcttgcagGCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
EST: gi|66913473|gb|CX100321.1|CX100321
EST:     AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAG                         GCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
genomic: AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAGgttctaatcc ... gatcttgcagGCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
EST: gi|86522330|gb|CI162536.1|CI162536
EST:     AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAG                         GCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
genomic: AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAGgttctaatcc ... gatcttgcagGCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
EST: gi|88849985|gb|CI091280.1|CI091280
EST:     AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAG                         GCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
genomic: AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAGgttctaatcc ... gatcttgcagGCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
EST: gi|86854994|gb|CI263061.1|CI263061
EST:     AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAG                         GCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
genomic: AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAGgttctaatcc ... gatcttgcagGCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
EST: gi|88226817|gb|CI224802.1|CI224802
EST:     AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAG                         GCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
genomic: AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAGgttctaatcc ... gatcttgcagGCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
EST: gi|88902197|gb|CI374805.1|CI374805
EST:     AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAG                         GCAAAGTTTGATGCCAAATCGCCACTTGAGGCCCTGCGAGAAGTTAGGAAG
genomic: AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAGgttctaatcc ... gatcttgcagGCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
EST: gi|86508887|gb|CI151520.1|CI151520
EST:     AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAG                         GCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG
genomic: AGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAGgttctaatcc ... gatcttgcagGCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAG

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: 71 (upstream exon), 40 (downstream exon)
Score: 6

TCAAAAGCAGCGTGAAGCAAACCAACCAACTATTCCATCAACTATAGGAGAGGAATTTGAGACAAACACCTTCATGCGTGTTGATCTGCCAGAAATACAGgttctaatcc ... gatcttgcagGCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAGACCAAGGATAACTGGAAAAGTTAATACCGATGCAACTGTTACTCTTCGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagatagttcctttgccggtgatgcttatgcagataatgccatcgatcttgcagGCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAGACCAAGGATAACTGGAAAAGTTAATACCGATGCAACTGTTACTCTTCGT
                                agataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcggtcttactgacaagaatcaacaactatcaattcttaatttcgaagatagttcctttgccggtgatgcttatgcagataatgccatcgatcttgcagGCAAAGTTTGGTGCCAAGTCGCCAGTTGAGGCCCTGCGAGAAGTTAGGAAGACCAAGGATAACTGGAAAAGTTAATACCGATGCAACTGTTACTCTTCGT

- - - cttactg
- - - - - - - - - - -caacaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgccatc