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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACGTCGTCGGGGCCGAAGGAGGCGCCGGCAAACAACCCGGGCCTCCAGGCGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctcttcgctaggctatttcactccgctggttgatcgctcttcgagttttcgttttggtagaattgggtgtctgatctgtggattggaagagag...

Basic information

species Oryza sativa
transcript LOC_Os05g22970.1
intron # 2
splice site 5'
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|33818513|gb|CF335087.1|CF335087
EST:     CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACG                         ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
genomic: CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctc ... ttccttgcagATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
EST: gi|88343329|gb|CI627289.1|CI627289
EST:     CGCCGTCGGAGAAGGACCC-GCGACCAAGGGCTACTTCATGCAGCAGACG                         ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
genomic: CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctc ... ttccttgcagATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
EST: gi|33819107|gb|CF335378.1|CF335378
EST:     CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACG                         ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
genomic: CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctc ... ttccttgcagATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
EST: gi|88364009|gb|CI610353.1|CI610353
EST:     CGCCGTCGGAGAAGGACCCCGGGACCAAGGGCTACTTCATGCAGCAGACG                         ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTANTCGCGTGTG
genomic: CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctc ... ttccttgcagATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
EST: gi|88396511|gb|CI600994.1|CI600994
EST:     CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTATTTCATGCAGCAGACG                         ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
genomic: CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctc ... ttccttgcagATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
EST: gi|38478143|gb|CF962276.1|CF962276
EST:     CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACG                         ATGTTCCGTGTAGAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
genomic: CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctc ... ttccttgcagATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
EST: gi|66918847|gb|CX105695.1|CX105695
EST:     CGCCGTCGGAGAAGGACCCCGCGAACAAGGGCTACTTCATGCAGCAGACG                         ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
genomic: CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctc ... ttccttgcagATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
EST: gi|38482501|gb|CF966535.1|CF966535
EST:     CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACG                         ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
genomic: CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctc ... ttccttgcagATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
EST: gi|87021271|gb|CI295330.1|CI295330
EST:     CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACG                         ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
genomic: CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctc ... ttccttgcagATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
EST: gi|88329315|gb|CI653229.1|CI653229
EST:     CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACG                         ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
genomic: CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctc ... ttccttgcagATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
EST: gi|25800681|gb|CA756642.1|CA756642
EST:     CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACG                         ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
genomic: CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctc ... ttccttgcagATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
EST: gi|33813839|gb|CF332805.1|CF332805
EST:     CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACG                         ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
genomic: CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctc ... ttccttgcagATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
EST: gi|88364025|gb|CI610369.1|CI610369
EST:     CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACG                         ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGAATTCTACTCGCGTGTG
genomic: CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctc ... ttccttgcagATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
EST: gi|58687672|gb|CK076359.1|CK076359
EST:     CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACG                         ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
genomic: CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctc ... ttccttgcagATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
EST: gi|33815680|gb|CF333691.1|CF333691
EST:     CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACG                         ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
genomic: CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctc ... ttccttgcagATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
EST: gi|88314674|gb|CI606742.1|CI606742
EST:     CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACG                         ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
genomic: CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctc ... ttccttgcagATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
EST: gi|88725675|gb|CI748934.1|CI748934
EST:     CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACG                         ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
genomic: CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctc ... ttccttgcagATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
EST: gi|88575843|gb|CI669988.1|CI669988
EST:     CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACG                         ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
genomic: CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctc ... ttccttgcagATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
EST: gi|58588133|gb|CF986441.1|CF986441
EST:     CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACG                         ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
genomic: CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctc ... ttccttgcagATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
EST: gi|88401847|gb|CI591174.1|CI591174
EST:     CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACG                         ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
genomic: CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctc ... ttccttgcagATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
EST: gi|88331273|gb|CI639684.1|CI639684
EST:     CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACG                         ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
genomic: CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctc ... ttccttgcagATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
EST: gi|58692806|gb|CK081493.1|CK081493
EST:     CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACG                         ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
genomic: CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctc ... ttccttgcagATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
EST: gi|88330299|gb|CI658610.1|CI658610
EST:     CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACG                         ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
genomic: CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctc ... ttccttgcagATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
EST: gi|9457296|gb|AU063064.2|AU063064
EST:     CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACG                         ATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG
genomic: CGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctc ... ttccttgcagATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTG

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: 61 (upstream exon), 71 (downstream exon)
Score: 64

GACGTCGTCGGGGCCGAAGGAGGCGCCGGCAAACAACCCGGGCCTCCAGGCGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctc ... ttccttgcagATGTTCCGTGTAAAGGATCCAAAAGTGAGTCTCGACTTCTACTCGCGTGTGATGGGCATGTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACGTCGTCGGGGCCGAAGGAGGCGCCGGCAAACAACCCGGGCCTCCAGGCGCCGTCGGAGAAGGACCCCGCGACCAAGGGCTACTTCATGCAGCAGACGgtaatccctcttcgctaggctatttcactccgctggttgatcgctcttcgagttttcgttttggtagaattgggtgtctgatctgtggattggaagagag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cactccgc