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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGACGGAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAGgtaataaaaattactccgatcctcttatactgatacaacactatattctaagcctgcctatgggctttctggagcaacaaaatatggaaacataatcctg...

Basic information

species Oryza sativa
transcript LOC_Os03g64020.2
intron # 3
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|38475301|gb|CF959434.1|CF959434
EST:     GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAG                         GTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
genomic: GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAGgtaataaaaa ... cctggcgcagGTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
EST: gi|117243743|gb|CT843209.1|CT843209
EST:     GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAG                         GTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
genomic: GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAGgtaataaaaa ... cctggcgcagGTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
EST: gi|218487328|gb|FG968259.1|FG968259
EST:     GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAG                         GTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTTCTGCTAAATGTT
genomic: GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAGgtaataaaaa ... cctggcgcagGTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
EST: gi|58030632|gb|CX728175.1|CX728175
EST:     AGGTCCCAGGTGCAGTCTACGCAGCCGAAAG                         GTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
genomic: AGGTCCCAGGTGCAGTCTACGCAGCCGAAAGgtaataaaaa ... cctggcgcagGTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
EST: gi|38475842|gb|CF959975.1|CF959975
EST:     GAAGTGACATT-TCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAG                         GTGTACAGTGATTTGACCGTGGGCTACCTAAAGATGTTCCTGCTAAATGTT
genomic: GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAGgtaataaaaa ... cctggcgcagGTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
EST: gi|33801214|gb|CF326480.1|CF326480
EST:     GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAG                         GTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
genomic: GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAGgtaataaaaa ... cctggcgcagGTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
EST: gi|29687940|gb|CB684215.1|CB684215
EST:     GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAG                         GTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
genomic: GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAGgtaataaaaa ... cctggcgcagGTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
EST: gi|29687939|gb|CB684214.1|CB684214
EST:     GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAG                         GTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
genomic: GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAGgtaataaaaa ... cctggcgcagGTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
EST: gi|29682412|gb|CB678687.1|CB678687
EST:     GAAGGTCCCAGGTGCCTTCTACGCAGCCGAAAG                         GTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
genomic: GAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAGgtaataaaaa ... cctggcgcagGTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT

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: 75 (upstream exon), 49 (downstream exon)
Score: 58

AAAGACGGAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAGgtaataaaaa ... cctggcgcagGTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTTCCAGCAACTACTCTTGCTCTAGGACT




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