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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCAAACAAAGGAGAGGATCAAGTGATGTTATTGGAGGAGGGTGTCCAAGCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAGgttgtttgtgatgtatgatttctccttcatgttgtatataaacgttgagatatcaacattactaaggcactgacaaagataatctgttgcacag

Basic information

species Oryza sativa
transcript LOC_Os03g19970.1
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|88315624|gb|CI615496.1|CI615496
EST:     GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAG                         ACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGTTGAG
genomic: GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAGgttgtttgtg ... tgttgcacagACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGTTGAG
EST: gi|88851822|gb|CI679380.1|CI679380
EST:     GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAG                         ACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGTTG
genomic: GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAGgttgtttgtg ... tgttgcacagACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGTTG
EST: gi|58664540|gb|CK053226.1|CK053226
EST:     GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAG                         ACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGTTGAG
genomic: GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAGgttgtttgtg ... tgttgcacagACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGTTGAG
EST: gi|88369930|gb|CI680610.1|CI680610
EST:     GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAG                         ACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGT
genomic: GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAGgttgtttgtg ... tgttgcacagACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGT
EST: gi|58674145|gb|CK062831.1|CK062831
EST:     GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAG                         ACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGTTGAG
genomic: GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAGgttgtttgtg ... tgttgcacagACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGTTGAG
EST: gi|88330229|gb|CI658538.1|CI658538
EST:     GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAG                         ACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGTT
genomic: GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAGgttgtttgtg ... tgttgcacagACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGTT
EST: gi|88310897|gb|CI659500.1|CI659500
EST:     GCACCAGTGCAAAAGCCAGTCTATGCTTCTCTCANATCACAAATGTTCAG                         ACTTTTCTTGTTGGACCACGCACTCATTCTAGAGAAT
genomic: GCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAGgttgtttgtg ... tgttgcacagACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAAT

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: 57 (upstream exon), 63 (downstream exon)
Score: 23

GCTCAAACAAAGGAGAGGATCAAGTGATGTTATTGGAGGAGGGTGTCCAAGCACCAGTGCAAAAGCCAGTTTATGCTTCTCTCACATCACAAATGTTCAGgttgtttgtg ... tgttgcacagACTTTTCTTGTTGGACCAGGCACTTATTCTAGAGAATCGATTGACGTTGAGAGCAAT




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