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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcttcagtctcctagatgtcctcatctatttgttcggcaatcttttgatatctatttatttttcagACGCTCGAGGAATTTTCCCTTGAAGCTGAAAAGGTTGAGAAGGGATACAGCCCTGCTGAATATGCTACTGGCCTGCCAAAAATCCATGGTCTCAGCAATG

Basic information

species Oryza sativa
transcript LOC_Os04g31190.1
intron # 19
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|87015202|gb|CI275392.1|CI275392
EST:     GTTCTTGAACAGGCTCATAGG                         ACGCTCGAGGAATTTTCCCTTGAAGCTGAAAAGGTTGAGAAGGGATACAGC
genomic: GTTCTTGAACAGGCTCATAGGgtatcttcag ... tatttttcagACGCTCGAGGAATTTTCCCTTGAAGCTGAAAAGGTTGAGAAGGGATACAGC
EST: gi|89184146|gb|CI046711.1|CI046711
EST:     GAAGGCAGCGTATACAAGAAACACTCCAAGTTCTTGAACAGGCTCATAGG                         ACGCTCGAGGAATTTTCCCTTGAAGCTGAAAAGGTTGAGAAGGGATACAGC
genomic: GAAGGCAGCGTATACAAGAAACACTCCAAGTTCTTGAACAGGCTCATAGGgtatcttcag ... tatttttcagACGCTCGAGGAATTTTCCCTTGAAGCTGAAAAGGTTGAGAAGGGATACAGC
EST: gi|89189718|gb|CI049257.1|CI049257
EST:     ACAAGAAACACTCCAAGTTCTTGAACAGGCTCATAGG                         ACGCTCGAGGAATTTTCCCTTGAAGCTGAAAAGGTTGAGAAGGGATACAGC
genomic: ACAAGAAACACTCCAAGTTCTTGAACAGGCTCATAGGgtatcttcag ... tatttttcagACGCTCGAGGAATTTTCCCTTGAAGCTGAAAAGGTTGAGAAGGGATACAGC
EST: gi|33802600|gb|CF327172.1|CF327172
EST:     GAAGGCAGCGTATACAAGAAACACTCCAAGTTCTTGAACAGGCTCATAGG                         ACGCTCGAGGAATTTTCCCTTGAAGCTGAAAAGGTTGAGAAGGGATACAGC
genomic: GAAGGCAGCGTATACAAGAAACACTCCAAGTTCTTGAACAGGCTCATAGGgtatcttcag ... tatttttcagACGCTCGAGGAATTTTCCCTTGAAGCTGAAAAGGTTGAGAAGGGATACAGC
EST: gi|87039859|gb|CI194481.1|CI194481
EST:     GAAGGCAGCGTATACAAGAAACACTCCAAGTTCTTGAACAGGCTCATAGG                         ACGCTCGAGGAATTTTCCCTTGAAGCTGAAAAGGTTGAGAAGGGATACAGC
genomic: GAAGGCAGCGTATACAAGAAACACTCCAAGTTCTTGAACAGGCTCATAGGgtatcttcag ... tatttttcagACGCTCGAGGAATTTTCCCTTGAAGCTGAAAAGGTTGAGAAGGGATACAGC

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: 58 (upstream exon), 32 (downstream exon)
Score: 3

AGAAAACCTGCTGGATGAAATGCTGAGGGAAACTGATGAAGTAATTATCAGAAGGCAGCGTATACAAGAAACACTCCAAGTTCTTGAACAGGCTCATAGGgtatcttcag ... tatttttcagACGCTCGAGGAATTTTCCCTTGAAGCTGAAAAGGTTGAGAAGGGATACAGCCCTGCTGAATATGCTACTGGCCTGCCAAAAATCCATGGTCTCAGCAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagatgtcctcatctatttgttcggcaatcttttgatatctatttatttttcagACGCTCGAGGAATTTTCCCTTGAAGCTGAAAAGGTTGAGAAGGGATACAGCCCTGCTGAATATGCTACTGGCCTGCCAAAAATCCATGGTCTCAGCAATG
                               ttttgat  putative branch site (score: 3)
                                       tctatttatttttc  CT-rich tract
                           aatcttttgatatcta  TA-rich tract