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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagcagtaattatctcgcgaatcatattatttgttgcgtgcgcactaatttctgacatggcatctaatttcttctcagGTACAAAGTGATAAGGGAGATAGGCGATGGCACCTGTGGGAATGTTTTTAGGGCTTATAACACTGAAACAAATGAAATT

Basic information

species Oryza sativa
transcript LOC_Os03g63020.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63020.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G045241_T01 (Zea mays), 3'ss of exon 3
gtcagcagtaattatc--tcgcgaatcatattatttgttgcgtgcgcactaatttctgacatggcatctaatttcttctcagGTACAAAGTGATAAGGGAGATAGGCGATGGCACCTGTGGGAATGTTTTTAGGGCTTATAACACTGAAACAAATGAAATT
|| || ||||| |     |  |   |  || | |   | |  ||     | | ||    | |  | ||  |||||||  |||||||||| ||||| || ||||||| ||||| ||||||||||||||||||| ||||| |||    ||||| |||||||||
gtaagtagtaagtgctcttttcactttttactttagatggtctggaaggttaatttgacctttacttcctatttctta-cagGTACAAATTGATACGGAAGATAGGTGATGGAACCTGTGGGAATGTTTTTATGGCTTCTAATGTAGAAACTAATGAAATT

upper sequence: LOC_Os03g63020.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G045241_T06 (Zea mays), 3'ss of exon 2
gtcagcagtaattatc--tcgcgaatcatattatttgttgcgtgcgcactaatttctgacatggcatctaatttcttctcagGTACAAAGTGATAAGGGAGATAGGCGATGGCACCTGTGGGAATGTTTTTAGGGCTTATAACACTGAAACAAATGAAATT---------------------
|| || ||||| |     |  |   |  || | |   | |  ||     | | ||    | |  | ||  |||||||  |||||||||| ||||| || ||||||| ||||| ||||||||||||||||||| ||||| |||    ||||| |||||||||                     
gtaagtagtaagtgctcttttcactttttactttagatggtctggaaggttaatttgacctttacttcctatttctta-cagGTACAAATTGATACGGAAGATAGGTGATGGAACCTGTGGGAATGTTTTTATGGCTTCTAATGTAGAAACTAATGAAATTGTAAGTGCAAGAACTCACCAA
















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|88571817|gb|CI663190.1|CI663190
EST:     TCAGTGACTCTTGGCAAAAGTTCTCTTGTAAAATCGACGACGATGGAAAG                         GTACAAAGTGATAAGG
genomic: TCAGTGACTCTTGGCAAAAGTTCTCTTGTAAAATCGACGACGATGGAAAGgtcagcagta ... ttcttctcagGTACAAAGTGATAAGG
EST: gi|88718034|gb|CI741544.1|CI741544
EST:     TCAGTGACTCTTGGCAAAAGTTCTCTTGTAAAATCGACGACGATGGAAAG                         GTACAAAGTGATAAGGGAGATAGGCGATGGCACCTGTGGGAATGTTTTTA
genomic: TCAGTGACTCTTGGCAAAAGTTCTCTTGTAAAATCGACGACGATGGAAAGgtcagcagta ... ttcttctcagGTACAAAGTGATAAGGGAGATAGGCGATGGCACCTGTGGGAATGTTTTTA
EST: gi|29656191|gb|CB652466.1|CB652466
EST:     TCAGTGACTCTTGGCAAAAGTTCTCTTGTAAAATCGACGACGATGGAAAG                         GTACAAAGTGATAAGGGAGATAGGCGATGGCACCTGTGGGAATGTTTTTAG
genomic: TCAGTGACTCTTGGCAAAAGTTCTCTTGTAAAATCGACGACGATGGAAAGgtcagcagta ... ttcttctcagGTACAAAGTGATAAGGGAGATAGGCGATGGCACCTGTGGGAATGTTTTTAG
EST: gi|29663526|gb|CB659801.1|CB659801
EST:     TCAGTGACTCTTGGCAAAAGTTCTCTTGTAAAATCGACGACGATGGAAAG                         GTACAAAGTGATAAGGGAGATAGGCGATGGCACCTGTGGGAATGTTTTTAG
genomic: TCAGTGACTCTTGGCAAAAGTTCTCTTGTAAAATCGACGACGATGGAAAGgtcagcagta ... ttcttctcagGTACAAAGTGATAAGGGAGATAGGCGATGGCACCTGTGGGAATGTTTTTAG
EST: gi|88415452|gb|CI586658.1|CI586658
EST:     TCAGTGACTCTTGGCAAAAGTTCTCTTGTAAAATCGACGACCATGGAAAG                         GTACAAAGTGATAAGGGAGATAGGC
genomic: TCAGTGACTCTTGGCAAAAGTTCTCTTGTAAAATCGACGACGATGGAAAGgtcagcagta ... ttcttctcagGTACAAAGTGATAAGGGAGATAGGC
EST: gi|88417218|gb|CI576292.1|CI576292
EST:     TCAGTGACTCTTGGCAAAAGTTCTCTTGTAAAATCGACGACGATGGAAAG                         GTACAAAGTGATAAGGGAGAT
genomic: TCAGTGACTCTTGGCAAAAGTTCTCTTGTAAAATCGACGACGATGGAAAGgtcagcagta ... ttcttctcagGTACAAAGTGATAAGGGAGAT
EST: gi|88324687|gb|CI587656.1|CI587656
EST:     TCAGTGACTCTTGGCAAAAGTTCTCTTGTAAAATCGACGACGATGGAAAG                         GTACAAAGTGATAAGGGAGATAGGCGATGGCACCTGTGGGAATGTTTTTAG
genomic: TCAGTGACTCTTGGCAAAAGTTCTCTTGTAAAATCGACGACGATGGAAAGgtcagcagta ... ttcttctcagGTACAAAGTGATAAGGGAGATAGGCGATGGCACCTGTGGGAATGTTTTTAG
EST: gi|88367674|gb|CI568446.1|CI568446
EST:     TCAGTGACTCTTGGCAAAAGTTCTCTTGTAAAATCGACGACGATGGAAAG                         GTACAAAGTGATAAGGGAGATAGGCGATGGCACCTGTGGGAATGTTTTTAG
genomic: TCAGTGACTCTTGGCAAAAGTTCTCTTGTAAAATCGACGACGATGGAAAGgtcagcagta ... ttcttctcagGTACAAAGTGATAAGGGAGATAGGCGATGGCACCTGTGGGAATGTTTTTAG
EST: gi|29644978|gb|CB649985.1|CB649985
EST:     TCAGTGACTCTTGGCAAAAGTTCTCTTGTAAAATCGACGACGATGGAAAG                         GTACAAAGTGATAAGGGAGATAGGCGATGGCACCTGTGGGAATGTTTTTAG
genomic: TCAGTGACTCTTGGCAAAAGTTCTCTTGTAAAATCGACGACGATGGAAAGgtcagcagta ... ttcttctcagGTACAAAGTGATAAGGGAGATAGGCGATGGCACCTGTGGGAATGTTTTTAG
EST: gi|29613119|gb|CB618132.1|CB618132
EST:     TCAGTGACTCTTGGCAAAAGTTCTCTTGTAAAATCGACGACGATGGAAAG                         GTACAAAGTGATAAGGGAGATAGGCGATGGCACCTGTGGGAATGTTTTTAG
genomic: TCAGTGACTCTTGGCAAAAGTTCTCTTGTAAAATCGACGACGATGGAAAGgtcagcagta ... ttcttctcagGTACAAAGTGATAAGGGAGATAGGCGATGGCACCTGTGGGAATGTTTTTAG
EST: gi|29613394|gb|CB618407.1|CB618407
EST:     TCAGTGACTCTTGGCAAAAGTTCTCTTGTAAAATCGACGACGATGGAAAG                         GTACAAAGTGATAAGGGAGATAGGCGATGGCACCTGTGGGAATGTTTTTAG
genomic: TCAGTGACTCTTGGCAAAAGTTCTCTTGTAAAATCGACGACGATGGAAAGgtcagcagta ... ttcttctcagGTACAAAGTGATAAGGGAGATAGGCGATGGCACCTGTGGGAATGTTTTTAG
EST: gi|88693186|gb|CI736761.1|CI736761
EST:     TCAGTGACTCTTGGCAAAAGTTCTCTTGTAAAATCGACGACGATGGAAAG                         GTACAAAGTGATAAGGGAGATAGGCGATGGCACCTGTGGGAATGTT
genomic: TCAGTGACTCTTGGCAAAAGTTCTCTTGTAAAATCGACGACGATGGAAAGgtcagcagta ... ttcttctcagGTACAAAGTGATAAGGGAGATAGGCGATGGCACCTGTGGGAATGTT

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: 74 (upstream exon), 72 (downstream exon)
Score: 49

ATGAGTTTTAGAGGTGGTGCGGGTTCGATCACGTGGAGTTCTATTGGTGTTCAGTGACTCTTGGCAAAAGTTCTCTTGTAAAATCGACGACGATGGAAAGgtcagcagta ... ttcttctcagGTACAAAGTGATAAGGGAGATAGGCGATGGCACCTGTGGGAATGTTTTTAGGGCTTATAACACTGAAACAAATGAAATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattatttgttgcgtgcgcactaatttctgacatggcatctaatttcttctcagGTACAAAGTGATAAGGGAGATAGGCGATGGCACCTGTGGGAATGTTTTTAGGGCTTATAACACTGAAACAAATGAAATT
                                       tctaatttcttctc  CT-rich tract
                                      atctaattt  TA-rich tract