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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaatgatctcagtatttttgtacagttacgcagcttggcttatatatggtgtagaaacatcaatcttgttcattgcttccttattataatgtttatttttcatttcattgaagatctcatttcaatttttgcagGTCAGATAGGGAGCTTTTGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAG

Basic information

species Oryza sativa
transcript LOC_Os03g49420.4
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49420.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G033619_T01 (Zea mays), 3'ss of exon 17
gtaagtaatgatctcagtatttttgtacagttacgcagcttggcttatatatggtgtagaaacatcaatcttgttcattgcttccttattataatgtttatttttca--tttcattgaagatctcatttcaatttttgcagGTCAGATAGGGAGCTTTTGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAG
|||||||||   | || | | ||| | |||    |  ||||  | |  | ||     |  |    | ||| | |  | | ||   ||||| | | |||| |||  ||  | | |||         | |  |  ||   |||||| || |||||||||||||||||||| || |||||||||||||||||||| ||| ||||||| |||
gtaagtaattcccacaatttgtttctgcaga---gttgcttttcctg-agattaaccaatactccctatcatctagacttctgttttatt-tcacgtttctttaacagctattattttttcgtgtaatcaacgttcaacagGTCTGAGAGGGAGCTTTTGGGTCATAATAATCAGTATCTTCCAAAGATTGTGTCTGTTTTTGCAGAG
















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|88849788|gb|CI001494.1|CI001494
EST:     ACGATGCTTGAGAA                         GTCAGATAGGGAGCTTTTGGGTCATAACAACCAGTATCTTCCCAAGATTGT
genomic: ACGATGCTTGAGAAgtaagtaatg ... atttttgcagGTCAGATAGGGAGCTTTTGGGTCATAACAACCAGTATCTTCCAAAGATTGT
EST: gi|86597066|gb|CI272661.1|CI272661
EST:     GAACGACTCTGTACGATGCTTGAGAA                         GTCAGATAGGGAGCTTTTGGGTCATAACCACCAGTATCTTCCAAAGATTGT
genomic: GAACAACTCTGTACGATGCTTGAGAAgtaagtaatg ... atttttgcagGTCAGATAGGGAGCTTTTGGGTCATAACAACCAGTATCTTCCAAAGATTGT
EST: gi|29629841|gb|CB634850.1|CB634850
EST:     TTAATCGAGGCCAAGATAGTTCATGAACAACTCTGTACGATGCTTGAGAA                         GTCAGATAGGGAGCTTTTGGGTCATAACAACCAGTATCTTCCAAAGATTGT
genomic: TTAATCGAGGCCAAGATAGTTCATGAACAACTCTGTACGATGCTTGAGAAgtaagtaatg ... atttttgcagGTCAGATAGGGAGCTTTTGGGTCATAACAACCAGTATCTTCCAAAGATTGT
EST: gi|27576974|gb|CA999668.1|CA999668
EST:     TTAATCGAGGCCAAGATAGTTCATGAACAACTCTGTACGATGCTTGAGAA                         GTCAGATAGGGAGCTTTTGGGTCATAACAACCAGTATCTTCCAAAGATTGT
genomic: TTAATCGAGGCCAAGATAGTTCATGAACAACTCTGTACGATGCTTGAGAAgtaagtaatg ... atttttgcagGTCAGATAGGGAGCTTTTGGGTCATAACAACCAGTATCTTCCAAAGATTGT
EST: gi|29629241|gb|CB634252.1|CB634252
EST:     TTAATCGAGGCCAAGATAGTTCATGAACAACTCTGTACGATGCTTGAG-A                         ---A-ATAGGGAGCTTTTGGGTCATAACAACCAGTATCTTCCAAAGATTGT
genomic: TTAATCGAGGCCAAGATAGTTCATGAACAACTCTGTACGATGCTTGAGAAgtaagtaatg ... atttttgcagGTCAGATAGGGAGCTTTTGGGTCATAACAACCAGTATCTTCCAAAGATTGT
EST: gi|29679232|gb|CB675507.1|CB675507
EST:     TTAATCGAGGCCAAGATAGTTCATGAACAACTCTGTACGATGCTTGAGAA                         GTCAGATAGGGAGCTTTTGGGTCATAACAACCAGTATCTTCCAAAGATTGT
genomic: TTAATCGAGGCCAAGATAGTTCATGAACAACTCTGTACGATGCTTGAGAAgtaagtaatg ... atttttgcagGTCAGATAGGGAGCTTTTGGGTCATAACAACCAGTATCTTCCAAAGATTGT
EST: gi|29681491|gb|CB677766.1|CB677766
EST:     TTAATCGAGGCCAAGATAGTTCATGAACAACTCTGTACGATGCTTGAGAA                         GTCAGATAGGGAGCTTTTGGGTCATAACAACCAGTATCTTCCAAAGATTGT
genomic: TTAATCGAGGCCAAGATAGTTCATGAACAACTCTGTACGATGCTTGAGAAgtaagtaatg ... atttttgcagGTCAGATAGGGAGCTTTTGGGTCATAACAACCAGTATCTTCCAAAGATTGT

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: 62 (upstream exon), 67 (downstream exon)
Score: 14

GTTGTTCCTGCTTGGTTAAGTTGTTTGCCAATAAAAAATGACTTAATCGAGGCCAAGATAGTTCATGAACAACTCTGTACGATGCTTGAGAAgtaagtaatg ... atttttgcagGTCAGATAGGGAGCTTTTGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttattataatgtttatttttcatttcattgaagatctcatttcaatttttgcagGTCAGATAGGGAGCTTTTGGGTCATAACAACCAGTATCTTCCAAAGATTGTCTCTATTTTTGCGGAG
                                              tttttgc  CT-rich tract
     tataatgtttattttt  TA-rich tract