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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGGgtatgaacttaaataatatcttgtgttggtcaaggcaacctgagtattggattgtctcgtcttttaacagttatgcttcgggttgtgcag

Basic information

species Oryza sativa
transcript LOC_Os02g57180.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57180.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G143651_T01 (Zea mays), 5'ss of exon 10
GCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGGgtatgaacttaaataatatcttg-----tgttggtcaaggcaacctgagtattggattgtctcgtcttttaac--agttatgcttcgggttgtgcag
|||||||||||||| |||||||| || ||||||||| | ||  || |||| ||||||||| ||||||||||||||| |||| ||  |          |  ||| ||  | || | | | ||  | | | |||   |  | ||  |  | ||  || |         
GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGGgtatgaatttaattaccaggccagtacatactggcca--gaaaacggggcatcaggtagactctcgtactgacttatgtgtgtctcag---------
















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|11442907|gb|BF430806.1|BF430806
EST:     CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGG                         GCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
genomic: CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGGgtatgaactt ... ggttgtgcagGCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
EST: gi|4714677|gb|AU055794.1|AU055794
EST:     ATTACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCCTATTGCAAGG                         NCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCCGTT
genomic: A-TACGTGAATGGCCACGGTACATCGATGTTCCTCTT-CCTATTGCAAGGgtatgaactt ... ggttgtgcagGCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTT-CCGTT
EST: gi|86422921|gb|CI060494.1|CI060494
EST:     CGATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGG                         GCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
genomic: CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGGgtatgaactt ... ggttgtgcagGCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
EST: gi|88246401|gb|CI246250.1|CI246250
EST:     CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGG                         GCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
genomic: CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGGgtatgaactt ... ggttgtgcagGCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
EST: gi|86496928|gb|CI139561.1|CI139561
EST:     CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGG                         GCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
genomic: CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGGgtatgaactt ... ggttgtgcagGCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
EST: gi|29673109|gb|CB669384.1|CB669384
EST:     CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGG                         GCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
genomic: CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGGgtatgaactt ... ggttgtgcagGCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
EST: gi|88227607|gb|CI227087.1|CI227087
EST:     CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGG                         GCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
genomic: CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGGgtatgaactt ... ggttgtgcagGCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
EST: gi|86423690|gb|CI062451.1|CI062451
EST:     CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGG                         GCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
genomic: CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGGgtatgaactt ... ggttgtgcagGCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
EST: gi|88222421|gb|CI222377.1|CI222377
EST:     GTTCCTCTTCCTATTGCAAGG                         GCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
genomic: GTTCCTCTTCCTATTGCAAGGgtatgaactt ... ggttgtgcagGCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
EST: gi|88985739|gb|CI033068.1|CI033068
EST:     CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGG                         GCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
genomic: CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGGgtatgaactt ... ggttgtgcagGCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
EST: gi|86831290|gb|CI297559.1|CI297559
EST:     CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGG                         GCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
genomic: CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGGgtatgaactt ... ggttgtgcagGCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
EST: gi|86599963|gb|CI258303.1|CI258303
EST:     CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGG                         GCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
genomic: CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGGgtatgaactt ... ggttgtgcagGCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
EST: gi|86435376|gb|CI106609.1|CI106609
EST:     CAATACGTGAATGGCCCCGGTACATCGATGTTCCTCTTCCTATTGCAAGG                         GCTATCGCATCTCCAAGGGAAATGCTGCTAAACCAAGTGCCCTTTCCGTTG
genomic: CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGGgtatgaactt ... ggttgtgcagGCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
EST: gi|11564837|gb|AU165473.1|AU165473
EST:     TCTTCCTTATTGCAA-G                         GNTATCGCATCTCCAAGGGAATTGNTGCTAAACAAAGTGCCNTTTCCGTTG
genomic: TCTTCC-TATTGCAAGGgtatgaactt ... ggttgtgcagGCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
EST: gi|88834503|gb|CI077786.1|CI077786
EST:     CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGG                         GCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
genomic: CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGGgtatgaactt ... ggttgtgcagGCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
EST: gi|29671359|gb|CB667634.1|CB667634
EST:     CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGG                         GCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
genomic: CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGGgtatgaactt ... ggttgtgcagGCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
EST: gi|86435209|gb|CI106442.1|CI106442
EST:     CTCTTCCTATTGCAAGG                         GCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
genomic: CTCTTCCTATTGCAAGGgtatgaactt ... ggttgtgcagGCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
EST: gi|86837459|gb|CI345692.1|CI345692
EST:     TCTTCCTATTGC-A-G                         GCTATCGCATCTCCAA-GGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
genomic: TCTTCCTATTGCAAGGgtatgaactt ... ggttgtgcagGCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
EST: gi|86508531|gb|CI151164.1|CI151164
EST:     TGTTCCTCTTCCTATTGCAAGG                         GCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
genomic: TGTTCCTCTTCCTATTGCAAGGgtatgaactt ... ggttgtgcagGCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
EST: gi|86895469|gb|CI331314.1|CI331314
EST:     ACATCGATGTTCCTCTTCCTATTGCAAGG                         GCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
genomic: ACATCGATGTTCCTCTTCCTATTGCAAGGgtatgaactt ... ggttgtgcagGCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
EST: gi|8856604|gb|AU093922.1|AU093922
EST:     CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGG                         G-TATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
genomic: CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGGgtatgaactt ... ggttgtgcagGCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
EST: gi|88730417|gb|CI754030.1|CI754030
EST:     CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGG                         GCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG
genomic: CAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGGgtatgaactt ... ggttgtgcagGCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTG

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

GCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGGgtatgaactt ... ggttgtgcagGCTATCGCATCTCCAAGGGAAATGCTGCTAAACAAAGTGCCCTTTCCGTTGCCAACCCCATCAATTTTCAACAAAGATCAGATTAATGCATTTTCTGTAG




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