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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCGGGAACATGTTTTATGGAACGACAAAGATACCAATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATGgcaagtcacaatctcgaacttctattaggagtacctttatctcaacaatgaaggcagcaactcatctcttgaatgattcatctttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g13200.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g13200.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G123540_T01 (Zea mays), 5'ss of exon 10
GTTCCGGGAACATGTTTTATGGAACGACAAAGATACCAATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATGgcaagtcacaatctcgaacttctattaggagtacctttatctcaacaatgaaggcagcaactcatctcttgaatgattcatctttgcag
|| |  |||||||||| |||||| ||| | ||| ||||||||||| ||||| |||||| |||| ||||||||||||||||| || ||||  ||||   ||||| | ||| ||   | | |    |           |       ||  ||    | ||  |||    | ||||||||
GTACAAGGAACATGTTGTATGGACCGATAGAGACACCAATTTGAAACTTTTAAGGAAGAGTGTCTTGACACGCATATATGCGCCCATGgttagtcctgatctcaatcttgta--ggcattcagctcgaggagttgtttcttattgctgctgcattttt--atgcccaacctttgcag
















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|24208830|gb|AU225857.1|AU225857
EST:     ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATG                         GCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
genomic: ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATGgcaagtcaca ... atctttgcagGCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
EST: gi|86494800|gb|CI137433.1|CI137433
EST:     ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATG                         GCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
genomic: ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATGgcaagtcaca ... atctttgcagGCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
EST: gi|86494153|gb|CI136786.1|CI136786
EST:     ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATG                         GCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
genomic: ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATGgcaagtcaca ... atctttgcagGCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
EST: gi|88227787|gb|CI227267.1|CI227267
EST:     ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATG                         GCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
genomic: ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATGgcaagtcaca ... atctttgcagGCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
EST: gi|87016754|gb|CI275756.1|CI275756
EST:     ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATG                         GCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
genomic: ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATGgcaagtcaca ... atctttgcagGCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
EST: gi|86495100|gb|CI137733.1|CI137733
EST:     ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATG                         GCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
genomic: ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATGgcaagtcaca ... atctttgcagGCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
EST: gi|86502915|gb|CI145548.1|CI145548
EST:     ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATG                         GCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
genomic: ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATGgcaagtcaca ... atctttgcagGCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
EST: gi|87038260|gb|CI192882.1|CI192882
EST:     ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATG                         GCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
genomic: ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATGgcaagtcaca ... atctttgcagGCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
EST: gi|86593837|gb|CI260066.1|CI260066
EST:     ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATG                         GCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
genomic: ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATGgcaagtcaca ... atctttgcagGCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
EST: gi|38474929|gb|CF959062.1|CF959062
EST:     ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATG                         GCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
genomic: ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATGgcaagtcaca ... atctttgcagGCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
EST: gi|86505703|gb|CI148336.1|CI148336
EST:     ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATG                         GCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
genomic: ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATGgcaagtcaca ... atctttgcagGCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
EST: gi|112787139|gb|EE592124.1|EE592124
EST:     ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATG                         GGCTATCATTTCGTGGTCTCAAGGGAATCCGGCGTATTCACCACCGCGGTA
genomic: ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATGgcaagtcaca ... atctttgcagG-CTATCATT-CGTGGTCTCAAGG-AATCCGGCGTATTCACCACCGCGGTA
EST: gi|27576085|gb|CA998779.1|CA998779
EST:     ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATG                         GCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
genomic: ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATGgcaagtcaca ... atctttgcagGCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
EST: gi|86518976|gb|CI159182.1|CI159182
EST:     ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATG                         GCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
genomic: ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATGgcaagtcaca ... atctttgcagGCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT
EST: gi|86500934|gb|CI143567.1|CI143567
EST:     ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATG                         GCTATCATTCGTGGTCTCCAAGGAATCCGGCGTATTCACCACCGCGGTAAC
genomic: ATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATGgcaagtcaca ... atctttgcagGCTATCATTCGTGGTCT-CAAGGAATCCGGCGTATTCACCACCGCGGTAAC
EST: gi|88233306|gb|CI233155.1|CI233155
EST:     GACACGCATATATGCCCCAATG                         GCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACTACCGCGGTAACT
genomic: GACACGCATATATGCCCCAATGgcaagtcaca ... atctttgcagGCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACT

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: 73 (upstream exon), 71 (downstream exon)
Score: 47

GTTCCGGGAACATGTTTTATGGAACGACAAAGATACCAATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATGgcaagtcaca ... atctttgcagGCTATCATTCGTGGTCTCAAGGAATCCGGCGTATTCACCACCGCGGTAACTTCAGCAAAAGCGCATGCAAAATTTAAGTCATCAAATACGGATCTCAAAA




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCCGGGAACATGTTTTATGGAACGACAAAGATACCAATTTGAAGCTTTTGAGGAAGGGTGTGTTGACACGCATATATGCCCCAATGgcaagtcacaatctcgaacttctattaggagtacctttatctcaacaatgaaggcagcaactcatctcttgaatgattcatctttgcag

- - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - -  TGAAGC