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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtctttttccatgtttgttgccatgcctcactagtcattaggttagttctagctacctgatcatttctgcttacttttcattgcttcagGGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTGCTAATGCTGGTGAAGAGAAACAAAATACAGACTCCAAGGGTATGATAGA

Basic information

species Oryza sativa
transcript LOC_Os11g40510.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 8
gtgagtctttt---tccatgtttgttgcc-atgcctcactagtcattaggttagttctagctacctgatcatttctgcttacttttcattgcttcagGGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTGCTAATGCTGGTGAAGAGAAACAAAATACAGACTCCAAGGGTATGATAGA
||| ||  | |   ||||||||| |  |  |||  ||| |  | |     | || | |  | |  |||| |   | | | ||||||| |     ||||||||||||| || ||||||||| ||||||||||||||||||| || |||||||||||||||||||||||||| | |   ||| | |||| |    |   
gtgtgttctctagttccatgtttctaacttatgtttcattt-tgaagtcctaagctttcacaaggtgattacacccgttcacttttc-tactggcagGGAAGTGGCTTGGGAACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTGCTAATGCTGGTGAAGAGAAACAGATTCTGGACACTAAGGTTGACCTGTC
















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|58688359|gb|CK077046.1|CK077046
EST:     GACGCACAAAATGCCATAAATGAACTGAATG                         GGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
genomic: GACGCACAAAATGCCATAAATGAACTGAATGgtgagtcttt ... attgcttcagGGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
EST: gi|58687280|gb|CK075967.1|CK075967
EST:     GACGCACAAAATGCCATAAATGAACTGAATG                         GGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
genomic: GACGCACAAAATGCCATAAATGAACTGAATGgtgagtcttt ... attgcttcagGGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
EST: gi|87006051|gb|CI289468.1|CI289468
EST:     GACGCACAAAATGCCATAAATGAACTGAATG                         GGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
genomic: GACGCACAAAATGCCATAAATGAACTGAATGgtgagtcttt ... attgcttcagGGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
EST: gi|58602505|gb|CK013033.1|CK013033
EST:     GACGCACAAAATGCCATAAATGAACTGAATG                         GGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
genomic: GACGCACAAAATGCCATAAATGAACTGAATGgtgagtcttt ... attgcttcagGGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
EST: gi|33680119|gb|CF308358.1|CF308358
EST:     GACGCACAAAATGCCATAAATGAACTGAATG                         GGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
genomic: GACGCACAAAATGCCATAAATGAACTGAATGgtgagtcttt ... attgcttcagGGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
EST: gi|88572117|gb|CI663688.1|CI663688
EST:     GACGCACAAAATGCCATAAATGAACTGAATG                         GGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
genomic: GACGCACAAAATGCCATAAATGAACTGAATGgtgagtcttt ... attgcttcagGGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
EST: gi|218497207|gb|FG946437.1|FG946437
EST:     GACGCACAAAATGCCATAAATGAACTGAATG                         GGAAGTGGCTTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGT
genomic: GACGCACAAAATGCCATAAATGAACTGAATGgtgagtcttt ... attgcttcagGGAAGTGGCT-CGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGT
EST: gi|86905007|gb|CI289154.1|CI289154
EST:     GACGCACAAAATGCCATAAATGAACTGAATG                         GGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
genomic: GACGCACAAAATGCCATAAATGAACTGAATGgtgagtcttt ... attgcttcagGGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
EST: gi|88321854|gb|CI672999.1|CI672999
EST:     GACGCACAAAATGCCATAAATGAACTGAATG                         GGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
genomic: GACGCACAAAATGCCATAAATGAACTGAATGgtgagtcttt ... attgcttcagGGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
EST: gi|58678674|gb|CK067361.1|CK067361
EST:     GACGCACAAAATGCCATAAATGAACTGAATG                         GGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
genomic: GACGCACAAAATGCCATAAATGAACTGAATGgtgagtcttt ... attgcttcagGGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
EST: gi|58690866|gb|CK079553.1|CK079553
EST:     GACGCACAAAATGCCATAAATGAACTGAATG                         GGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
genomic: GACGCACAAAATGCCATAAATGAACTGAATGgtgagtcttt ... attgcttcagGGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
EST: gi|58694246|gb|CK082933.1|CK082933
EST:     GACGCACAAAATGCCATAAATGAACTGAATG                         GGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
genomic: GACGCACAAAATGCCATAAATGAACTGAATGgtgagtcttt ... attgcttcagGGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
EST: gi|25797088|gb|CA753049.1|CA753049
EST:     GACGCACAAAATGCCATAAATGAACTGAATG                         GGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAAGGGT
genomic: GACGCACAAAATGCCATAAATGAACTGAATGgtgagtcttt ... attgcttcagGGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAA-GGGT
EST: gi|218500911|gb|FG960833.1|FG960833
EST:     GACGCACAAAATGCCATAAATGAACTGAATG                         GGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
genomic: GACGCACAAAATGCCATAAATGAACTGAATGgtgagtcttt ... attgcttcagGGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
EST: gi|58597389|gb|CK007917.1|CK007917
EST:     GACGCACAAAATGCCATAAATGAACTGAATG                         GGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
genomic: GACGCACAAAATGCCATAAATGAACTGAATGgtgagtcttt ... attgcttcagGGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
EST: gi|325494350|gb|JG458874.1|JG458874
EST:     GACGCACAAAATGCCATAAATGAACTGAATG                         GGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
genomic: GACGCACAAAATGCCATAAATGAACTGAATGgtgagtcttt ... attgcttcagGGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
EST: gi|58606512|gb|CK034545.1|CK034545
EST:     GACGCACAAAATGCCATAAATGAACTGAATG                         GGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
genomic: GACGCACAAAATGCCATAAATGAACTGAATGgtgagtcttt ... attgcttcagGGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
EST: gi|58601763|gb|CK012291.1|CK012291
EST:     GACGCACAAAATGCCATAAATGAACTGAATG                         GGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
genomic: GACGCACAAAATGCCATAAATGAACTGAATGgtgagtcttt ... attgcttcagGGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
EST: gi|86596642|gb|CI286555.1|CI286555
EST:     GACGCACAAAATGCCATAAATGAACTGAATG                         GGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
genomic: GACGCACAAAATGCCATAAATGAACTGAATGgtgagtcttt ... attgcttcagGGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
EST: gi|87004665|gb|CI300987.1|CI300987
EST:     GACGCACAAAATGCCATAAATGAACTGAATG                         GGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG
genomic: GACGCACAAAATGCCATAAATGAACTGAATGgtgagtcttt ... attgcttcagGGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattaggttagttctagctacctgatcatttctgcttacttttcattgcttcagGGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTGCTAATGCTGGTGAAGAGAAACAAAATACAGACTCCAAGGGTATGATAGA
                                 tgcttac  putative branch site (score: 2)
                                       cttttcattgcttc  CT-rich tract
                                    ttactttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtctttttccatgtttgttgccatgcctcactagtcattaggttagttctagctacctgatcatttctgcttacttttcattgcttcagGGAAGTGGCTCGGCAACCGTCAAGTTCGTTGCAATTGGGCAACAAAGGGTGCTAATGCTGGTGAAGAGAAACAAAATACAGACTCCAAGGGTATGATAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA