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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacgtatcttgctatgtatttctgtctcctatttaagttcaaatatattaaatgagtttcagaaattacatttgaaaacatgcagGAGAGAGGTCATTGATGAGGACGGTTGGTTGCACACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTTTAAAAATTATAGATAG

Basic information

species Oryza sativa
transcript LOC_Os11g04980.2
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 8
gtaacgtatcttgctatgtatttctgtctccta--tttaagttcaaatatattaaat---gagtt-tcagaaattacatttgaaaacatgcagGAGAGAGGTCATTGATGAGGACGGTTGGTTGCACACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTTTAAAAATTATAGATAG
     |||  || ||||   |  ||    | ||  |||    | ||  || || ||     | || |||  || ||||||| ||||  | ||| | ||| ||||||||||| || ||||||||||||||||||||||||||| ||||||| |||||||| |||||||| || || |||||
-----gtaaatttctatccgtcacttaaacatagctttgtactgaatgatcttcaactgcaacttatcaataaatacattttaaaaactacagAAAAGAAGTCATTGATGAAGATGGTTGGTTGCACACTGGAGACATAGGTCTGTGGCTACCTGGAGGACGTTTAAAGATCATCGATAG

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 17
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 17
---gtaacgtatcttgctatgtatttctgtctcctatttaagttcaaatatattaaatgagtttcagaaattacatttgaaaacatg-----cagGAGAGAGGTCATTGATGAGGACGGTTGGTTGCACACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTTTAAAAATTATAGATAG
     |||   |  |||  || |  |   |||   | |  |    || | ||  ||| |   || |   ||| || |  ||   ||      ||||| |||||| |||||||| || || ||| | ||||||||||| |||||| |||||||||| ||||| ||| |||||||||| || ||
gtataaacacctactgcattggaaattcctctttcact--aaccaaagtgtaccaaaag---tttaattatttcagtaaaacgtattattttcagGAAAGAGGTGATTGATGAAGATGGATGGCTTCACACTGGAGATATAGGTCTGTGGCTGCCGGGAGGACGTCTAAAAATTATTGACAG

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 17
gtaacgtatcttgctatgtatttctgtctcctatttaagttca--aatatattaaa--tgagtttcagaaattacatt-tgaaaacatgcagGAGAGAGGTCATTGATGAGGACGGTTGGTTGCACACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTTTAAAAATTATAGATAG
||| |  | |||||  |||  | |||  || | |  | |||    | | | | |||  ||  |       ||||  |  | |||     |||||||||||| |||||||| || || ||| | || || |||||||||||||| ||| | |||||||| ||  |||| || || |||||
gtacc-caccttgcc-tgttctgctggttcttttgaatgttgtgcattttgtcaaaattggatacatctgattatgtgatcaaattgaacagGAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAG

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|66919239|gb|CX106087.1|CX106087
EST:     GTTAGGGGAACTACGATATTTTTTGGTTACTATAAGGATGAAATCCAAAC                         GAGAGAGGTCATTGATGAGGACGGTTGGTTGCACACTGGAGACATAGGTTT
genomic: GTTAGGGGAACTACGATATTTTTTGGTTACTATAAGGATGAAATCCAAACgtaacgtatc ... aaacatgcagGAGAGAGGTCATTGATGAGGACGGTTGGTTGCACACTGGAGACATAGGTTT
EST: gi|58590451|gb|CF988759.1|CF988759
EST:     GTTAGGGGAACTACGATATTTTTTGGTTACTATAAGGATGAAATCCAAAC                         GAGAGAGGTCATTGATGAGGACGGTTGGTTGCACACTGGAGACATAGGTTT
genomic: GTTAGGGGAACTACGATATTTTTTGGTTACTATAAGGATGAAATCCAAACgtaacgtatc ... aaacatgcagGAGAGAGGTCATTGATGAGGACGGTTGGTTGCACACTGGAGACATAGGTTT
EST: gi|58595336|gb|CF993644.1|CF993644
EST:     GTTAGGGGAACTACGATATTTTTTGGTTACTGGGAGGATGAAATCCAAAC                         GAGAGAGGTCATTGATGAGGACGGTTGGTTGCACACTGGAGACATAGGTTT
genomic: GTTAGGGGAACTACGATATTTTTTGGTTACTATAAGGATGAAATCCAAACgtaacgtatc ... aaacatgcagGAGAGAGGTCATTGATGAGGACGGTTGGTTGCACACTGGAGACATAGGTTT
EST: gi|27577334|gb|CB000029.1|CB000029
EST:     GTTAGGGGAACTACGATATTTTTTGGTTACTATAAGGATGAAATCCAAAC                         GAGAGAGGTCATTGATGAGGACGGTTGGTTGCACACTGGAGACATAGGTTT
genomic: GTTAGGGGAACTACGATATTTTTTGGTTACTATAAGGATGAAATCCAAACgtaacgtatc ... aaacatgcagGAGAGAGGTCATTGATGAGGACGGTTGGTTGCACACTGGAGACATAGGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttaagttcaaatatattaaatgagtttcagaaattacatttgaaaacatgcagGAGAGAGGTCATTGATGAGGACGGTTGGTTGCACACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTTTAAAAATTATAGATAG
          aaatatattaaatgag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacgtatcttgctatgtatttctgtctcctatttaagttcaaatatattaaatgagtttcagaaattacatttgaaaacatgcagGAGAGAGGTCATTGATGAGGACGGTTGGTTGCACACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTTTAAAAATTATAGATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG