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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgaactaggagagcatgagctcccccatttccattagaagaaacaacctttgaaggttgataactgattccatgtatgtgtggcaactttatttctagGAGGATATACAACGTAGTGGATGACGACCCTGCCCCAAGATCTGAGGTTTTCGCATTTGCTCGGAGCTTGGTTGAGAGGAAGCATCCTGGCCTGATAATG

Basic information

species Oryza sativa
transcript LOC_Os01g15660.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15660.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G119749_T04 (Zea mays), 3'ss of exon 5
tttgaactaggagagcatgagctcccccatttccattagaagaaac--aacctttgaaggttgataactgattccatgt-atgtgtggcaactttatttctagGAGGATATACAACGTAGTGGATGACGACCCTGCCCCAAGATCTGAGGTTTTCGCATTTGCTCGGAGCTTGGTTGAGAGGAAGCATCCTGGCCTGATAATG
 ||  ||  |    |  |  | ||  |||   | | |    ||||    |  | |   | ||   || |  |  | | | |||| |  ||| | |||| | ||||  ||||  || || |||||||||||||||||||||||| |||| ||||| || ||||||  ||| ||| |  ||||||   ||||||   ||||||  
-ttagacatgtttggttttggttcttccacagcgactgagtgaaatctgaaatatcctgtttaccaattattcacttctcatgttta-caattctatt-ccagGAAAATATTTAATGTGGTGGATGACGACCCTGCCCCAAGAGCTGAAGTTTTTGCGTTTGCTACGAGTTTGATACAGAGGAGATATCCTGATATGATAACT
















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|29674694|gb|CB670969.1|CB670969
EST:     GCTGACATTTGTCAGGCTATCCTGGCTAGCATGAGCATCAGAAGTGCAAG                         GAGGATATACAACGTAGTGGATGACGACCCTGCCCCAAGATCTGAGGTTTT
genomic: GCTGACATTTGTCAGGCTATCCTGGCTAGCATGAGCATCAGAAGTGCAAGgtttgtttgt ... ttatttctagGAGGATATACAACGTAGTGGATGACGACCCTGCCCCAAGATCTGAGGTTTT
EST: gi|29677177|gb|CB673452.1|CB673452
EST:     GCTGACATTTGTCAGGCTATCCTGGCTAGCATGAGCATCAGAAGTGCAAG                         GAGGATATACAACGTAGTGGATGACGACCCTGCCCCAAGATCTGAGGTTTT
genomic: GCTGACATTTGTCAGGCTATCCTGGCTAGCATGAGCATCAGAAGTGCAAGgtttgtttgt ... ttatttctagGAGGATATACAACGTAGTGGATGACGACCCTGCCCCAAGATCTGAGGTTTT
EST: gi|88265547|gb|CI376449.1|CI376449
EST:     ATGAGCATCAGAAGTGCAAG                         GAGGATATACAACGTAGTGGATGACGACCCTGCCCCAAGATCTGAGGTTTT
genomic: ATGAGCATCAGAAGTGCAAGgtttgtttgt ... ttatttctagGAGGATATACAACGTAGTGGATGACGACCCTGCCCCAAGATCTGAGGTTTT
EST: gi|89177289|gb|CI250738.1|CI250738
EST:     GCTGACATTTGTCAGGCTATCCTGGCTAGCATGAGCATCAGAAGTGCAAG                         GAGGATATACAACGTAGTGGATGACGACCCTGCCCCAAGATCTGAGGTTTT
genomic: GCTGACATTTGTCAGGCTATCCTGGCTAGCATGAGCATCAGAAGTGCAAGgtttgtttgt ... ttatttctagGAGGATATACAACGTAGTGGATGACGACCCTGCCCCAAGATCTGAGGTTTT
EST: gi|88986554|gb|CI033697.1|CI033697
EST:     GCTGACATTTGTCAGGCTATCCTGGCTAGCATGAGCATCAGAAGTGCAAG                         GAGGATATACAACGTAGTGGATGACGACCCTGCCCCAAGATCTGAGGTTTT
genomic: GCTGACATTTGTCAGGCTATCCTGGCTAGCATGAGCATCAGAAGTGCAAGgtttgtttgt ... ttatttctagGAGGATATACAACGTAGTGGATGACGACCCTGCCCCAAGATCTGAGGTTTT
EST: gi|86483066|gb|CI125699.1|CI125699
EST:     GCTGACATTTGTCAGGCTATCCTGGCTAGCATGAGCATCAGAAGTGCAAG                         GAGGATATACAACGTAGTGGATGACGACCCTGCCCCAAGATCTGAGGTTTT
genomic: GCTGACATTTGTCAGGCTATCCTGGCTAGCATGAGCATCAGAAGTGCAAGgtttgtttgt ... ttatttctagGAGGATATACAACGTAGTGGATGACGACCCTGCCCCAAGATCTGAGGTTTT
EST: gi|29642827|gb|CB647834.1|CB647834
EST:     GCTGACATTTGTCAGGCTATCCTGGCTAGCATGAGCATCAGAAGTGCAAG                         GAGGATATACAACGTAGTGGATGACGACCCTGCCCCAAGATCTGAGGTTTT
genomic: GCTGACATTTGTCAGGCTATCCTGGCTAGCATGAGCATCAGAAGTGCAAGgtttgtttgt ... ttatttctagGAGGATATACAACGTAGTGGATGACGACCCTGCCCCAAGATCTGAGGTTTT
EST: gi|88472748|gb|CI410019.1|CI410019
EST:     GCTAGCATGAGCATCAGAAGTGCAAG                         GAGGATATACAACGTAGTGGATGACGACCCTGCCCCAAGATCTGAGGTTTT
genomic: GCTAGCATGAGCATCAGAAGTGCAAGgtttgtttgt ... ttatttctagGAGGATATACAACGTAGTGGATGACGACCCTGCCCCAAGATCTGAGGTTTT
EST: gi|66921834|gb|CX108682.1|CX108682
EST:     GCTGACATTTGTCAGGCTATCCTGGCTAGCATGAGCATCAGAAGTGCAAG                         GAGGATATACAACGTAGTGGATGACGACCCTGCCCCAAGATCTGAGGTTTT
genomic: GCTGACATTTGTCAGGCTATCCTGGCTAGCATGAGCATCAGAAGTGCAAGgtttgtttgt ... ttatttctagGAGGATATACAACGTAGTGGATGACGACCCTGCCCCAAGATCTGAGGTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacctttgaaggttgataactgattccatgtatgtgtggcaactttatttctagGAGGATATACAACGTAGTGGATGACGACCCTGCCCCAAGATCTGAGGTTTTCGCATTTGCTCGGAGCTTGGTTGAGAGGAAGCATCCTGGCCTGATAATG
                                           ctttatttct  CT-rich tract
                                         aactttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgaactaggagagcatgagctcccccatttccattagaagaaacaacctttgaaggttgataactgattccatgtatgtgtggcaactttatttctagGAGGATATACAACGTAGTGGATGACGACCCTGCCCCAAGATCTGAGGTTTTCGCATTTGCTCGGAGCTTGGTTGAGAGGAAGCATCCTGGCCTGATAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA