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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattagcacatctaatggcattgctctgcgttattcttataaaaaatggaacaagattcaatcaattttttttttgattctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTTTCAAATGTATTAAATGTGTTAGTCTCTTCTGGAGCTGATGCGCAG

Basic information

species Oryza sativa
transcript LOC_Os03g14980.2
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G550865_T02 (Zea mays), 3'ss of exon 8
gtattagcacatctaatggcattgctctgcgttattcttataaaaaatggaacaagattcaatcaattttttttttgattctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTTTCAAATGTATTAAATGTGTTAGTCTCTTCTGGAGCTGATGCGCAG----
      | |     | |||| ||| | |      |  ||  |   ||  | |||   || | |  ||   || ||| |||||||| ||||||||||||||| ||  | || |||||||||| ||| || || ||||| |||||||||||  ||||||| ||||||||||| ||||||||||| |||    
------gtattcacagtggctttgtttt------tctttccattgaacaggacacagtt-agtatatggcttattt-attctttgtacagGTCAAAAGCAAGCTCAGGGGTCACTCTAAGAGAATCACGGGTCTTGCCTTTTCAAATGTGCTAAATGTCTTAGTCTCTTCCGGAGCTGATGCTCAGGTTA

upper sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G550865_T01 (Zea mays), 3'ss of exon 8
gtattagcacatctaatggcattgctctgcgttattcttataaaaaatggaacaagattcaatcaattttttttttgattctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTTTCAAATGTATTAAATGTGTTAGTCTCTTCTGGAGCTGATGCGCAG
      | |     | |||| ||| | |      |  ||  |   ||  | |||   || | |  ||   || ||| |||||||| ||||||||||||||| ||  | || |||||||||| ||| || || ||||| |||||||||||  ||||||| ||||||||||| ||||||||||| |||
------gtattcacagtggctttgtttt------tctttccattgaacaggacacagtt-agtatatggcttattt-attctttgtacagGTCAAAAGCAAGCTCAGGGGTCACTCTAAGAGAATCACGGGTCTTGCCTTTTCAAATGTGCTAAATGTCTTAGTCTCTTCCGGAGCTGATGCTCAG

upper sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G030422_T03 (Zea mays), 3'ss of exon 23
gtattagcacatctaatggcattgctctgcgttattcttataaaaaatggaacaagattcaatcaattttttttttgattctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTTTCAAATGTATTAAATGTGTTAGTCTCTTCTGGAGCTGATGCGCAG
      | |    |  |||| ||| | | | ||  |   | | | |  | |   |  |   |   ||||          |||||| ||||||||||||||| ||  |||| |||||||||| ||| || || ||||| |||||||||||  ||||||| |||||||| || ||||||||||| |||
------gtattcatggtggctttgtttttctttcattgcacagata--gaagttaagtatgacttattt--------gctctttgtacagGTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTTTCAAATGTGCTAAATGTTTTAGTCTCGTCAGGAGCTGATGCCCAG

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|27554431|gb|CA998331.1|CA998331
EST:     TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|58657128|gb|CK045808.1|CK045808
EST:     TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|58677432|gb|CK066119.1|CK066119
EST:     TTGGAATGGATGAGTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|58655231|gb|CK043911.1|CK043911
EST:     TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|58691548|gb|CK080235.1|CK080235
EST:     TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|58594272|gb|CF992580.1|CF992580
EST:     TTGGAATGGATGACTCAACCATCCAAATGTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|58657970|gb|CK046650.1|CK046650
EST:     TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|163926688|gb|EG713704.1|EG713704
EST:     TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|58656462|gb|CK045142.1|CK045142
EST:     TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|218501279|gb|FG957977.1|FG957977
EST:     GGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: GGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|218487225|gb|FG954419.1|FG954419
EST:     TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|29680680|gb|CB676955.1|CB676955
EST:     TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|58689471|gb|CK078158.1|CK078158
EST:     TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|58694923|gb|CK083610.1|CK083610
EST:     TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|29673860|gb|CB670135.1|CB670135
EST:     TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
EST: gi|58590233|gb|CF988541.1|CF988541
EST:     TTGGGATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAG                         GTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcac ... ctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttataaaaaatggaacaagattcaatcaattttttttttgattctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTTTCAAATGTATTAAATGTGTTAGTCTCTTCTGGAGCTGATGCGCAG
                                     ttttgat  putative branch site (score: 4)
                               ttttttttttgattct  CT-rich tract
                     attcaatcaatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattagcacatctaatggcattgctctgcgttattcttataaaaaatggaacaagattcaatcaattttttttttgattctttgcacagGTCAAAAGCAAACTTCGAGGGCACTCTAAGAAAATTACTGGACTTGCTTTTTCAAATGTATTAAATGTGTTAGTCTCTTCTGGAGCTGATGCGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT