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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatcttgcgtgttcttaatcttttttgcatgcatatatggtggctttggattttaaaattgcctttatatcttcataatagacctgcttttattttgcagCTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTG

Basic information

species Oryza sativa
transcript LOC_Os06g33710.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g33710.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G047867_T01 (Zea mays), 3'ss of exon 7
------------------------------------------tatcttgc-gtgttcttaatcttttttgcatgcatatatggtggctttggattt--taaaattgcctttatatc-ttcataatagacctgcttttattttgcagCTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTG
                                          |  |  || ||    |    |  | |||  |  |      |   |||||  | |  |    |||   |  |||  |||||| || || |||| || |||||||||||| |||||| |||| ||| | || ||||| |||||||||||||| ||||| |||||||| || |||||||
gtatgttcaaaagctggtacctggtggtactttatatgactgtgacaggctgtaggatatgccactattgtttatagcctcaggcactttgtttctgctggtcttgatctcttatagttcatagtatacttgctatt-ttttgcagCTGTTGATTTCCTGAGGAATTCTCCCGAAGGAAAATATGATGCTATTATTGTAGATTCATCAGATCCAATTG

upper sequence: LOC_Os06g33710.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT5G53120.4 (Arabidopsis thaliana), 3'ss of exon 8
-tatcttgcgtgttcttaatctt-ttttgcatgcatatatggtggctttggattttaaaattgcctttatatcttcataatagacctgcttttattttgcagCTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTG
 ||  ||  |  |||||   ||| || |   | || | |  || |      ||||     |||  || |||||               ||||  | | |||||||  || ||| |  | ||  ||||||||||||| |||||||| |||||||||||||| || || ||  | |
gtaa-ttaagcattcttctacttgttctctgttcacaaaacgtagtcaaaaattt---gcttgtgttgatatc--------------actttcctctggcagCTGCTGAGTTCCTCCGTAAATCCCCTGAAGGGAAGTATGATGCCATCATTGTTGATTCTTCAGATCCCGTAG

upper sequence: LOC_Os06g33710.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 7
------------------tatctt--gcgtgttcttaatcttttttgcatgcatata-tggtggctttggat----tttaaaattgcctt--tatatcttcataatagacctgcttttattttg-cagCTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTG
                  ||  ||    | | ||||| | | |  |   |   || | |  || |||  | |    |||   | |  |||  | || |||| | ||     |    | |||||| ||||||| || ||  | ||| |||  ||||||||||| |||||||| || |||||||||||||| || ||  | |
gtatgttcattctcaaaataatttcaaagagatcttactttatcctatgtaactagaataatgacttcagctgcttttttccaatatcttgctgtaccttcttgatttcattttcatgattttggcagCTGTTGAATTTCTTAGACATGTACCTGAAGGGAAGTATGATGCAATTATTGTTGATTCATCAGATCCTGTGG

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|33686636|gb|CF314875.1|CF314875
EST:     ACTATCTGTTGGATTCAAAGATCCCCGTGTTCAACTTCATGTTGGTGACG                         CTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTG
genomic: ACTATCTGTTGGATTCAAAGATCCCCGTGTTCAACTTCATGTTGGTGACGgtatgtttag ... tattttgcagCTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTG
EST: gi|29681267|gb|CB677542.1|CB677542
EST:     ACTATCTGTTGGATTCAAAGATCCCCGTGTTCAACTTCATGTTGGTGACG                         CTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTG
genomic: ACTATCTGTTGGATTCAAAGATCCCCGTGTTCAACTTCATGTTGGTGACGgtatgtttag ... tattttgcagCTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTG
EST: gi|29678039|gb|CB674314.1|CB674314
EST:     ACTATCTGTTGGATTCAAAGATCCCCGTGTTCAACTTCATGTTGGTGACG                         CTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTG
genomic: ACTATCTGTTGGATTCAAAGATCCCCGTGTTCAACTTCATGTTGGTGACGgtatgtttag ... tattttgcagCTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTG
EST: gi|29661773|gb|CB658048.1|CB658048
EST:     ACTATCTGTTGGATTCAAAGATCCCCGTGTTCAACTTCATGTTGGTGACG                         CTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTG
genomic: ACTATCTGTTGGATTCAAAGATCCCCGTGTTCAACTTCATGTTGGTGACGgtatgtttag ... tattttgcagCTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTG
EST: gi|29674257|gb|CB670532.1|CB670532
EST:     ACTATCTGTTGGATTCAAAGATCCCCGTGTTCAACTTCATGTTGGTGACG                         CTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTG
genomic: ACTATCTGTTGGATTCAAAGATCCCCGTGTTCAACTTCATGTTGGTGACGgtatgtttag ... tattttgcagCTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTG
EST: gi|38468529|gb|CF952660.1|CF952660
EST:     ACTATCTGTTGGATTCAAAGATCCCCGTGTTCAACTTCATGTTGGTGACG                         CTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTG
genomic: ACTATCTGTTGGATTCAAAGATCCCCGTGTTCAACTTCATGTTGGTGACGgtatgtttag ... tattttgcagCTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTG
EST: gi|58690531|gb|CK079218.1|CK079218
EST:     A-TATCTGT-GGATTCAAAGATCCCCGTGTTCAACTTCATGTTGGTGACG                         CTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTG
genomic: ACTATCTGTTGGATTCAAAGATCCCCGTGTTCAACTTCATGTTGGTGACGgtatgtttag ... tattttgcagCTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTG
EST: gi|29660327|gb|CB656602.1|CB656602
EST:     ACTATCTGTTGGATTCAAAGATCCCCGTGTTCAACTTCATGTTGGTGACG                         CTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTG
genomic: ACTATCTGTTGGATTCAAAGATCCCCGTGTTCAACTTCATGTTGGTGACGgtatgtttag ... tattttgcagCTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggattttaaaattgcctttatatcttcataatagacctgcttttattttgcagCTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTG
                                     cctgcttttatttt  CT-rich tract
                  tttatatcttcataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatcttgcgtgttcttaatcttttttgcatgcatatatggtggctttggattttaaaattgcctttatatcttcataatagacctgcttttattttgcagCTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG