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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAAAGTGAAGATTGCAGAGCATAAGCTTACAGGACACAGAGTTGCTATAAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctccttttctaaagagaccattttaatcaatctattatcttctgtgctcatatgatcttaagttacttgcttcctgtagtggtctgatctgtgaa...

Basic information

species Oryza sativa
transcript LOC_Os03g17980.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G107867_T04 (Zea mays), 5'ss of exon 1
GGAAAAGTGAAGATTGCAGAGCATAAGCTTACAGGACACAGAGTTGCTATAAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgta-acctccttttctaaagagac--cattttaatcaatctattatcttctgtgctcatatgatcttaagttacttgcttcctgtagtggt-ctgatctgtgaa----------------------------------------------
|||||||||||||||||||||||||||||||| ||||| || ||||||||||||||| | ||| |||||||||||||||||||||||||||| ||||||||||    |  || || |   |     |||||| |  ||| |    | || ||     | |  |  |||  ||   |  | | | |  |  |  | ||   || |                                              
GGAAAAGTGAAGATTGCAGAGCATAAGCTTACTGGACATAGGGTTGCTATAAAGATCATCAACTGCCGCCAAATGAGAAATATGGAAATGGAAGAGAAAGgtatggtttgttatccagtcattttgcattttcactaatat----ttttttgataataaacaagtttagttttaatagtgcttttgataatattaatacatggagttgctttgataattaagaccacatccctccctatcatgtttccag

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA13G05700.1 (Glycine max), 5'ss of exon 2
GGAAAAGTGAAGATTGCAGAGCATAAGCTTACAGGACACAGAGTTGCTATAAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctccttttctaaagagaccattttaatcaatctattatct------tctgtgctcatatgatcttaagttacttgcttcctgtagtggtctgatctgtgaa
|| || ||||| ||||| ||||||   |  || || || | |||||||||||||||||| ||||||| | | || | ||| ||||||||||| || ||||||  |    |  | |  | | |  ||||| |    |    || ||      ||||   | |  || | | |  || | |   |  |  ||    |   | | ||  
GGCAAGGTGAAAATTGCTGAGCATGTACGGACTGGTCATAAAGTTGCTATAAAGATCCTTAACCGCCACAAGATTAAAAACATGGAAATGGAAGAAAAAGgt--ctgaatcatttgcatacataattttgactgtttatctaactgcaggatctgattttaattgttttcagttttcctatatttttaagca--caagtatatg--
















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|58666860|gb|CK055546.1|CK055546
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|58674399|gb|CK063085.1|CK063085
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|88316515|gb|CI622761.1|CI622761
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCACCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|58604235|gb|CK014763.1|CK014763
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|29627233|gb|CB632244.1|CB632244
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|58679972|gb|CK068659.1|CK068659
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|88436650|gb|CI691382.1|CI691382
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|58659927|gb|CK048607.1|CK048607
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|88451891|gb|CI694666.1|CI694666
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|29663426|gb|CB659701.1|CB659701
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|117237395|gb|CT861888.1|CT861888
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|58670476|gb|CK059162.1|CK059162
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|33678911|gb|CF307150.1|CF307150
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|88593233|gb|CI709394.1|CI709394
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|58678394|gb|CK067081.1|CK067081
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|58605908|gb|CK033941.1|CK033941
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         N
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacag-
EST: gi|58605908|gb|CK033941.1|CK033941
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         N
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacag-
EST: gi|58675377|gb|CK064064.1|CK064064
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|58672618|gb|CK061304.1|CK061304
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|38471514|gb|CF955645.1|CF955645
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|88391925|gb|CI683743.1|CI683743
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|58671476|gb|CK060162.1|CK060162
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|29616519|gb|CB621531.1|CB621531
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|88250467|gb|CI348697.1|CI348697
EST:     AAAGATCCTGAACCCCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|29614995|gb|CB620008.1|CB620008
EST:     AGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|58668341|gb|CK057027.1|CK057027
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|58680986|gb|CK069673.1|CK069673
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|29672730|gb|CB669005.1|CB669005
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|58598230|gb|CK008758.1|CK008758
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|58690725|gb|CK079412.1|CK079412
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|33797130|gb|CF324430.1|CF324430
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|58669222|gb|CK057908.1|CK057908
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|58658129|gb|CK046809.1|CK046809
EST:     AAAGATGGTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
EST: gi|88321968|gb|CI673117.1|CI673117
EST:     AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAG                         CAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC
genomic: AAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctcct ... ttgtttacagCAAAGAGAGAAATCAAGATACTGAGATTGTTCATTCATCCCCATATCATTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAAAGTGAAGATTGCAGAGCATAAGCTTACAGGACACAGAGTTGCTATAAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaacctccttttctaaagagaccattttaatcaatctattatcttctgtgctcatatgatcttaagttacttgcttcctgtagtggtctgatctgtgaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA