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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGTTGTGATGGAGTACTGCAAGTTTGGAGAACTGTTTGATTACATTGTTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgaccttactcatttctttcacttgttaaacacgctcttttagcatttacttccaactttaatgcttgcttattttcaccattcaaaacctatgg...

Basic information

species Oryza sativa
transcript LOC_Os03g17980.2
intron # 3
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 3
lower sequence: GRMZM2G107867_T02 (Zea mays), 5'ss of exon 3
ATATGTTGTGATGGAGTACTGCAAGTTTGGAGAACTGTTTGATTACATTGTTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgaccttactcatttctt-tcacttgtta-aacacgctcttttagcatt----tacttccaactttaatgcttgcttattttcaccattcaaaacctatgg
||||||||||||||| || || |||| ||| ||  | |||||||||||||||||||||||||| || ||||||||||| ||||| |||||||||||||||||| ||  |  |  || |  ||  | |||| |   |||| ||| |||| |  |     ||  |     |  ||     | ||  | |      |   ||       
ATATGTTGTGATGGAATATTGTAAGTATGGCGAGTTATTTGATTACATTGTTGAGAAAGGCAGATTACAGGAAGATGAAGCTCGTCGAATCTTCCAGCAGgtatttatcacttttcttggctggttacttctagtaacatgctttttttgagtcacaataggtagttatcaaagaacggttttatcttgttgctttgaat------

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 3
ATATGTTGTGATGGAGTACTGCAAGTTTGGAGAACTGTTTGATTACATTGTTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgaccttactcatttctttcacttgttaaacacgctcttttagcatttacttccaactttaatgcttgcttattttcaccattcaaaacctatgg
|||| |||| ||||||||    |||| |||||| ||||| ||||||||||| ||||| |||||||||||||||||||| |||||     | || |||||||||       ||||| ||||  |  | ||   | | ||  | |  |  ||   | || | |   ||||   || || ||   | ||              
ATATTTTGTCATGGAGTATGTGAAGTCTGGAGAGCTGTTCGATTACATTGTAGAGAAGGGCAGGTTGCAGGAAGATGAAGCTCGTAATTTTTTTCAGCAGgtaggattgtttact-attttgtgtaatta--agagactttttcatgtcacagattttccaagctaatttctgatt-ttggaagcag-------------

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 4
ATATGTTGTGATGGAGTACTGCAAGTTTGGAGAACTGTTTGATTACATTGTTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgaccttactcatttctttcacttgttaaacacgctcttttagcatttacttccaactttaatgcttgcttattttcaccattcaaaacctatgg
||||||||| ||||||||    |||| |||||| || || |||||||| || ||||| || ||||||||||||||||| |||||     | || |||||||||       ||  | | |  |||    |  | || ||  |   ||  ||   | ||   |   ||||   || || ||   | ||              
ATATGTTGTCATGGAGTATGTGAAGTCTGGAGAGCTTTTCGATTACATAGTAGAGAAGGGTAGGTTGCAGGAAGATGAAGCTCGTAATTTTTTTCAGCAGgta----ggattgtttacta-ttttgtgtagtgaagacttttgcttgtcacagatttttcaagctaatttctgatt-ttggaagcag-------------

upper sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G29160.3 (Arabidopsis thaliana), 5'ss of exon 3
ATATGTTGTGATGGAGTACTGCAAGTTTGGAGAACTGTTTGATTACATTGTTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgaccttactcatttctttcacttgttaaacacgctcttttagcatttacttccaactttaatgcttgcttattttcaccattcaaaaccta-tgg
 |||||||||||||||||   ||||| |||||| || |||||||| ||||||||||||||||| || || ||||||||||||||     | |||||||||||  |||   || ||| || |  | ||  ||          | | |    |   |||  |  || | || ||| || | ||    | ||| | || | | |
TTATGTTGTGATGGAGTATGTCAAGTCTGGAGAGCTCTTTGATTATATTGTTGAGAAAGGCAGATTACAAGAAGATGAGGCTCGTAACTTTTTCCAGCAGgt--ttg--ttttctctttaccataaccagtgtgtttgtagcgtatcatgtcatctttgagtttgagtg-ttgtttgtgtttg--actcatatccgaatag

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:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTAGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|58674399|gb|CK063085.1|CK063085
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTAGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|29627233|gb|CB632244.1|CB632244
EST:     TTGAGAAAGGCAGGTTGCACGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTAGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|58679972|gb|CK068659.1|CK068659
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTAGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|58659927|gb|CK048607.1|CK048607
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTAGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|29663426|gb|CB659701.1|CB659701
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|117237395|gb|CT861888.1|CT861888
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTAGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|58670476|gb|CK059162.1|CK059162
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTAGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|33678911|gb|CF307150.1|CF307150
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|58678394|gb|CK067081.1|CK067081
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTAGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|58672618|gb|CK061304.1|CK061304
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTAGAATACTGACACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|58671476|gb|CK060162.1|CK060162
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTAGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|29616519|gb|CB621531.1|CB621531
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTAGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|88250467|gb|CI348697.1|CI348697
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|29614995|gb|CB620008.1|CB620008
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTAGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|33381730|gb|CF197073.1|CF197073
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTAGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|58668341|gb|CK057027.1|CK057027
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGT
EST: gi|58680986|gb|CK069673.1|CK069673
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTAGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|29672730|gb|CB669005.1|CB669005
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|218488644|gb|FG955529.1|FG955529
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTAGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|58598230|gb|CK008758.1|CK008758
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGGCGAATCTTCCAGCAG                         ATTATATCTGGGGTAGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|33797130|gb|CF324430.1|CF324430
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATTATCTGGGGTTGAATACTGCCACAGAAACATGGGGTGGTTCATCGT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTAT-ATCTGGGGTTGAATACTGCCACAGAAACATGG--TGGTTCATCGT
EST: gi|58669222|gb|CK057908.1|CK057908
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTAGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
EST: gi|58658129|gb|CK046809.1|CK046809
EST:     TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAG                         ATTATATCTGGGGTAGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT
genomic: TTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgacc ... tatggaacagATTATATCTGGGGTTGAATACTGCCACAGAAACATGGTGGTTCATCGTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATGTTGTGATGGAGTACTGCAAGTTTGGAGAACTGTTTGATTACATTGTTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgaccttactcatttctttcacttgttaaacacgctcttttagcatttacttccaactttaatgcttgcttattttcaccattcaaaacctatgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG