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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttaagatttttgtcaatgccagaccaactgaaacaccctgacagcaatatcctgatttgctaactactgaacttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATGCTAAGAAGCAATGTGCCTTCTTAGGATTATGAGCAGACAGTTCATACAC

Basic information

species Oryza sativa
transcript LOC_Os01g19150.5
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g19150.5 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G075992_T01 (Zea mays), 3'ss of exon 7
-----------gtaagttaag-atttttgtcaatgccagaccaactg--aaacaccctgacagcaatatcctgatttgctaactactga--acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATGCTAAGAAGCAATGTGCCTTCTTAGGATTATGAGCAGACAGTTCATACAC
           |  ||   || |  |  |||    |  |    | |   ||||||  |   || || |||||||| | | |  |  | |   ||||||||||| ||| ||||| | ||  ||| ||| ||||| | ||| | || ||||||||||||||||||||||| ||||||||| | |||| |  |||||||     
caataacaattgagagcggagcagctccgtcccaccatgcttcagtaccaaacactatctaagtaa-atcctgatgtaccacatcttcattgcttgaacagAGTTGAGAGGAGTACCAGAGGAGTTTGTTGTGCAATTGATCCCTCAGCATGCTAAGAAGCAATGTGCTTTCTTAGGAGTTTGAGAAAGCAGTTCAATTTT
















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|29637278|gb|CB642287.1|CB642287
EST:     CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
genomic: CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|86503762|gb|CI146395.1|CI146395
EST:     CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
genomic: CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|29670122|gb|CB666397.1|CB666397
EST:     CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
genomic: CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|29632836|gb|CB637845.1|CB637845
EST:     ATTCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
genomic: ATTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|29668964|gb|CB665239.1|CB665239
EST:     CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
genomic: CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|8856575|gb|AU093893.1|AU093893
EST:     CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
genomic: CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|29666430|gb|CB662705.1|CB662705
EST:     CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
genomic: CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|29619093|gb|CB624105.1|CB624105
EST:     CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTGTTGTGAAGTTGGTTCCACAGCATG
genomic: CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|29634101|gb|CB639110.1|CB639110
EST:     TTACCAAATGGCCGTACTCTTCCCCCCACTATTCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
genomic: TTACCAAATGGCCGTACTCTT-CCCCCACTATTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|29614478|gb|CB619491.1|CB619491
EST:     CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTGTTGTGAAGTTGGTTCCACAGCATG
genomic: CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|29675686|gb|CB671961.1|CB671961
EST:     CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
genomic: CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|29624000|gb|CB629011.1|CB629011
EST:     CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTGTTGTGAAGTTGGTTCCACAGCATG
genomic: CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|29633505|gb|CB638514.1|CB638514
EST:     TTCAATTTCAAGCTTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
genomic: TTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|29666643|gb|CB662918.1|CB662918
EST:     CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
genomic: CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|29645803|gb|CB650810.1|CB650810
EST:     CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
genomic: CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|29676371|gb|CB672646.1|CB672646
EST:     CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
genomic: CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|29666992|gb|CB663267.1|CB663267
EST:     CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
genomic: CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|29666993|gb|CB663268.1|CB663268
EST:     CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
genomic: CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|29632504|gb|CB637513.1|CB637513
EST:     CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
genomic: CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|29666642|gb|CB662917.1|CB662917
EST:     CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
genomic: CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|29633965|gb|CB638974.1|CB638974
EST:     TTACCAAATGGCCGTACTCTTCCCCCCACTATTCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
genomic: TTACCAAATGGCCGTACTCTT-CCCCCACTATTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|33808948|gb|CF330360.1|CF330360
EST:     TCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
genomic: TCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|29674068|gb|CB670343.1|CB670343
EST:     CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
genomic: CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|33683225|gb|CF311464.1|CF311464
EST:     TCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
genomic: TCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|29628249|gb|CB633260.1|CB633260
EST:     CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTGTTGTGAAGTTGGTTCCACAGCATG
genomic: CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|29623354|gb|CB628365.1|CB628365
EST:     CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTGTTGTGAAGTTGGTTCCACAGCATG
genomic: CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|29668829|gb|CB665104.1|CB665104
EST:     CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
genomic: CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
EST: gi|33808952|gb|CF330361.1|CF330361
EST:     CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTG                         AGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG
genomic: CTTACCAAATGGCCGTACTCTTCCCCCACTATTCAATTTCAAGCCTCGTGgtaagttaag ... acttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactgaaacaccctgacagcaatatcctgatttgctaactactgaacttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATGCTAAGAAGCAATGTGCCTTCTTAGGATTATGAGCAGACAGTTCATACAC
                                tgctaac  putative branch site (score: 1)
                    aatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttaagatttttgtcaatgccagaccaactgaaacaccctgacagcaatatcctgatttgctaactactgaacttgaacagAGCTGAAAGGAGCATCAATGGAATTTCTTGTGAAGTTGGTTCCACAGCATGCTAAGAAGCAATGTGCCTTCTTAGGATTATGAGCAGACAGTTCATACAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG