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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtaatccacagacgaaagatttcccaaagtttcatctgtttaatgcctctttgcttaccttactgttagcaattgaaacacaatctgacttaattatggatttaatagAATGGTGGTGATCCAGCATCTAGAAGCATCGATATAAAGCCTAGAATTTCAGAAGAAAGGCCCGATAAAGCAAAACCCTGGGAGCTGATGGAAGTCCTAA

Basic information

species Oryza sativa
transcript LOC_Os01g15020.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 17
gtatggtaatccacagacgaaagatttcccaaagtttcatctgtttaatgcctctttgcttaccttactgttagcaattgaaacacaatctgacttaattatggatttaatagAATGGTGGTGATCCAGCATCTAGAAGCATCGATATAAAGCCTAGAATTTCAGAAGAAAGGCCCGATAAAGCAAAACCCTGGGAGCTGATGGAAGTCCTAA
                  | | |||       |||||||       ||    || |||||||||| | | | |  |||| ||  |  ||||||||| || |    || ||||||||||||| ||| ||||||| || ||||| ||||||||||| ||||| |||||||||| ||| |||||||||||||| ||||| || |||||||| ||||
------------------gtatgatgattttcagtttcacaca---aaaagttccttgcttacct-attatcaataatttaagtaacatctgacttgataa--atttgaatagAATGGTGGGGATACAGCATCAAGGAGCATAGATATAAAGCCAAGAATCTCAGAAGAAAAGCCTGATAAAGCAAAACCTTGGGAACTAATGGAAGTTCTAA

upper sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 15
gtatggtaatccacagacgaaagatttcccaaagtttcatctgtttaatgcctctttgcttaccttactgttagcaattgaaacacaatctgacttaattatggattt-aatagAATGGTGGTGATCCAGCATCTAGAAGCATCGATATAAAGCCTAGAATTTCAGAAGAAAGGCCCGATAAAGCAAAACCCTGGGAGCTGATGGAAGTCCTAA
                  | | | |    ||  ||||||   |   || |  || |||| |  | || | | |  | || ||| | | |||||||| || |   |||| |||||| |||||| ||| ||||||| |||||||| ||||||||| | ||||| |||||||||| | | |||||||||||| | | ||| || ||||| || ||||
------------------gtatggtgattcatggtttca---gacaaaaggttccttgccttacctattatcaatagtttaaata-actctgacttgatgacaaatttgaatagACTGGTGGCGATACAGCATCAAGAAGCATAGATATAAAGGCAAGAATCTCAGAAGAAAAGTCTGATAAAGCAAAAGCTTCGGAACTAATGGAGGTTCTAA
















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|58595855|gb|CK006383.1|CK006383
EST:     GGATGGATCACATCGACAGGAATTCTCCTGCAAAGCCATCTCCTATAATG                         AATGGTGGTGATCCAGCATCTAGAAGCATCGATGTGGAGCCTAGAATTTCA
genomic: GGATGGATCACATCGACAGGAATTCTCCTGCAAAGCCATCTCCTATAATGgtatggtaat ... gatttaatagAATGGTGGTGATCCAGCATCTAGAAGCATCGATATAAAGCCTAGAATTTCA
EST: gi|58679784|gb|CK068471.1|CK068471
EST:     GGATGGATCACATCGACAGGAATTCTCCTGCAAAGCCATCTCCTATAATG                         AATGGTGGTGATCCAGCATCTAGAAGCATCGATATAAAGCCTAGAATTTCA
genomic: GGATGGATCACATCGACAGGAATTCTCCTGCAAAGCCATCTCCTATAATGgtatggtaat ... gatttaatagAATGGTGGTGATCCAGCATCTAGAAGCATCGATATAAAGCCTAGAATTTCA
EST: gi|58661141|gb|CK049821.1|CK049821
EST:     GGATGGATCACATCGACAGGAATTCTCCTGCAAAGCCATCTCCTATAATG                         AATGGTGGTGATCCAGCATCTAGAAGCATCGATATAAAGCCTAGAATTTCA
genomic: GGATGGATCACATCGACAGGAATTCTCCTGCAAAGCCATCTCCTATAATGgtatggtaat ... gatttaatagAATGGTGGTGATCCAGCATCTAGAAGCATCGATATAAAGCCTAGAATTTCA
EST: gi|29625565|gb|CB630576.1|CB630576
EST:     GGATGGATCACATCGACAGGAATTCTCCTGCAAAGCCATCTCCTATAATG                         AATGGTGGTGATCCAGCATCTAGAAGCATCGATATAAAGCCTAGAATTTCA
genomic: GGATGGATCACATCGACAGGAATTCTCCTGCAAAGCCATCTCCTATAATGgtatggtaat ... gatttaatagAATGGTGGTGATCCAGCATCTAGAAGCATCGATATAAAGCCTAGAATTTCA
EST: gi|58606459|gb|CK034492.1|CK034492
EST:     GGATGGATCACATCGACAGGAATTCTCCTGCAAAGCCATCTCCTATAATG                         AAGTGGTGGTGATCCAGCATCTAGAAGCATCGATGTAAAGCCTAGAATTTC
genomic: GGATGGATCACATCGACAGGAATTCTCCTGCAAAGCCATCTCCTATAATGgtatggtaat ... gatttaatagAA-TGGTGGTGATCCAGCATCTAGAAGCATCGATATAAAGCCTAGAATTTC
EST: gi|58601227|gb|CK011755.1|CK011755
EST:     AGGAATTCTCCTGCAAAGCCATCTCCTATAATG                         AATGGTGGTGATCCAGCATCTAGAAGCGTCGATATAAAGCCTAGAATTTCA
genomic: AGGAATTCTCCTGCAAAGCCATCTCCTATAATGgtatggtaat ... gatttaatagAATGGTGGTGATCCAGCATCTAGAAGCATCGATATAAAGCCTAGAATTTCA
EST: gi|29626131|gb|CB631142.1|CB631142
EST:     GGATGGATCACATCGACAGGAATTCTCCTGCAAAGCCATCTCCTATAATG                         AATGGTGGTGATCCAGCATCTAGAAGCATCGATATAAAGCCTAGAATTTCA
genomic: GGATGGATCACATCGACAGGAATTCTCCTGCAAAGCCATCTCCTATAATGgtatggtaat ... gatttaatagAATGGTGGTGATCCAGCATCTAGAAGCATCGATATAAAGCCTAGAATTTCA
EST: gi|29619450|gb|CB624462.1|CB624462
EST:     GGATGGATCACATCGACAGGAATTCTCCTGCAAAGCCATCTCCTATAATG                         AATGGTGGTGATCCAGCATCTAGAAGCATCGATATAAAGCCTAGAATTTCA
genomic: GGATGGATCACATCGACAGGAATTCTCCTGCAAAGCCATCTCCTATAATGgtatggtaat ... gatttaatagAATGGTGGTGATCCAGCATCTAGAAGCATCGATATAAAGCCTAGAATTTCA
EST: gi|29630393|gb|CB635402.1|CB635402
EST:     GGATGGATCACATCGACAGGAATTCTCCTGCAAAGCCATCTCCTATAATG                         AATGGTGGTGATCCAGCATCTAGAAGCATCGATATAAAGCCTAGAATTTCA
genomic: GGATGGATCACATCGACAGGAATTCTCCTGCAAAGCCATCTCCTATAATGgtatggtaat ... gatttaatagAATGGTGGTGATCCAGCATCTAGAAGCATCGATATAAAGCCTAGAATTTCA
EST: gi|29625310|gb|CB630321.1|CB630321
EST:     GGATGGATCACATCGACAGGAATTCTCCTGCAAAGCCATCTCCTATAATG                         AATGGTGGTGATCCAGCATCTAGAAGCATCGATATAAAGCCTAGAATTTCA
genomic: GGATGGATCACATCGACAGGAATTCTCCTGCAAAGCCATCTCCTATAATGgtatggtaat ... gatttaatagAATGGTGGTGATCCAGCATCTAGAAGCATCGATATAAAGCCTAGAATTTCA
EST: gi|33675602|gb|CF303841.1|CF303841
EST:     GGATGGATCACATCGACAGGAATTCTCCTGCAAAGCCATCTCCTATAATG                         AATGGTGGTGATCCAGCATCTAGAAGCATCGATATAAAGCCTAGAATTTCA
genomic: GGATGGATCACATCGACAGGAATTCTCCTGCAAAGCCATCTCCTATAATGgtatggtaat ... gatttaatagAATGGTGGTGATCCAGCATCTAGAAGCATCGATATAAAGCCTAGAATTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaccttactgttagcaattgaaacacaatctgacttaattatggatttaatagAATGGTGGTGATCCAGCATCTAGAAGCATCGATATAAAGCCTAGAATTTCAGAAGAAAGGCCCGATAAAGCAAAACCCTGGGAGCTGATGGAAGTCCTAA
                                    ttaattatggatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggtaatccacagacgaaagatttcccaaagtttcatctgtttaatgcctctttgcttaccttactgttagcaattgaaacacaatctgacttaattatggatttaatagAATGGTGGTGATCCAGCATCTAGAAGCATCGATATAAAGCCTAGAATTTCAGAAGAAAGGCCCGATAAAGCAAAACCCTGGGAGCTGATGGAAGTCCTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG