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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCCTTGTACAGAAGGACGCAGGCATACATTGAGCTTGCTGATCTGGAACTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAGgtgaagctcaagttcatcagaacatgttaaataccaccatatctccataatttgtgactcactgttgctgttctcttctcag

Basic information

species Oryza sativa
transcript LOC_Os04g28420.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g28420.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G154685_T01 (Zea mays), 5'ss of exon 10
AGGCCTTGTACAGAAGGACGCAGGCATACATTGAGCTTGCTGATCTGGAACTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAGgtgaagct-----caagttcatcag------aacatgttaaataccaccatatctccataatt-tgtgactcactgttg-ctgttctcttc-tcag-
||||||||||||||||| |||| |||||||| ||||||| ||| || || ||||||||||||||||| |||||||||||||| ||||||||||| |||||||     |     ||| ||| |         |   |   ||  |  |   |  || ||  ||  ||  | | |||  || || || ||    |||  
AGGCCTTGTACAGAAGGGCGCAAGCATACATCGAGCTTGTTGACCTAGAGCTAGCAGAGTTGGATGTGAAGAAAGCACTGGAAATTGATCCTGATAACAGgtatgattagtgccaaattctttgattcttaagtcttgcaaggattattgttgcttcagcatggtgaaattaactcctgactattttcgcgatcaag
















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|86412554|gb|CI066959.1|CI066959
EST:     CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAG                         GGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
genomic: CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAGgtgaagctca ... ctcttctcagGGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
EST: gi|218489779|gb|FG969223.1|FG969223
EST:     CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAG                         GGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
genomic: CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAGgtgaagctca ... ctcttctcagGGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
EST: gi|3762939|gb|AU029691.1|AU029691
EST:     TANCAGAGTTGGATGTCCAAGAAAGCACTGGAGATTGATCCTGACAACAG                         GGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACCA
genomic: TAGCAGAGTTGGATGT-CAAGAAAGCACTGGAGATTGATCCTGACAACAGgtgaagctca ... ctcttctcagGGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTA-CA
EST: gi|86506588|gb|CI149221.1|CI149221
EST:     CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAG                         GGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
genomic: CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAGgtgaagctca ... ctcttctcagGGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
EST: gi|89163178|gb|CI100068.1|CI100068
EST:     CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAG                         GGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
genomic: CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAGgtgaagctca ... ctcttctcagGGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
EST: gi|2312019|gb|C28174.1|C28174
EST:     CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAG                         GGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
genomic: CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAGgtgaagctca ... ctcttctcagGGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
EST: gi|218488949|gb|FG960628.1|FG960628
EST:     CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAG                         GGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
genomic: CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAGgtgaagctca ... ctcttctcagGGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
EST: gi|86484135|gb|CI126768.1|CI126768
EST:     AGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAG                         GGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
genomic: AGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAGgtgaagctca ... ctcttctcagGGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
EST: gi|86528735|gb|CI168941.1|CI168941
EST:     CTAGCAGAGTTGGGTGTCAAGAAAGCACTGGAGATTGATCCTGACAACAG                         GGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
genomic: CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAGgtgaagctca ... ctcttctcagGGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
EST: gi|86485367|gb|CI128000.1|CI128000
EST:     CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAG                         GGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
genomic: CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAGgtgaagctca ... ctcttctcagGGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
EST: gi|89181155|gb|CI045238.1|CI045238
EST:     CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAG                         GGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
genomic: CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAGgtgaagctca ... ctcttctcagGGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
EST: gi|89184352|gb|CI046917.1|CI046917
EST:     ACTGGAGATTGATCCTGACNACAG                         GGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
genomic: ACTGGAGATTGATCCTGACAACAGgtgaagctca ... ctcttctcagGGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
EST: gi|86528371|gb|CI168577.1|CI168577
EST:     CTAGCAGAGTTGGGTGTCAAGAAAGCACTGGAGATTGATCCTGACAACAG                         GGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
genomic: CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAGgtgaagctca ... ctcttctcagGGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
EST: gi|86832739|gb|CI345153.1|CI345153
EST:     CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAG                         GGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
genomic: CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAGgtgaagctca ... ctcttctcagGGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
EST: gi|88569754|gb|CI660929.1|CI660929
EST:     CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAG                         GGATGTGAAGATGGTGTATAAGAC
genomic: CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAGgtgaagctca ... ctcttctcagGGATGTGAAGATGGTGTATAAGAC
EST: gi|88849661|gb|CI089767.1|CI089767
EST:     CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAG                         GGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
genomic: CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAGgtgaagctca ... ctcttctcagGGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
EST: gi|15847220|gb|BI795496.1|BI795496
EST:     CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAG                         GGATGTGAAGATGGTGTATAAGACATTGAAGGAGTAAGATCAAGGAGTACA
genomic: CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAGgtgaagctca ... ctcttctcagGGATGTGAAGATGGTGTATAAGACATTGAAGGAG-AAGATCAAGGAGTACA
EST: gi|86427218|gb|CI072315.1|CI072315
EST:     CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAG                         GGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
genomic: CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAGgtgaagctca ... ctcttctcagGGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
EST: gi|8527213|gb|AU092028.1|AU092028
EST:     CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAG                         GGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
genomic: CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAGgtgaagctca ... ctcttctcagGGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
EST: gi|88989314|gb|CI043813.1|CI043813
EST:     CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAG                         GGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
genomic: CTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAGgtgaagctca ... ctcttctcagGGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
EST: gi|10794673|gb|AU108639.1|AU108639
EST:     TAGCCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGANCCTGACAACAG                         GGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
genomic: TAG-CAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAGgtgaagctca ... ctcttctcagGGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
EST: gi|86483317|gb|CI125950.1|CI125950
EST:     GCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAG                         GGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA
genomic: GCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAGgtgaagctca ... ctcttctcagGGATGTGAAGATGGTGTATAAGACATTGAAGGAGAAGATCAAGGAGTACAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCCTTGTACAGAAGGACGCAGGCATACATTGAGCTTGCTGATCTGGAACTAGCAGAGTTGGATGTCAAGAAAGCACTGGAGATTGATCCTGACAACAGgtgaagctcaagttcatcagaacatgttaaataccaccatatctccataatttgtgactcactgttgctgttctcttctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT