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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACAATAGGCTACGCCCGTTGAGCTATCGTGGCGCTGATGTTTTCCTGCTGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaatcttgccgcccactttctttgctctctctccatgaagtaccttagcttagtcaacctgttatcttgcactgacacatatatatttctgttgtcag

Basic information

species Oryza sativa
transcript LOC_Os02g58730.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58730.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G375002_T03 (Zea mays), 5'ss of exon 3
CTACAATAGGCTACGCCCGTTGAGCTATCGTGGCGCTGATGTTTTCCTGCTGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaatcttgccgcccactttctttgctctctctccatgaagtac---cttagcttagtcaacctgttatcttgca---ctgacacat-atatatttctgttgtcag------
 |||||||| || || ||||||||||||||||| ||||||||||| ||||| ||||||||||| |||||||||||||||||||||||||| ||||| ||||||||||  | |  | ||||||||||||  | |   | |  |  | | |   ||||  |   | | | | ||  ||||||   ||  || || |  | |   ||| ||         
TTACAATAGACTGCGTCCGTTGAGCTATCGTGGTGCTGATGTTTTTCTGCTCGCCTTTTCTCTTATCAGCAAAGCAAGCTATGAGAATGTCTCTAAGAAGgcaataatctttccctgcccactttcttgccccggccccggtttaatgcattcttatttattttagcttcttgacttgcatttcttgcatattacctgtgcatgtcgttttttccag

upper sequence: LOC_Os02g58730.2 (Oryza sativa), 5'ss of exon 3
lower sequence: AT4G35020.3 (Arabidopsis thaliana), 5'ss of exon 5
CTACAATAGGCTACGCCCGTTGAGCTATCGTGGCGCTGATGTTTTCCTGCTGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaatcttgccgcccactttctttgctctctctccatgaagtaccttagcttagtcaacctgttatcttgcactgacacatatatatttctgttgtcag
||||||||| ||| | || ||||||||||| || || ||||| ||| | || || || || ||  |||||||||| |||||||| ||||||||||||||||   | |  | | | |  |  ||     | || ||      |        |    | ||| |  ||| ||   | || |     || |   |||   || | ||
CTACAATAGACTAAGACCTTTGAGCTATCGCGGTGCAGATGTCTTCTTACTTGCATTCTCACTTGTCAGCAAAGCTAGCTATGAAAATGTTTCTAAAAAGgtt-tgatctgtggtcttctcctgaaacttctttcctgttttattcagtttacattcagtgattctgatagaatacatttg-gtatcttgcttttgattcttag
















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|218483315|gb|FG958115.1|FG958115
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|88362335|gb|CI608726.1|CI608726
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAAT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAAT
EST: gi|163919913|gb|EG714915.1|EG714915
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTC
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTC
EST: gi|30228239|gb|CB966130.1|CB966130
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|11233552|gb|AU164964.1|AU164964
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|58593555|gb|CF991863.1|CF991863
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|325493533|gb|JG458057.1|JG458057
EST:     TGGACTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTATCTAAAAAG                         TGGATACCTGAA
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAA
EST: gi|88832933|gb|CI369823.1|CI369823
EST:     CAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: CAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|86900291|gb|CI296334.1|CI296334
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGC
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGC
EST: gi|25807453|gb|CA763414.1|CA763414
EST:     TGGCCTNTTCTCTGATCAGCAAAGCAAGCTACGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|88410858|gb|CI578664.1|CI578664
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATAC-TGAATTA-GGCAT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCAT
EST: gi|30229558|gb|CB967449.1|CB967449
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCNATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|218501655|gb|FG956603.1|FG956603
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAA
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAA
EST: gi|88337442|gb|CI630739.1|CI630739
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGCAATTAAGGCATCATGCTC
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTG-AATTAAGGCATTATGCTC
EST: gi|4714260|gb|AU058227.1|AU058227
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|117226289|gb|CT846197.1|CT846197
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|32947879|gb|BP184451.1|BP184451
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|163920990|gb|EG710403.1|EG710403
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|33802327|gb|CF327037.1|CF327037
EST:     TGGCCTTTTCTCTGATCAGCGAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|86415824|gb|CI029835.1|CI029835
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCCATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|218499440|gb|FG950955.1|FG950955
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|218494722|gb|FG969779.1|FG969779
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|7134822|gb|AU082691.1|AU082691
EST:     CAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: CAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|25802725|gb|CA758686.1|CA758686
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|58591734|gb|CF990042.1|CF990042
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|3763167|gb|AU029919.1|AU029919
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|14980894|gb|BI305572.1|BI305572
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|58594206|gb|CF992514.1|CF992514
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
EST: gi|7134824|gb|AU082692.1|AU082692
EST:     TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAG                         TGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT
genomic: TGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaat ... ctgttgtcagTGGATACCTGAATTAAGGCATTATGCTCCTGGTGTGCCAATAATTCTCGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTACAATAGGCTACGCCCGTTGAGCTATCGTGGCGCTGATGTTTTCCTGCTGGCCTTTTCTCTGATCAGCAAAGCAAGCTATGAGAATGTTTCTAAAAAGgcaataaaatcttgccgcccactttctttgctctctctccatgaagtaccttagcttagtcaacctgttatcttgcactgacacatatatatttctgttgtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT