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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAAGATTTTGTTGTCTTGACGGAGCTTCTTATGATGGAGCTGCTGAAACTTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggccattatacatctcaacatgattggtcatggcttatctcatataatacaaattcaattactagtactggtgctgaaatattggtcatccta...

Basic information

species Oryza sativa
transcript LOC_Os01g61500.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g61500.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G014720_T01 (Zea mays), 5'ss of exon 3
TAAAGATTTTGTTGTCTTGACGGAGCTTCTTATGATGGAGCTGCTGAAACTTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggccattatacatctc-aacatgattggtcatggcttatctcatataata-caaattcaattactagtactggtgctgaaatattggtcatccta
|||||| |||||||||||||||||||| ||||||||| ||||||||||||| |||||||| || || || ||||||||||||||||| |||||||||||||||||      |  |  |    |  | ||  |    | ||    ||||   || | |    |||  |      | | || |  |||  || ||  ||||   
TAAAGAATTTGTTGTCTTGACGGAGCTGCTTATGATGCAGCTGCTGAAACTCGATGGCATTGAAGCTGAAGGAGAAGCAAGGGCACAGAGGAAGGCTGAGgtacacaactaaacaatcgctgctgatattttcaaacgtgctacatcttcaatgagaatgcattacagcgactgaaatgtttatgatgtaatg--catcagg

upper sequence: LOC_Os01g61500.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G046418_T01 (Zea mays), 5'ss of exon 3
TAAAGATTTTGTTGTCTTGACGGAGCTTCTTATGATGGAGCTGCTGAAACTTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggccattatacatctcaaca-tgattggtcatggcttatctcatataatacaaattcaattactagtactggtgctgaaatattg-gtcatccta-
|||||| ||||| ||||||||||| || ||||||||  ||||||||||||| |||||||| || || || ||||||||||||||||| |||||||||||||||||    | |  | || |        || ||   || |   || ||  |  |||   ||| || ||||   |||||        ||  ||   |  |  | 
TAAAGAATTTGTCGTCTTGACGGAACTGCTTATGATACAGCTGCTGAAACTCGATGGCATCGAAGCTGAAGGAGAAGCAAGGGCACAGAGGAAGGCTGAGgtaca-caactaaaacacttgctgctgctgttttcacacgtgcta-cttgttcaatgagaatgca-ttacagctactgaaatatttatgatgtaacgcctcag
















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|86415279|gb|CI069682.1|CI069682
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGGAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|88850183|gb|CI091676.1|CI091676
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|33675385|gb|CF303624.1|CF303624
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|33676925|gb|CF305164.1|CF305164
EST:     AGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: AGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|88475199|gb|CI412470.1|CI412470
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAG
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGT-GTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAG
EST: gi|33676487|gb|CF304726.1|CF304726
EST:     TGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|86542293|gb|CI182499.1|CI182499
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|88469155|gb|CI406426.1|CI406426
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|88477386|gb|CI414657.1|CI414657
EST:     GGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: GGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|88451090|gb|CI534083.1|CI534083
EST:     CAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: CAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|86504097|gb|CI146730.1|CI146730
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|66927949|gb|CX114797.1|CX114797
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|86599345|gb|CI251303.1|CI251303
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|88376312|gb|CI533214.1|CI533214
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|88963710|gb|CI029483.1|CI029483
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|88473485|gb|CI410756.1|CI410756
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGTTGTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|33674802|gb|CF303041.1|CF303041
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|88487843|gb|CI425114.1|CI425114
EST:     GGCATNAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: GGCAT-AGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|86420400|gb|CI056389.1|CI056389
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|218486310|gb|FG947933.1|FG947933
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCGAGGTCTTGTGGAGAC
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGAC
EST: gi|86835390|gb|CI347847.1|CI347847
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|22305160|gb|BQ906382.1|BQ906382
EST:     TGATGGCATAGAGGCANGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TGATGGCATAGAGGCA-GAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|58685366|gb|CK074053.1|CK074053
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|89188214|gb|CI115463.1|CI115463
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|218494744|gb|FG957721.1|FG957721
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGACACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|88256833|gb|CI354614.1|CI354614
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|33675145|gb|CF303384.1|CF303384
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|88469156|gb|CI406427.1|CI406427
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|88516400|gb|CI444054.1|CI444054
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|86842371|gb|CI335269.1|CI335269
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCGAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|33675421|gb|CF303660.1|CF303660
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|89192518|gb|CI016527.1|CI016527
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|86433949|gb|CI094292.1|CI094292
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
EST: gi|33676869|gb|CF305108.1|CF305108
EST:     TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAG                         GTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA
genomic: TTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggc ... tgcattgcagGTACGCCGTGTCCAAGGTCTTGTGGAGACGTTGGATAAGCTGAAGGCAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAAGATTTTGTTGTCTTGACGGAGCTTCTTATGATGGAGCTGCTGAAACTTGATGGCATAGAGGCAGAGGGAGAAGCAAGGGCACAAAGGAAGGCTGAGgtacagtggccattatacatctcaacatgattggtcatggcttatctcatataatacaaattcaattactagtactggtgctgaaatattggtcatccta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA