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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccagacagataagctaccattgcagataatagtgttgcttattagatctgtaacatcacacattatcacaccctgttgcattataattgattaac...

Basic information

species Zea mays
transcript GRMZM2G047855_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047855_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g55389.1 (Oryza sativa), 5'ss of exon 9
GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccagacagataagctaccattgcagataatagtgttgcttattagatctgtaacatcacacattatcacaccctgttgcattataattgattaac
||  |||||||||| |||||||| || || |||||||||||||||||||||||||||||||||||||||||||| |   |     || ||  |||    | | |         || |   | |||   |    | |||  |      |||  || |||      || ||
GCTGTAGATTTTCTTGATAAGCTTCTACGTTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagtctaccccgacagataatatttgttacattccaagaagatactgattttgtttgactggatatttcctatttatgtaacagtattgactgttcac
















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|71761092|gb|DR959029.1|DR959029
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|6095381|gb|AW120048.1|AW120048
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGNGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|149085357|gb|EE174864.2|EE174864
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|37388000|gb|CF631204.1|CF631204
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|31998439|gb|CD662075.1|CD662075
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|149097606|gb|EE183499.2|EE183499
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|211352561|gb|FL469240.1|FL469240
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAMCGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|32925527|gb|CF030339.1|CF030339
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|31997697|gb|CD661720.1|CD661720
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|60345677|gb|DN212650.1|DN212650
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|5607774|gb|AI901441.1|AI901441
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|7216891|gb|AW563013.1|AW563013
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAATCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGGGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|32924942|gb|CF029754.1|CF029754
EST:     GCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: GCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|71446426|gb|DR827476.1|DR827476
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|5525642|gb|AI861535.1|AI861535
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|110941068|gb|EE161225.1|EE161225
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|30705895|gb|CD058961.1|CD058961
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|14203981|gb|BG837658.1|BG837658
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|60340774|gb|DN207747.1|DN207747
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|7227707|gb|AW566348.1|AW566348
EST:     AGCTCCTGCGCTATGATCGCCAAGATAGGCTCACTGCACGTGAATCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|30706066|gb|CD059017.1|CD059017
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|148929900|gb|EE285653.2|EE285653
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|5922209|gb|AW055479.1|AW055479
EST:     AGCTCCTGCGCTATGATCCCCAAGATAGGCTCCCTGCACGTGAAGCTATG                         GCCCATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGACCAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|7135599|gb|AW498168.1|AW498168
EST:     AGCTCCTGCGCTATGATCNCCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|32870873|gb|CF010555.1|CF010555
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|149109954|gb|EE293763.2|EE293763
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|30087041|gb|CB885249.1|CB885249
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|149039472|gb|EE046612.2|EE046612
EST:     AGCTCCTGCGCTATGATCACCAAGATGGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|18177159|gb|BM378369.1|BM378369
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|67020854|gb|CO449603.1|CO449603
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
EST: gi|19436338|gb|BM952748.1|BM952748
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAA
EST: gi|6095382|gb|AW120049.1|AW120049
EST:     AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG                         GCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA
genomic: AGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 107

GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGACCACAATAATCGTTGTCTACACCCTCGAAATGAAGTTGTTGCTAATTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 171

GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGACCACAATAATCGTTGTCTACACCCTCGAAATGAAGTTGTTGCTAATTTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 177

GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGACCACAATAATCGTTGTCTACACCCTCGAAATGAAGTTGTTGCTAATTTC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 119

GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccaga ... ataaatgtagGCACATCCCTACTTCCTCCAAGTCAGAGCTGTGGAGAACAGTAGAACGAGACCACAATAATCGTTGTCTACACCCTCGAAATGAAGTTGTTGCTAATTTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATGgtaagccagacagataagctaccattgcagataatagtgttgcttattagatctgtaacatcacacattatcacaccctgttgcattataattgattaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC