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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGTGCAGCGAAAAGGGGTATGATTCTCTATCTGTGAGTGATGCAAAGCAAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttagtcggggtgtttgggactgcttcactccacggaatctagcttagcttcataaaactctagccaaacactctcaacttcatcagctcagctt...

Basic information

species Zea mays
transcript GRMZM2G121452_T01
intron # 5
splice site 5'
intron type U2

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|78118214|gb|DV536601.1|DV536601
EST:     AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
EST: gi|50322448|gb|CO517574.1|CO517574
EST:     AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
EST: gi|31350060|gb|CD434417.1|CD434417
EST:     AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAAGAACG
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACG
EST: gi|76925420|gb|DV170446.1|DV170446
EST:     AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGG-G
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
EST: gi|32858209|gb|CD997890.1|CD997890
EST:     AAATGCTTATGTTCAGTTCTGACCTAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
EST: gi|33101497|gb|CF061457.1|CF061457
EST:     AAATGCTTATGTTCAGTTCTGACCTAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
EST: gi|76290008|gb|DV029576.1|DV029576
EST:     AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
EST: gi|50322447|gb|CO517573.1|CO517573
EST:     AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
EST: gi|71447603|gb|DR828653.1|DR828653
EST:     AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGGATTGGGAGATTAGGAACGGTGCTGT
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAAT-GGGAGATTAAGAACGGTGCTGT
EST: gi|74245478|gb|DT653392.1|DT653392
EST:     AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAN                         GAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
EST: gi|74246334|gb|DT654248.1|DT654248
EST:     AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
EST: gi|76285525|gb|DV025093.1|DV025093
EST:     AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAANGCG
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
EST: gi|32910062|gb|CF014874.1|CF014874
EST:     AAATGCTTATGTTCAGTTCTGACCTAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
EST: gi|211410327|gb|FL477489.1|FL477489
EST:     AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
EST: gi|71421222|gb|DR805345.1|DR805345
EST:     AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTTTTCCAGAAGGCG
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
EST: gi|32944421|gb|CF049240.1|CF049240
EST:     GTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
genomic: GTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
EST: gi|78123250|gb|DV541634.1|DV541634
EST:     AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
EST: gi|32907102|gb|CF011915.1|CF011915
EST:     AAATGCTTATGTTCAGTTCTGACCTAGATCTGCACGAGTACATCACTGAG                         GTGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
EST: gi|76290007|gb|DV029575.1|DV029575
EST:     AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGGG
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
EST: gi|33104279|gb|CF064239.1|CF064239
EST:     AAATGCTTATGTTCAGTTCTGACCTAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
EST: gi|71444673|gb|DR825723.1|DR825723
EST:     AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
EST: gi|31351657|gb|CD436014.1|CD436014
EST:     AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
EST: gi|91049533|gb|EB159951.1|EB159951
EST:     AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAAGAACGGTGC
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGC
EST: gi|76282323|gb|DV021891.1|DV021891
EST:     AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
EST: gi|93282632|gb|EB674896.1|EB674896
EST:     AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAGGAACGGTGCT
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCT
EST: gi|211394133|gb|FL452938.1|FL452938
EST:     AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
EST: gi|76014276|gb|DT941446.1|DT941446
EST:     AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTTTTCCAGAAGGCG
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
EST: gi|31352805|gb|CD437162.1|CD437162
EST:     AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
EST: gi|31355614|gb|CD439971.1|CD439971
EST:     AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAG                         GAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG
genomic: AAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCG

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: 431

TGGGTGCAGCGAAAAGGGGTATGATTCTCTATCTGTGAGTGATGCAAAGCAAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCGAAGGAATCACAGCCCTGCAAGGAGATCCCATCCTTGCAGCTTATCAACC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 364

TGGGTGCAGCGAAAAGGGGTATGATTCTCTATCTGTGAGTGATGCAAAGCAAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCGAAGGAATCACAGCCCTGCAAGGAGATCCCATCCTTGCAGCTTATCAACC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 271

TGGGTGCAGCGAAAAGGGGTATGATTCTCTATCTGTGAGTGATGCAAAGCAAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCGAAGGAATCACAGCCCTGCAAGGAGATCCCATCCTTGCAGCTTATCAACC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 295

TGGGTGCAGCGAAAAGGGGTATGATTCTCTATCTGTGAGTGATGCAAAGCAAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttag ... tcgttaacagGAGCACCCGGAATGGGAGATTAAGAACGGTGCTGTCTTCTTCCAGAAGGCGAAGGAATCACAGCCCTGCAAGGAGATCCCATCCTTGCAGCTTATCAACC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGTGCAGCGAAAAGGGGTATGATTCTCTATCTGTGAGTGATGCAAAGCAAATGCTTATGTTCAGTTCTGACCAAGATCTGCACGAGTACATCACTGAGgtaaccttagtcggggtgtttgggactgcttcactccacggaatctagcttagcttcataaaactctagccaaacactctcaacttcatcagctcagctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cataaaac