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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGATTTATACTGTATGGGATTCCTGGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAGgtatgatcaagcagttctattattgatatacttgtttcttctatatgttgcttgacttgcttctaaagttcacgagctctgtcgcag

Basic information

species Zea mays
transcript GRMZM2G411333_T01
intron # 8
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|5871584|gb|AW018055.1|AW018055
EST:     AGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAG                         ACTTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
genomic: AGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAGgtatgatcaa ... tctgtcgcagACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
EST: gi|71309093|gb|DR790816.1|DR790816
EST:     CCTCTTAGGAG                         ACCGGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
genomic: CCTCTTAGGAGgtatgatcaa ... tctgtcgcagACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
EST: gi|78105425|gb|DV523843.1|DV523843
EST:     GGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAG                         ACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
genomic: GGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAGgtatgatcaa ... tctgtcgcagACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
EST: gi|6031461|gb|AW076363.1|AW076363
EST:     GGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAG                         ACTTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
genomic: GGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAGgtatgatcaa ... tctgtcgcagACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
EST: gi|91051044|gb|EB161462.1|EB161462
EST:     GGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAG                         ACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
genomic: GGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAGgtatgatcaa ... tctgtcgcagACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
EST: gi|32836424|gb|CD976102.1|CD976102
EST:     ACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAG                         ACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
genomic: ACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAGgtatgatcaa ... tctgtcgcagACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
EST: gi|5901323|gb|AW042423.1|AW042423
EST:     GGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAG                         ACTTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
genomic: GGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAGgtatgatcaa ... tctgtcgcagACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
EST: gi|78022284|gb|DV490671.1|DV490671
EST:     GGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAG                         ACTTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
genomic: GGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAGgtatgatcaa ... tctgtcgcagACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
EST: gi|32836575|gb|CD976253.1|CD976253
EST:     ACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAG                         ACCTGGTCCTCTCAACCAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
genomic: ACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAGgtatgatcaa ... tctgtcgcagACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
EST: gi|71443427|gb|DR824477.1|DR824477
EST:     GGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCTTCTTAGGAG                         ACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
genomic: GGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAGgtatgatcaa ... tctgtcgcagACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
EST: gi|93283751|gb|EB676015.1|EB676015
EST:     GGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAG                         ACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
genomic: GGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAGgtatgatcaa ... tctgtcgcagACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
EST: gi|149010273|gb|EE042100.2|EE042100
EST:     GGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTTTTAGGAG                         ACCTGGTCCTTTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
genomic: GGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAGgtatgatcaa ... tctgtcgcagACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
EST: gi|211364468|gb|FL432340.1|FL432340
EST:     GGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAG                         ACTTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
genomic: GGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAGgtatgatcaa ... tctgtcgcagACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
EST: gi|50335616|gb|CO530742.1|CO530742
EST:     GGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAG                         ACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
genomic: GGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAGgtatgatcaa ... tctgtcgcagACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
EST: gi|5668501|gb|AI932016.1|AI932016
EST:     GGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAG                         ACTTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA
genomic: GGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAGgtatgatcaa ... tctgtcgcagACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTA

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: 39 (upstream exon), 24 (downstream exon)
Score: 2

AATGATTTATACTGTATGGGATTCCTGGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAGgtatgatcaa ... tctgtcgcagACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACT


Block sizes: 41 (upstream exon), 17 (downstream exon)
Score: 6

AATGATTTATACTGTATGGGATTCCTGGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAGgtatgatcaa ... tctgtcgcagACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACT


Block sizes: 47 (upstream exon), 24 (downstream exon)
Score: 9

AATGATTTATACTGTATGGGATTCCTGGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAGgtatgatcaa ... tctgtcgcagACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACT


Block sizes: 45 (upstream exon), 11 (downstream exon)
Score: 5

AATGATTTATACTGTATGGGATTCCTGGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAGgtatgatcaa ... tctgtcgcagACCTGGTCCTCTCAAACAAACTAGTAGTTTATGACTTGGAAAAAGAAGTTATTGGATGGACAGACTACAACT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGATTTATACTGTATGGGATTCCTGGATGGTGGTGTACAGACTAAAGATGGGAAAGATATGCTCCTCTTAGGAGgtatgatcaagcagttctattattgatatacttgtttcttctatatgttgcttgacttgcttctaaagttcacgagctctgtcgcag

- - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC