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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtatttctcgtcacgagttgttatccactggatttattctctacttttgtgaaatttctttgttcttcacttttcag

Basic information

species Zea mays
transcript GRMZM2G058366_T01
intron # 13
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|88746461|gb|DY530602.1|DY530602
EST:     TGTTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT                         GTTTTTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
genomic: TG-TTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
EST: gi|148965008|gb|EE015841.2|EE015841
EST:     TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT                         GTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
genomic: TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
EST: gi|211324539|gb|FL445891.1|FL445891
EST:     TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT                         GTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
genomic: TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
EST: gi|18163479|gb|BM333318.1|BM333318
EST:     TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT                         GTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
genomic: TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
EST: gi|5069977|gb|AI737942.1|AI737942
EST:     TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT                         GTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
genomic: TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
EST: gi|211158731|gb|FL327701.1|FL327701
EST:     TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT                         GTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAA
genomic: TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAA
EST: gi|32865528|gb|CF005210.1|CF005210
EST:     TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT                         GTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
genomic: TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
EST: gi|5361078|gb|AI795693.1|AI795693
EST:     GATGTTGATGGTGGTAACAGCCGGACT                         GTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
genomic: GATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
EST: gi|211198572|gb|FL471183.1|FL471183
EST:     TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT                         GTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
genomic: TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
EST: gi|211340444|gb|FL354255.1|FL354255
EST:     TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT                         GTTTCTGAGAAGAAGGGCTAAA
genomic: TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGG-CTAAA
EST: gi|5005902|gb|AI711964.1|AI711964
EST:     AGATCGATGTTGATGGTGGTAACAGCCGGACT                         GTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
genomic: AGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
EST: gi|211435902|gb|FL357604.1|FL357604
EST:     TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT                         GTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
genomic: TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
EST: gi|20803409|gb|BQ294459.1|BQ294459
EST:     TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT                         GTTTCTGAGAAGAAGGCTAAAG
genomic: TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAG
EST: gi|211522124|gb|FL314742.1|FL314742
EST:     TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT                         GTTTCTGAGAAGAAGGCTAAAGCAT
genomic: TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCAT
EST: gi|15100485|gb|BI396276.1|BI396276
EST:     TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT                         GTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
genomic: TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
EST: gi|60353761|gb|DN220734.1|DN220734
EST:     TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT                         GTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
genomic: TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
EST: gi|211093130|gb|FL308874.1|FL308874
EST:     TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT                         GTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
genomic: TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
EST: gi|16921014|gb|BM074941.1|BM074941
EST:     TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT                         GTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
genomic: TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
EST: gi|211514505|gb|FL430894.1|FL430894
EST:     TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT                         GTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
genomic: TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
EST: gi|16916424|gb|BM072835.1|BM072835
EST:     TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT                         GTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
genomic: TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
EST: gi|211267809|gb|FL345566.1|FL345566
EST:     TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT                         GTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
genomic: TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
EST: gi|149062811|gb|EE157528.2|EE157528
EST:     TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT                         GTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
genomic: TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
EST: gi|148965007|gb|EE015840.2|EE015840
EST:     TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT                         GTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
genomic: TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
EST: gi|78021263|gb|DV489650.1|DV489650
EST:     TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT                         GTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
genomic: TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
EST: gi|86469050|gb|DY235420.1|DY235420
EST:     TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT                         GTTTTTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
genomic: TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCC
EST: gi|211165712|gb|FL359024.1|FL359024
EST:     TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACT                         GTTTCTGAGAAGAAGGCT
genomic: TTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCT

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: 49 (upstream exon), 48 (downstream exon)
Score: 346

GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCCTACTTTGAGACGTCGGCTAAAGAGGGCTTCAATGTAGAGGCTGCATTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 274

GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCCTACTTTGAGACGTCGGCTAAAGAGGGCTTCAATGTAGAGGCTGCATTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 225

GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCCTACTTTGAGACGTCGGCTAAAGAGGGCTTCAATGTAGAGGCTGCATTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 377

GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtattt ... cacttttcagGTTTCTGAGAAGAAGGCTAAAGCATGGTGTGCTTCAAAGGGAAACATCCCCTACTTTGAGACGTCGGCTAAAGAGGGCTTCAATGTAGAGGCTGCATTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCAGCCCATCAGACCCAGAGAATTTCCCATTTGTTGTGCTTGGTAACAAGATCGATGTTGATGGTGGTAACAGCCGGACTgtgagtatttctcgtcacgagttgttatccactggatttattctctacttttgtgaaatttctttgttcttcacttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG