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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatcaattcaatgttgtttatgaagtgtgtgctgttcctttccttccacggtctctgttttttttttggaaaaaaaaatgattcttctttttttatactgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACAGCTCCAGAACCTTTGCAATGTCTATGCCCTCTACATTCTCCACAAGCAC

Basic information

species Zea mays
transcript GRMZM5G864319_T01
intron # 12
splice site 3'
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|78092060|gb|DV520434.1|DV520434
EST:     GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA                         GTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
genomic: GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
EST: gi|78089951|gb|DV518325.1|DV518325
EST:     AGTAGCTCACATCCAGTTGGTCATTGTAACCAA                         GTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
genomic: AGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
EST: gi|33104324|gb|CF064284.1|CF064284
EST:     GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA                         GTTCATTGCGAAGGT
genomic: GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGT
EST: gi|13382067|gb|BG458742.1|BG458742
EST:     GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA                         GTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
genomic: GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
EST: gi|71759064|gb|DR957001.1|DR957001
EST:     GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA                         GTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
genomic: GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
EST: gi|32835294|gb|CD974972.1|CD974972
EST:     GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA                         GTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
genomic: GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
EST: gi|149044449|gb|EE047570.2|EE047570
EST:     GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA                         GTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
genomic: GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
EST: gi|32834719|gb|CD974397.1|CD974397
EST:     GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA                         GTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
genomic: GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
EST: gi|113703173|gb|EE680677.1|EE680677
EST:     GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA                         GTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
genomic: GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
EST: gi|60395837|gb|DN228707.1|DN228707
EST:     GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA                         GTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
genomic: GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
EST: gi|19436236|gb|BM952646.1|BM952646
EST:     GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA                         GTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
genomic: GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
EST: gi|60356985|gb|DN223958.1|DN223958
EST:     GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA                         GTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
genomic: GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
EST: gi|213179269|gb|FM196444.1|FM196444
EST:     GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA                         GTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
genomic: GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
EST: gi|31405924|gb|CD484656.1|CD484656
EST:     GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA                         GTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
genomic: GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
EST: gi|9732140|gb|BE510892.1|BE510892
EST:     GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA                         GTTCATTGCGAAGGTACAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
genomic: GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
EST: gi|22490101|gb|BU050024.1|BU050024
EST:     GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA                         GTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
genomic: GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
EST: gi|19351144|gb|BM895676.1|BM895676
EST:     GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA                         GTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTG
genomic: GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTG
EST: gi|33101745|gb|CF061705.1|CF061705
EST:     GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA                         GTTCATTGCGAAGGT
genomic: GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGT
EST: gi|18655285|gb|BM500090.1|BM500090
EST:     TTTGCTAGAGGCNTGCAGTAGCTCACATCCAGTTGGTCATATGTAACCAA                         GTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAAC
genomic: TTTGCTAGAGGC-TGCAGTAGCTCACATCCAGTTGGTCAT-TGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAAC
EST: gi|60358249|gb|DN225222.1|DN225222
EST:     GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA                         GTTCATTGCGAAGGTACAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
genomic: GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
EST: gi|14204220|gb|BG837897.1|BG837897
EST:     GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA                         GTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
genomic: GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
EST: gi|87153521|gb|DY398310.1|DY398310
EST:     GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA                         GTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA
genomic: GATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACA

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), 46 (downstream exon)
Score: 116

GTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACAGCTCCAGAACCTTTGCAATGTCTATGCCCTCTACATTCTCCACAAGCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 355

GTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACAGCTCCAGAACCTTTGCAATGTCTATGCCCTCTACATTCTCCACAAGCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 501

GTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACAGCTCCAGAACCTTTGCAATGTCTATGCCCTCTACATTCTCCACAAGCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 458

GTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatca ... actgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACAGCTCCAGAACCTTTGCAATGTCTATGCCCTCTACATTCTCCACAAGCAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctgttttttttttggaaaaaaaaatgattcttctttttttatactgctatagGTTCATTTCGAAGGTGCAGCAGGACATTCCTGGACCTGGAGTGAAGGAACAGCTCCAGAACCTTTGCAATGTCTATGCCCTCTACATTCTCCACAAGCAC
                              ttcttctttttttata  CT-rich tract
      ttttttttttggaaaa  TA-rich tract