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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcattttaacttttgatttcacctttttttttgagatactacatgcttatttagcctagagaaagtttttttcatttattcttgtattgcaatccctaactttgtgcaccgattggcttttttttgtttgatccagGGAGCGGACACAATCAGCCTCTGGTGCAG

Basic information

species Zea mays
transcript GRMZM2G057158_T02
intron # 5
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|26558010|gb|CA830245.1|CA830245
EST:     TCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAACTGGACA                         GGAGCGGACACAATCAGCCTCTGGTGCAG
genomic: TCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAACTGGACAgtgagcattt ... tttgatccagGGAGCGGACACAATCAGCCTCTGGTGCAG
EST: gi|21828621|gb|BQ703305.1|BQ703305
EST:     TCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAACTGGACA                         GGAGCGGACACAATCAGCCTCTGGTGCAG
genomic: TCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAACTGGACAgtgagcattt ... tttgatccagGGAGCGGACACAATCAGCCTCTGGTGCAG
EST: gi|67027074|gb|CO455823.1|CO455823
EST:     TCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAACTGGACA                         GGAGCGGACACAATCAGCCTCTGGTGCAG
genomic: TCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAACTGGACAgtgagcattt ... tttgatccagGGAGCGGACACAATCAGCCTCTGGTGCAG
EST: gi|87156460|gb|DY401249.1|DY401249
EST:     TCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAACTGGACA                         GGAGCGGACACAATCAGCCTCTGGTGCAG
genomic: TCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAACTGGACAgtgagcattt ... tttgatccagGGAGCGGACACAATCAGCCTCTGGTGCAG
EST: gi|113704257|gb|EE681761.1|EE681761
EST:     TCATTCCAGCAGTCTTTGATGTCACATCTTGGCCAACAACAAACTGGACA                         GGAGCGGACACAATCAGCCTCTGGTGCAG
genomic: TCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAACTGGACAgtgagcattt ... tttgatccagGGAGCGGACACAATCAGCCTCTGGTGCAG
EST: gi|78180947|gb|DV551320.1|DV551320
EST:     TCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAACTGGACA                         GGAGCGGACACAATCAGCCTCTGGTGCAG
genomic: TCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAACTGGACAgtgagcattt ... tttgatccagGGAGCGGACACAATCAGCCTCTGGTGCAG
EST: gi|94473208|gb|EB702166.1|EB702166
EST:     TCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAACTGGACA                         GGAGCGGACACAATCAGCCTCTGGTGCAG
genomic: TCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAACTGGACAgtgagcattt ... tttgatccagGGAGCGGACACAATCAGCCTCTGGTGCAG

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: 47 (upstream exon), 49 (downstream exon)
Score: 336

CAATTAATTTCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAACTGGACAgtgagcattt ... tttgatccagGGAGCGGACACAATCAGCCTCTGGTGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 345

CAATTAATTTCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAACTGGACAgtgagcattt ... tttgatccagGGAGCGGACACAATCAGCCTCTGGTGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 308

CAATTAATTTCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAACTGGACAgtgagcattt ... tttgatccagGGAGCGGACACAATCAGCCTCTGGTGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 280

CAATTAATTTCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAACTGGACAgtgagcattt ... tttgatccagGGAGCGGACACAATCAGCCTCTGGTGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtattgcaatccctaactttgtgcaccgattggcttttttttgtttgatccagGGAGCGGACACAATCAGCCTCTGGTGCAG
                                   cttttttttgttt  CT-rich tract
                                    ttttttttgtttgat  TA-rich tract