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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaagaaaggggctgttaaaaatttcgacttctggtgcaccgttcacggttcatcaatcagtgtttttctcccgaatggccggttgcagGGGATTCTGAACTTGGGGTTTGTTCCGGGGACCGATTCTGGCATCGGCAGACGGGATGTCAGCCCCCCTCGACCGACTTGCTAGGCCAT

Basic information

species Zea mays
transcript GRMZM2G355610_T01
intron # 1
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|31358202|gb|CD442559.1|CD442559
EST:     GCTCTCCTCGTGGACAAAACCACCGGCTCCCGATATCCAAATTGGAACAG                         GGGATTCTGAACTTGGGGTTTGTTCCGGGGACCGATTCTGGCATCGGCAGA
genomic: GCTCTCCTCGTGGACAAAACCACCGGCTCCCGATATCCAAATTGGAACAGgtaagaagaa ... ccggttgcagGGGATTCTGAACTTGGGGTTTGTTCCGGGGACCGATTCTGGCATCGGCAGA
EST: gi|211129916|gb|FL015856.1|FL015856
EST:     GCTCTCCTCGTGGACAAAACCACCGGCTCCCGATATCCAAATTGGAACAG                         GGGATTCTGAACTTGGGGTTTGTTCCGGGGACCGATTCTGGCATCGGCAGA
genomic: GCTCTCCTCGTGGACAAAACCACCGGCTCCCGATATCCAAATTGGAACAGgtaagaagaa ... ccggttgcagGGGATTCTGAACTTGGGGTTTGTTCCGGGGACCGATTCTGGCATCGGCAGA
EST: gi|211129911|gb|FL015851.1|FL015851
EST:     GCTCTCCTCGTGGACAAAACCACCGGCTCCCGATATCCAAATTGGAACAG                         GGGATTCTGAACTTGGGGTTTGTTCCGGGGACCGATTCTGGCATCGGCAGA
genomic: GCTCTCCTCGTGGACAAAACCACCGGCTCCCGATATCCAAATTGGAACAGgtaagaagaa ... ccggttgcagGGGATTCTGAACTTGGGGTTTGTTCCGGGGACCGATTCTGGCATCGGCAGA
EST: gi|211129914|gb|FL015854.1|FL015854
EST:     GCTCTCCTCGTGGACAAAACCACCGGCTCCCGATATCCAAATTGGAACAG                         GGGATTCTGAACTTGGGGTTTGTTCCGGGGACCGATTCTGGCATCGGCAGA
genomic: GCTCTCCTCGTGGACAAAACCACCGGCTCCCGATATCCAAATTGGAACAGgtaagaagaa ... ccggttgcagGGGATTCTGAACTTGGGGTTTGTTCCGGGGACCGATTCTGGCATCGGCAGA
EST: gi|67026420|gb|CO455169.1|CO455169
EST:     GCTCTTCTCGTGGACAAAACCACCGGCTCCCGATATCCAAATTGGAACAG                         GGGATTCTGAACTTGGGGTTTGTTCCGGGGACCGATTCTGGCATCGGCAGA
genomic: GCTCTCCTCGTGGACAAAACCACCGGCTCCCGATATCCAAATTGGAACAGgtaagaagaa ... ccggttgcagGGGATTCTGAACTTGGGGTTTGTTCCGGGGACCGATTCTGGCATCGGCAGA

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: 43 (upstream exon), 49 (downstream exon)
Score: 42

AAAGCAGAGCGGCAGACTGGCAGAGGCAGGCGCTCTCGGCTCTCCTCGTGGACAAAACCACCGGCTCCCGATATCCAAATTGGAACAGgtaagaagaa ... ccggttgcagGGGATTCTGAACTTGGGGTTTGTTCCGGGGACCGATTCTGGCATCGGCAGACGGGATGTCAGCCCCCCTCGACCGACTTGCTAGGCCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 64

AAAGCAGAGCGGCAGACTGGCAGAGGCAGGCGCTCTCGGCTCTCCTCGTGGACAAAACCACCGGCTCCCGATATCCAAATTGGAACAGgtaagaagaa ... ccggttgcagGGGATTCTGAACTTGGGGTTTGTTCCGGGGACCGATTCTGGCATCGGCAGACGGGATGTCAGCCCCCCTCGACCGACTTGCTAGGCCAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 96

AAAGCAGAGCGGCAGACTGGCAGAGGCAGGCGCTCTCGGCTCTCCTCGTGGACAAAACCACCGGCTCCCGATATCCAAATTGGAACAGgtaagaagaa ... ccggttgcagGGGATTCTGAACTTGGGGTTTGTTCCGGGGACCGATTCTGGCATCGGCAGACGGGATGTCAGCCCCCCTCGACCGACTTGCTAGGCCAT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 89

AAAGCAGAGCGGCAGACTGGCAGAGGCAGGCGCTCTCGGCTCTCCTCGTGGACAAAACCACCGGCTCCCGATATCCAAATTGGAACAGgtaagaagaa ... ccggttgcagGGGATTCTGAACTTGGGGTTTGTTCCGGGGACCGATTCTGGCATCGGCAGACGGGATGTCAGCCCCCCTCGACCGACTTGCTAGGCCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcaccgttcacggttcatcaatcagtgtttttctcccgaatggccggttgcagGGGATTCTGAACTTGGGGTTTGTTCCGGGGACCGATTCTGGCATCGGCAGACGGGATGTCAGCCCCCCTCGACCGACTTGCTAGGCCAT
                           tgttttt  TA-rich tract