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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ggcttgttcggttagctctcaatccatgtggattgagcgggattggatgggtttgaatcccaaacagctcaaactttttcacaattttttccaatcccatccaatccatgtgtattgggaataaccgaacaagcccttagTGGCATCGACTTCCCGGTCCTCTGGACACGTCACAAATAGTAGGCGATAATTCAAACTGTGGTTTCTTAGTGAAAATACAACTATGCCGCAATAATTAGC

Basic information

species Zea mays
transcript GRMZM2G056393_T01
intron # 20
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|84980317|gb|DW530666.1|DW530666
EST:     GAGTGATTCTTCTTTTTACAGAAGAACAAATTTTGTTTGCGAACTTTTAG                         TGGCATCGACTTCCCGGTCCTCTGGACACGTCACAAATAGTAGGCGATAAT
genomic: GAGTGATTCTTCTTTTTACAGAAGAACAAATTTTGTTTGCGAACTTTTAGggcttgttcg ... aagcccttagTGGCATCGACTTCCCGGTCCTCTGGACACGTCACAAATAGTAGGCGATAAT
EST: gi|211492457|gb|FL459662.1|FL459662
EST:     GAGTGATTCTTCTTTTTACAGAAGAACAAATTTTGTTTGCGAACTTTTAG                         TGGCATCGACTTCCCGGTCCTCTGGACACGTCACAAATAGTAGGCGATAAT
genomic: GAGTGATTCTTCTTTTTACAGAAGAACAAATTTTGTTTGCGAACTTTTAGggcttgttcg ... aagcccttagTGGCATCGACTTCCCGGTCCTCTGGACACGTCACAAATAGTAGGCGATAAT
EST: gi|61119855|gb|DN560816.1|DN560816
EST:     GAGTGATTCTTCTTTTTACAGAAGAACAAATTTTGTTTGCGAACTTTTAG                         TGGCATCGACTTCCCGGTCCTCTGGACACGTCACAAATAGTAGGCGATAAT
genomic: GAGTGATTCTTCTTTTTACAGAAGAACAAATTTTGTTTGCGAACTTTTAGggcttgttcg ... aagcccttagTGGCATCGACTTCCCGGTCCTCTGGACACGTCACAAATAGTAGGCGATAAT

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), 49 (downstream exon)
Score: 76

AGGATGTGCAGATGCAACTAGTGACCTCGTACCAGGCGGCCAAGGGCACAGAGTGATTCTTCTTTTTACAGAAGAACAAATTTTGTTTGCGAACTTTTAGggcttgttcg ... aagcccttagTGGCATCGACTTCCCGGTCCTCTGGACACGTCACAAATAGTAGGCGATAATTCAAACTGTGGTTTCTTAGTGAAAATACAACTATGCCGCAATAATTAGC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 66

AGGATGTGCAGATGCAACTAGTGACCTCGTACCAGGCGGCCAAGGGCACAGAGTGATTCTTCTTTTTACAGAAGAACAAATTTTGTTTGCGAACTTTTAGggcttgttcg ... aagcccttagTGGCATCGACTTCCCGGTCCTCTGGACACGTCACAAATAGTAGGCGATAATTCAAACTGTGGTTTCTTAGTGAAAATACAACTATGCCGCAATAATTAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 61

AGGATGTGCAGATGCAACTAGTGACCTCGTACCAGGCGGCCAAGGGCACAGAGTGATTCTTCTTTTTACAGAAGAACAAATTTTGTTTGCGAACTTTTAGggcttgttcg ... aagcccttagTGGCATCGACTTCCCGGTCCTCTGGACACGTCACAAATAGTAGGCGATAATTCAAACTGTGGTTTCTTAGTGAAAATACAACTATGCCGCAATAATTAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 61

AGGATGTGCAGATGCAACTAGTGACCTCGTACCAGGCGGCCAAGGGCACAGAGTGATTCTTCTTTTTACAGAAGAACAAATTTTGTTTGCGAACTTTTAGggcttgttcg ... aagcccttagTGGCATCGACTTCCCGGTCCTCTGGACACGTCACAAATAGTAGGCGATAATTCAAACTGTGGTTTCTTAGTGAAAATACAACTATGCCGCAATAATTAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttccaatcccatccaatccatgtgtattgggaataaccgaacaagcccttagTGGCATCGACTTCCCGGTCCTCTGGACACGTCACAAATAGTAGGCGATAATTCAAACTGTGGTTTCTTAGTGAAAATACAACTATGCCGCAATAATTAGC
                                 gaataac  putative branch site (score: 61)
                                                ccctt  putative PPT
                                  aataa  TA-rich tract