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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttacgtatatgtccagactccagatcgactccaccagggcaccagcagagacgtgatcacgtactcacgtggtgcctttctctcagtttctccgagactacgtgcacgtttcatggaaaccggttcatgactctggggggacgtgtatttccacagGAGTGCAGCGGCTGTGGCGGGTGAGGGGTCGAGGACTACGCACAGAATTGCGTTCCGAGTGAGGTCGGACGAGGACGAGGTACTCGACGACGGCTACAAA

Basic information

species Zea mays
transcript GRMZM2G101405_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|32862978|gb|CF002660.1|CF002660
EST:     GCCGAGCGCGTCGTCCCGGACGCTGCTGCAGGCTACAGTAGTCATACTAG                         GAGTGCAGCGGCTGTGGCGGGTGAGGGGTCGAGGACTACGCACAGAATTGC
genomic: GCCGAGCGCGTCGTCCCGGACGCTGCTGCAGGCTACAGTAGTCATACTAGgtgagttacg ... atttccacagGAGTGCAGCGGCTGTGGCGGGTGAGGGGTCGAGGACTACGCACAGAATTGC
EST: gi|32863173|gb|CF002855.1|CF002855
EST:     GCCGAGCGCGTCGTCCCGGACGCTGCTGCAGGCTACAGTAGTCATACTAG                         GAGTGCAGCGGCTGTGGCGGGTGAGGGGTCGAGGACTACGCACAGAATTGC
genomic: GCCGAGCGCGTCGTCCCGGACGCTGCTGCAGGCTACAGTAGTCATACTAGgtgagttacg ... atttccacagGAGTGCAGCGGCTGTGGCGGGTGAGGGGTCGAGGACTACGCACAGAATTGC

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 3 RNA-Seq libraries.


Block sizes: 42 (upstream exon), 8 (downstream exon)
Score: 1

TCCCGGCAGCTGTACCTGGTGCGTTCGCGCCGCCGCCGCCGCTTATGCCGGCCGAGCGCGTCGTCCCGGACGCTGCTGCAGGCTACAGTAGTCATACTAGgtgagttacg ... atttccacagGAGTGCAGCGGCTGTGGCGGGTGAGGGGTCGAGGACTACGCACAGAATTGCGTTCCGAGTGAGGTCGGACGAGGACGAGGTACTCGACGACGGCTACAAA


Block sizes: 47 (upstream exon), 29 (downstream exon)
Score: 4

TCCCGGCAGCTGTACCTGGTGCGTTCGCGCCGCCGCCGCCGCTTATGCCGGCCGAGCGCGTCGTCCCGGACGCTGCTGCAGGCTACAGTAGTCATACTAGgtgagttacg ... atttccacagGAGTGCAGCGGCTGTGGCGGGTGAGGGGTCGAGGACTACGCACAGAATTGCGTTCCGAGTGAGGTCGGACGAGGACGAGGTACTCGACGACGGCTACAAA


Block sizes: 27 (upstream exon), 23 (downstream exon)
Score: 1

TCCCGGCAGCTGTACCTGGTGCGTTCGCGCCGCCGCCGCCGCTTATGCCGGCCGAGCGCGTCGTCCCGGACGCTGCTGCAGGCTACAGTAGTCATACTAGgtgagttacg ... atttccacagGAGTGCAGCGGCTGTGGCGGGTGAGGGGTCGAGGACTACGCACAGAATTGCGTTCCGAGTGAGGTCGGACGAGGACGAGGTACTCGACGACGGCTACAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcacgtttcatggaaaccggttcatgactctggggggacgtgtatttccacagGAGTGCAGCGGCTGTGGCGGGTGAGGGGTCGAGGACTACGCACAGAATTGCGTTCCGAGTGAGGTCGGACGAGGACGAGGTACTCGACGACGGCTACAAA
                                            tatttcc  CT-rich tract
                                          tgtattt  TA-rich tract