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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtttacaagttttctatttgtctaagttttagcatattgtttctgaaacttcagcacaaaaaaacatctatggttgcccagaaccttgattgcttatttgctaaatttatattttaatatgcttactataagtatctctgcacgtgcagGTTGTGAACAGGATCCAAAAATTACGGAAGACTGCTCAGCTTGAACCTGCTGATCCAGTTGATGTGTATTACGAATCTGTGGGCAGTGACAAAAACACAC

Basic information

species Zea mays
transcript GRMZM2G158627_T02
intron # 9
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|71432888|gb|DR813938.1|DR813938
EST:     TAGATCTACGAGCTGACCAGTCATTGTTTGAAGCTGGAGTGGCTCGAGAG                         GTTGTGAACAGGATCCAAAAATTACGGAAGACTGCTCAGCTTGAACCTGCT
genomic: TAGATCTACGAGCTGACCAGTCATTGTTTGAAGCTGGAGTGGCTCGAGAGgtagtttaca ... gcacgtgcagGTTGTGAACAGGATCCAAAAATTACGGAAGACTGCTCAGCTTGAACCTGCT
EST: gi|40334151|gb|CK368221.1|CK368221
EST:     TAGATCTACGAGCTGACCAGTCATTGTTTGAAGCTGGAGTGGCTCGAGAG                         GTTGTGAACAGGATCCAAAAATTACGGAAGACTGCTCAGCTTGAACCTGCT
genomic: TAGATCTACGAGCTGACCAGTCATTGTTTGAAGCTGGAGTGGCTCGAGAGgtagtttaca ... gcacgtgcagGTTGTGAACAGGATCCAAAAATTACGGAAGACTGCTCAGCTTGAACCTGCT
EST: gi|78022271|gb|DV490658.1|DV490658
EST:     CGAGCTGACCAGTCATT-TTTGAAGCTGGAGTGGCTCGAGAG                         GTTGTGAACACGATCCAAAAATTACGGAAGACTGCTCAGCTTGAACCTGCT
genomic: CGAGCTGACCAGTCATTGTTTGAAGCTGGAGTGGCTCGAGAGgtagtttaca ... gcacgtgcagGTTGTGAACAGGATCCAAAAATTACGGAAGACTGCTCAGCTTGAACCTGCT
EST: gi|74240586|gb|DT648500.1|DT648500
EST:     TAGATCTACGAGCTGACCAGTCATTGTTTGAAGCTGGAGTGGCTCGAGAG                         GTTGTGAACAGGATCCAAAAATTACGGAAGACTGCTCAGCTTGAACCTGCT
genomic: TAGATCTACGAGCTGACCAGTCATTGTTTGAAGCTGGAGTGGCTCGAGAGgtagtttaca ... gcacgtgcagGTTGTGAACAGGATCCAAAAATTACGGAAGACTGCTCAGCTTGAACCTGCT
EST: gi|45568479|gb|CK986083.1|CK986083
EST:     TAGATCTACGAGCTGACCAGTCATTGTTTGAAGCTGGAGTGGCTCGAGAG                         GTTGTGAACAGGATCCAAAAATTACGGAAGACTGCTCAGCTTGAACCTGCT
genomic: TAGATCTACGAGCTGACCAGTCATTGTTTGAAGCTGGAGTGGCTCGAGAGgtagtttaca ... gcacgtgcagGTTGTGAACAGGATCCAAAAATTACGGAAGACTGCTCAGCTTGAACCTGCT
EST: gi|211108629|gb|FL325826.1|FL325826
EST:     TAGATCTACGAGCTGACCAGTCATTGTTTGAAGCTGGAGTGGCTCGAGAG                         GTTGTGAACAGGATCCAAAAATTACGGAAGACTGCTCAGCTTGAACCTGCT
genomic: TAGATCTACGAGCTGACCAGTCATTGTTTGAAGCTGGAGTGGCTCGAGAGgtagtttaca ... gcacgtgcagGTTGTGAACAGGATCCAAAAATTACGGAAGACTGCTCAGCTTGAACCTGCT

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), 48 (downstream exon)
Score: 165

GCGACGTTTTAGTCATTTTAGATCTACGAGCTGACCAGTCATTGTTTGAAGCTGGAGTGGCTCGAGAGgtagtttaca ... gcacgtgcagGTTGTGAACAGGATCCAAAAATTACGGAAGACTGCTCAGCTTGAACCTGCTGATCCAGTTGATGTGTATTACGAATCTGTGGGCAGTGACAAAAACACAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 66

GCGACGTTTTAGTCATTTTAGATCTACGAGCTGACCAGTCATTGTTTGAAGCTGGAGTGGCTCGAGAGgtagtttaca ... gcacgtgcagGTTGTGAACAGGATCCAAAAATTACGGAAGACTGCTCAGCTTGAACCTGCTGATCCAGTTGATGTGTATTACGAATCTGTGGGCAGTGACAAAAACACAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 121

GCGACGTTTTAGTCATTTTAGATCTACGAGCTGACCAGTCATTGTTTGAAGCTGGAGTGGCTCGAGAGgtagtttaca ... gcacgtgcagGTTGTGAACAGGATCCAAAAATTACGGAAGACTGCTCAGCTTGAACCTGCTGATCCAGTTGATGTGTATTACGAATCTGTGGGCAGTGACAAAAACACAC


Block sizes: 43 (upstream exon), 44 (downstream exon)
Score: 29

GCGACGTTTTAGTCATTTTAGATCTACGAGCTGACCAGTCATTGTTTGAAGCTGGAGTGGCTCGAGAGgtagtttaca ... gcacgtgcagGTTGTGAACAGGATCCAAAAATTACGGAAGACTGCTCAGCTTGAACCTGCTGATCCAGTTGATGTGTATTACGAATCTGTGGGCAGTGACAAAAACACAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttgctaaatttatattttaatatgcttactataagtatctctgcacgtgcagGTTGTGAACAGGATCCAAAAATTACGGAAGACTGCTCAGCTTGAACCTGCTGATCCAGTTGATGTGTATTACGAATCTGTGGGCAGTGACAAAAACACAC
                         tgcttac  putative branch site (score: 29)
                                        tctctgc  putative PPT
       taaatttatattttaa  TA-rich tract