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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGGCGTTTGGGGATCATGGCGGCGCGGGCGGCTGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAGgtgggtgcgggcgacccaggctgatctcctcttgcattgtttgctgcgtcgcgagtccatgcctccatggttctgatctcctgatttgtgcag

Basic information

species Zea mays
transcript GRMZM2G138886_T01
intron # 2
splice site 5'
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|211247234|gb|FL156674.1|FL156674
EST:     TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAG                         ACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
genomic: TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAGgtgggtgcgg ... atttgtgcagACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
EST: gi|211249461|gb|FL156681.1|FL156681
EST:     TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAG                         ACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
genomic: TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAGgtgggtgcgg ... atttgtgcagACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
EST: gi|148972285|gb|EE023184.2|EE023184
EST:     TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAG                         ACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
genomic: TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAGgtgggtgcgg ... atttgtgcagACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
EST: gi|211249468|gb|FL156688.1|FL156688
EST:     TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAG                         ACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
genomic: TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAGgtgggtgcgg ... atttgtgcagACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
EST: gi|76283026|gb|DV022594.1|DV022594
EST:     TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAG                         ACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
genomic: TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAGgtgggtgcgg ... atttgtgcagACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
EST: gi|71319363|gb|DR796428.1|DR796428
EST:     TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAG                         ACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
genomic: TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAGgtgggtgcgg ... atttgtgcagACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
EST: gi|211249467|gb|FL156687.1|FL156687
EST:     TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAG                         ACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
genomic: TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAGgtgggtgcgg ... atttgtgcagACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
EST: gi|50324450|gb|CO519576.1|CO519576
EST:     TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAG                         ACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
genomic: TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAGgtgggtgcgg ... atttgtgcagACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
EST: gi|76294034|gb|DV033602.1|DV033602
EST:     TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAG                         ACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
genomic: TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAGgtgggtgcgg ... atttgtgcagACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
EST: gi|211249466|gb|FL156686.1|FL156686
EST:     TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAG                         ACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
genomic: TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAGgtgggtgcgg ... atttgtgcagACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
EST: gi|211004196|gb|FK981412.1|FK981412
EST:     TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAG                         ACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
genomic: TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAGgtgggtgcgg ... atttgtgcagACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
EST: gi|211004197|gb|FK981413.1|FK981413
EST:     TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAG                         ACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
genomic: TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAGgtgggtgcgg ... atttgtgcagACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
EST: gi|71439376|gb|DR820426.1|DR820426
EST:     TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAG                         ACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
genomic: TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAGgtgggtgcgg ... atttgtgcagACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
EST: gi|30307157|gb|CD001830.1|CD001830
EST:     TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAG                         ACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
genomic: TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAGgtgggtgcgg ... atttgtgcagACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
EST: gi|149081651|gb|EE170801.2|EE170801
EST:     TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAG                         ACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
genomic: TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAGgtgggtgcgg ... atttgtgcagACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
EST: gi|211249462|gb|FL156682.1|FL156682
EST:     TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAG                         ACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG
genomic: TGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAGgtgggtgcgg ... atttgtgcagACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTG

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: 124

GTCGGCGTTTGGGGATCATGGCGGCGCGGGCGGCTGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAGgtgggtgcgg ... atttgtgcagACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCA


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 4

GTCGGCGTTTGGGGATCATGGCGGCGCGGGCGGCTGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAGgtgggtgcgg ... atttgtgcagACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCA


Block sizes: 29 (upstream exon), 24 (downstream exon)
Score: 2

GTCGGCGTTTGGGGATCATGGCGGCGCGGGCGGCTGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAGgtgggtgcgg ... atttgtgcagACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCA


Block sizes: 40 (upstream exon), 45 (downstream exon)
Score: 5

GTCGGCGTTTGGGGATCATGGCGGCGCGGGCGGCTGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAGgtgggtgcgg ... atttgtgcagACATGGCGAGCCGGCGCGCGCTCACGGACATCAAGAACCTCGTCGGGGCTGCCCCGTACCCCTACGCCGTCGCCAAGAAGCCCATGCTGCA


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCGGCGTTTGGGGATCATGGCGGCGCGGGCGGCTGACGAGAACAGGAGACCGGCGGCAGGGAAGCCCGCGCCAGGCGTCCGAGgtgggtgcgggcgacccaggctgatctcctcttgcattgtttgctgcgtcgcgagtccatgcctccatggttctgatctcctgatttgtgcag

- - - - - - - - - - - - - - - - - - - - - - AGGAGA