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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGGAGGGCGGTGGCGGCGCAGTCGCTGCGGACGACCGCCACCGAGACGCTGACGGCGGATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAGgtgagtggcatcctttagctcttctgccttctccttgcacgtttgattgcttggcggtattagtgtacagctcctttccatttctgtgtgcgttggtgct...

Basic information

species Zea mays
transcript GRMZM2G144730_T01
intron # 1
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|148966755|gb|EE017835.2|EE017835
EST:     TGACGGCGGATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAG                         ATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGGCAGCTATTGCAAAT
genomic: TGACGGCGGATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAGgtgagtggca ... tctgatgcagATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGGCAGCTATTGCAAAT
EST: gi|88749445|gb|DY533586.1|DY533586
EST:     TGACGGCGGATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAG                         ATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGGCAGCTATTGCAAAT
genomic: TGACGGCGGATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAGgtgagtggca ... tctgatgcagATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGGCAGCTATTGCAAAT
EST: gi|88754995|gb|DY539136.1|DY539136
EST:     TGACGGCGGATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAG                         ATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGGCAGCTATTGCAAAT
genomic: TGACGGCGGATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAGgtgagtggca ... tctgatgcagATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGGCAGCTATTGCAAAT
EST: gi|94474601|gb|EB703559.1|EB703559
EST:     TGACGGCGGATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAG                         ATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGGCAGCTATTGCAAAT
genomic: TGACGGCGGATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAGgtgagtggca ... tctgatgcagATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGGCAGCTATTGCAAAT
EST: gi|211511546|gb|FL285065.1|FL285065
EST:     TGACGGCGGATCTCGCCGCCAGCACGACCAACGGCGTGGTGCATGCTCAG                         ATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGTCAGCTATTGCAAAT
genomic: TGACGGCGGATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAGgtgagtggca ... tctgatgcagATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGGCAGCTATTGCAAAT
EST: gi|148981227|gb|EE027511.2|EE027511
EST:     TGACGGCGGATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAG                         ATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGGCAGCTATTGCAAAT
genomic: TGACGGCGGATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAGgtgagtggca ... tctgatgcagATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGGCAGCTATTGCAAAT
EST: gi|148928929|gb|EC873987.2|EC873987
EST:     TGACGGCGGATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAG                         ATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGGCAGCTATTGCAAAT
genomic: TGACGGCGGATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAGgtgagtggca ... tctgatgcagATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGGCAGCTATTGCAAAT
EST: gi|32826011|gb|CD965689.1|CD965689
EST:     GATCTCGCCGCCAGCACGGCCTACGGCGCGGTGCATGCTCAG                         ATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGGCAGCTATTGCAAAT
genomic: GATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAGgtgagtggca ... tctgatgcagATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGGCAGCTATTGCAAAT
EST: gi|149048881|gb|EE048381.2|EE048381
EST:     TGACGGCGGATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAG                         ATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGGCAGCTATTGCAAAT
genomic: TGACGGCGGATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAGgtgagtggca ... tctgatgcagATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGGCAGCTATTGCAAAT
EST: gi|78075399|gb|DV503833.1|DV503833
EST:     TGACGGCGGATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAG                         ATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGGCAGCTATTGCAAAT
genomic: TGACGGCGGATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAGgtgagtggca ... tctgatgcagATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGGCAGCTATTGCAAAT
EST: gi|148958744|gb|EC905021.2|EC905021
EST:     TGACGGCGGATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAG                         ATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGGCAGCTATTGCAAAT
genomic: TGACGGCGGATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAGgtgagtggca ... tctgatgcagATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGGCAGCTATTGCAAAT

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: 440

TAGGAGGGCGGTGGCGGCGCAGTCGCTGCGGACGACCGCCACCGAGACGCTGACGGCGGATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAGgtgagtggca ... tctgatgcagATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGGCAGCTATTGCAAATTCTAGGAGGAAGACAAAGATAGTATGCACCATAGGTCCCTCAACCAACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 287

TAGGAGGGCGGTGGCGGCGCAGTCGCTGCGGACGACCGCCACCGAGACGCTGACGGCGGATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAGgtgagtggca ... tctgatgcagATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGGCAGCTATTGCAAATTCTAGGAGGAAGACAAAGATAGTATGCACCATAGGTCCCTCAACCAACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 286

TAGGAGGGCGGTGGCGGCGCAGTCGCTGCGGACGACCGCCACCGAGACGCTGACGGCGGATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAGgtgagtggca ... tctgatgcagATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGGCAGCTATTGCAAATTCTAGGAGGAAGACAAAGATAGTATGCACCATAGGTCCCTCAACCAACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 735

TAGGAGGGCGGTGGCGGCGCAGTCGCTGCGGACGACCGCCACCGAGACGCTGACGGCGGATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAGgtgagtggca ... tctgatgcagATGTATAGTGAGGCTAGTAGTGAAATCCCTTCACAGGCAGCTATTGCAAATTCTAGGAGGAAGACAAAGATAGTATGCACCATAGGTCCCTCAACCAACA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGGAGGGCGGTGGCGGCGCAGTCGCTGCGGACGACCGCCACCGAGACGCTGACGGCGGATCTCGCCGCCAGCACGGCCAACGGCGCGGTGCATGCTCAGgtgagtggcatcctttagctcttctgccttctccttgcacgtttgattgcttggcggtattagtgtacagctcctttccatttctgtgtgcgttggtgct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttctcc