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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGATTCCGAGAGCACTCATGCCGCTTGAGgtgtgtattaaaattattaactgtccttttcttctgttctcttctttgtgtgtaccattggtaattctactagttattactctgctctagcggctaactg...

Basic information

species Zea mays
transcript GRMZM2G008726_T01
intron # 3
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|211040038|gb|FK962663.1|FK962663
EST:     AGTGATTCCGAGAGCACTCATGCCGCTTGAG                         ATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
genomic: AGTGATTCCGAGAGCACTCATGCCGCTTGAGgtgtgtatta ... ctcaaactagATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
EST: gi|211166478|gb|FK962667.1|FK962667
EST:     AGTGATTCCGAGAGCACTCATGCCGCTTGAG                         ATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
genomic: AGTGATTCCGAGAGCACTCATGCCGCTTGAGgtgtgtatta ... ctcaaactagATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
EST: gi|211166479|gb|FK962668.1|FK962668
EST:     AGTGATTCCGAGAGCACTCATTCCGCTTGAG                         ATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
genomic: AGTGATTCCGAGAGCACTCATGCCGCTTGAGgtgtgtatta ... ctcaaactagATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
EST: gi|211166480|gb|FK962669.1|FK962669
EST:     AGTGATTCCGAGAGCACTCATGCCGCTTGAG                         ATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
genomic: AGTGATTCCGAGAGCACTCATGCCGCTTGAGgtgtgtatta ... ctcaaactagATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
EST: gi|211166481|gb|FK962670.1|FK962670
EST:     AGTGATTCCGAGAGCACTCATGCCGCTTGAG                         ATATCTGGTGCTAGCGTTGGGAGAAGTTAAGGTTTGTCTCCGACATGCACG
genomic: AGTGATTCCGAGAGCACTCATGCCGCTTGAGgtgtgtatta ... ctcaaactagATATCTGGTGCTAGCGTTGG-AGAAGTTAAGGTT-GTCTCCGACATGCACG
EST: gi|211040035|gb|FK962660.1|FK962660
EST:     AGTGATTCCGAGAGCACTCATGCCGCTTGAG                         ATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
genomic: AGTGATTCCGAGAGCACTCATGCCGCTTGAGgtgtgtatta ... ctcaaactagATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
EST: gi|32823039|gb|CD962748.1|CD962748
EST:     GGTGATTCCGAGAGCACTCATGCCGCTTGAG                         ATATCTGGTGCTAGCGTTGGAGAAGTTA
genomic: AGTGATTCCGAGAGCACTCATGCCGCTTGAGgtgtgtatta ... ctcaaactagATATCTGGTGCTAGCGTTGGAGAAGTTA
EST: gi|211040039|gb|FK962664.1|FK962664
EST:     AGTGATTCCGAGAGCACTCATGCCGCTTGAG                         ATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
genomic: AGTGATTCCGAGAGCACTCATGCCGCTTGAGgtgtgtatta ... ctcaaactagATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
EST: gi|211040036|gb|FK962661.1|FK962661
EST:     AGTGATTCCGAGAGCACTCATGCCGCTTGAG                         ATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
genomic: AGTGATTCCGAGAGCACTCATGCCGCTTGAGgtgtgtatta ... ctcaaactagATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
EST: gi|211040034|gb|FK962659.1|FK962659
EST:     AGTGATTCCGAGAGCACTCATTCCGCTTGAG                         ATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
genomic: AGTGATTCCGAGAGCACTCATGCCGCTTGAGgtgtgtatta ... ctcaaactagATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
EST: gi|211040037|gb|FK962662.1|FK962662
EST:     AGTGATTCCGAGAGCACTCATTCCGCTTGAG                         ATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
genomic: AGTGATTCCGAGAGCACTCATGCCGCTTGAGgtgtgtatta ... ctcaaactagATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
EST: gi|211166482|gb|FK962671.1|FK962671
EST:     AGTGATTCCGAGAGCACTCATGCCGCTTGAG                         ATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
genomic: AGTGATTCCGAGAGCACTCATGCCGCTTGAGgtgtgtatta ... ctcaaactagATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
EST: gi|211040041|gb|FK962666.1|FK962666
EST:     AGTGATTCCGAGAGCACTCATGCCGCTTGAG                         ATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
genomic: AGTGATTCCGAGAGCACTCATGCCGCTTGAGgtgtgtatta ... ctcaaactagATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
EST: gi|211040040|gb|FK962665.1|FK962665
EST:     AGTGATTCCGAGAGCACTCATGCCGCTTGAG                         ATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
genomic: AGTGATTCCGAGAGCACTCATGCCGCTTGAGgtgtgtatta ... ctcaaactagATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
EST: gi|211040031|gb|FK962656.1|FK962656
EST:     AGTGATTCCGAGAGCACTCATGCCGCTTGAK                         ATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAK
genomic: AGTGATTCCGAGAGCACTCATGCCGCTTGAGgtgtgtatta ... ctcaaactagATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
EST: gi|211040032|gb|FK962657.1|FK962657
EST:     AGTGATTCCGAGAGCACTCATGCCGCTTGAG                         ATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
genomic: AGTGATTCCGAGAGCACTCATGCCGCTTGAGgtgtgtatta ... ctcaaactagATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAG
EST: gi|211040033|gb|FK962658.1|FK962658
EST:     AGTGATTCCGAGAGCACTCATGCCGCTTGAG                         ATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCC
genomic: AGTGATTCCGAGAGCACTCATGCCGCTTGAGgtgtgtatta ... ctcaaactagATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCC

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: 31 (upstream exon), 49 (downstream exon)
Score: 11

AGTGATTCCGAGAGCACTCATGCCGCTTGAGgtgtgtatta ... ctcaaactagATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAGAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTG


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 27

AGTGATTCCGAGAGCACTCATGCCGCTTGAGgtgtgtatta ... ctcaaactagATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAGAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTG


Block sizes: 31 (upstream exon), 46 (downstream exon)
Score: 8

AGTGATTCCGAGAGCACTCATGCCGCTTGAGgtgtgtatta ... ctcaaactagATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAGAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTGATTCCGAGAGCACTCATGCCGCTTGAGgtgtgtattaaaattattaactgtccttttcttctgttctcttctttgtgtgtaccattggtaattctactagttattactctgctctagcggctaactg

- - - - - AGAGCA