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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAGgtgtgttgcaaggcattttcttctcttgtaaacacaggaaaaaatgttttgctgatgaatttaacaaatatagtcccccaatcttgcagtaagttactta...

Basic information

species Zea mays
transcript GRMZM2G014136_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014136_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os06g24704.1 (Oryza sativa), 5'ss of exon 6
AGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAGgtgtgttgcaaggcattttcttctcttgtaaacacaggaa-----aaaatgttttgctgatgaatttaacaaatatagtcccccaatcttgcagtaagttactta
||||||||||| ||  ||||||| ||||||||||||||||| || |||||||||||  | || || ||||||||||| |||     | | ||   ||    | || |||  |  |       ||||  || | || |   |  | | || |||  |   | | ||  || || ||     
AGGTTTGCAGCATTTTTATCTCCACTTACACTTGGTCGAGTTAATATTGCAGTTAATGCGGTTTATATTTCAAAGgtatgtcatgtgcccttccttttctatatatacatggagattgttcgaatgagttccagagggtatatatatatgtagctcaagattattatag-aatttg----
















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|32922586|gb|CF027398.1|CF027398
EST:     TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAG                         GTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
genomic: TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAGgtgtgttgca ... atggatacagGTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
EST: gi|32922930|gb|CF027742.1|CF027742
EST:     TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAG                         GTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
genomic: TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAGgtgtgttgca ... atggatacagGTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
EST: gi|32922923|gb|CF027735.1|CF027735
EST:     TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAG                         GTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
genomic: TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAGgtgtgttgca ... atggatacagGTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
EST: gi|50322995|gb|CO518121.1|CO518121
EST:     TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAG                         GTCAGCCTAACAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
genomic: TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAGgtgtgttgca ... atggatacagGTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
EST: gi|78118417|gb|DV536803.1|DV536803
EST:     TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAG                         GTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
genomic: TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAGgtgtgttgca ... atggatacagGTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
EST: gi|32923030|gb|CF027842.1|CF027842
EST:     TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAG                         GTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
genomic: TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAGgtgtgttgca ... atggatacagGTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
EST: gi|211534372|gb|FL093852.1|FL093852
EST:     TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAG                         GTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
genomic: TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAGgtgtgttgca ... atggatacagGTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
EST: gi|32923258|gb|CF028070.1|CF028070
EST:     TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAG                         GTCAGCCTATCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
genomic: TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAGgtgtgttgca ... atggatacagGTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
EST: gi|78122592|gb|DV540976.1|DV540976
EST:     TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAGAG                         GTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
genomic: TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAGgtgtgttgca ... atggatacagGTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
EST: gi|32921855|gb|CF026667.1|CF026667
EST:     TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAG                         GTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
genomic: TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAGgtgtgttgca ... atggatacagGTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
EST: gi|61119686|gb|DN560647.1|DN560647
EST:     TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAG                         GTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
genomic: TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAGgtgtgttgca ... atggatacagGTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
EST: gi|32923274|gb|CF028086.1|CF028086
EST:     TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAG                         GTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
genomic: TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAGgtgtgttgca ... atggatacagGTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
EST: gi|32921928|gb|CF026740.1|CF026740
EST:     TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAG                         GTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
genomic: TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAGgtgtgttgca ... atggatacagGTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
EST: gi|32922650|gb|CF027462.1|CF027462
EST:     TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAG                         GTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
genomic: TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAGgtgtgttgca ... atggatacagGTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
EST: gi|32920277|gb|CF025089.1|CF025089
EST:     TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAG                         GTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA
genomic: TTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAGgtgtgttgca ... atggatacagGTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCA

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), 45 (downstream exon)
Score: 44

AGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAGgtgtgttgca ... atggatacagGTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCAATTGCACCAGATGCCCCTGAAATGTTGTTGCTTGACTATCCCAGTCACC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 233

AGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAGgtgtgttgca ... atggatacagGTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCAATTGCACCAGATGCCCCTGAAATGTTGTTGCTTGACTATCCCAGTCACC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 243

AGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAGgtgtgttgca ... atggatacagGTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCAATTGCACCAGATGCCCCTGAAATGTTGTTGCTTGACTATCCCAGTCACC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 113

AGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAGgtgtgttgca ... atggatacagGTCAGCCTAGCAATTGCTGTGAGATACAGTTTGTCAAGGAGAGCCTTTTCAATTGCACCAGATGCCCCTGAAATGTTGTTGCTTGACTATCCCAGTCACC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGTTTGCAGCTTTCCTATCTCCGCTTACACTTGGTCGAGTAAACATTGCAGTTAACTCAGTCTACATTTCAAAGgtgtgttgcaaggcattttcttctcttgtaaacacaggaaaaaatgttttgctgatgaatttaacaaatatagtcccccaatcttgcagtaagttactta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaaata