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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTCCGGCGCCGCCGCCGCCGCCGATGACACCCCTTTCCTCTTCTGGCTCACCGGCGGCGACCGCTGCTCCGTCTTCAGCGGCCTCGCCTACGAGATCGgtacgccaagtatttggatgatgcatggagttggagtgagcgattttgatttgccttgtgtgaaaaataagatgctggatgctctctctcgcctcgcag

Basic information

species Zea mays
transcript GRMZM2G471269_T04
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|211361158|gb|FL409334.1|FL409334
EST:     CACCGGCGGCGACCGCTGCTCCGTCTTCAGCGGCCTCGCCTACGAGATCG                         GTCCCATCAGATTCGTCCTGGAAC
genomic: CACCGGCGGCGACCGCTGCTCCGTCTTCAGCGGCCTCGCCTACGAGATCGgtacgccaag ... cgcctcgcagGTCCCATCAGATTCGTCCTGGAAC
EST: gi|211348131|gb|FL378229.1|FL378229
EST:     CACCGGCGGCGACCGCTGCTCCGTCTTCAGCGGCCTCGCCTACGAGATCG                         GTCCCATCAGATTCGTCCTGGAACCCTACAACGGCACCCTGCCGCGCCTGC
genomic: CACCGGCGGCGACCGCTGCTCCGTCTTCAGCGGCCTCGCCTACGAGATCGgtacgccaag ... cgcctcgcagGTCCCATCAGATTCGTCCTGGAACCCTACAACGGCACCCTGCCGCGCCTGC
EST: gi|211073389|gb|FL369067.1|FL369067
EST:     CACCGGCGGCGACCGCTGCTCCGTCTTCAGCGGCCTCGCCTACGAGATCG                         GTCCCATCAGATTCGTCCTGGAACCCTACAACGGCACCCTGC
genomic: CACCGGCGGCGACCGCTGCTCCGTCTTCAGCGGCCTCGCCTACGAGATCGgtacgccaag ... cgcctcgcagGTCCCATCAGATTCGTCCTGGAACCCTACAACGGCACCCTGC
EST: gi|211214594|gb|FL385235.1|FL385235
EST:     ACCGGCGGCGACCGCTGCTCCGTCTTCAGCGGCCTCGCCTTACGAGATCG                         GTTCCCATCAGATTCGTCCTGGAACCCTACAACGGCACCCT
genomic: ACCGGCGGCGACCGCTGCTCCGTCTTCAGCGGCCTCGCCT-ACGAGATCGgtacgccaag ... cgcctcgcagGT-CCCATCAGATTCGTCCTGGAACCCTACAACGGCACCCT
EST: gi|211425791|gb|FL370217.1|FL370217
EST:     CACCGGCGGCGACCGCTGCTCCGTCTTCAGCGGCCTCGCCTACGAGATCG                         GTCCCATCAGATTCGTCCTGGAACCCTACAACGGCACCCTGCCGCGCTTGC
genomic: CACCGGCGGCGACCGCTGCTCCGTCTTCAGCGGCCTCGCCTACGAGATCGgtacgccaag ... cgcctcgcagGTCCCATCAGATTCGTCCTGGAACCCTACAACGGCACCCTGCCGCGCCTGC

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: 46 (upstream exon), 44 (downstream exon)
Score: 30

GAGTCCGGCGCCGCCGCCGCCGCCGATGACACCCCTTTCCTCTTCTGGCTCACCGGCGGCGACCGCTGCTCCGTCTTCAGCGGCCTCGCCTACGAGATCGgtacgccaag ... cgcctcgcagGTCCCATCAGATTCGTCCTGGAACCCTACAACGGCACCCTGCCGCGCCTGCGATACAACCACAACTCGTGGTCAAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 128

GAGTCCGGCGCCGCCGCCGCCGCCGATGACACCCCTTTCCTCTTCTGGCTCACCGGCGGCGACCGCTGCTCCGTCTTCAGCGGCCTCGCCTACGAGATCGgtacgccaag ... cgcctcgcagGTCCCATCAGATTCGTCCTGGAACCCTACAACGGCACCCTGCCGCGCCTGCGATACAACCACAACTCGTGGTCAAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 113

GAGTCCGGCGCCGCCGCCGCCGCCGATGACACCCCTTTCCTCTTCTGGCTCACCGGCGGCGACCGCTGCTCCGTCTTCAGCGGCCTCGCCTACGAGATCGgtacgccaag ... cgcctcgcagGTCCCATCAGATTCGTCCTGGAACCCTACAACGGCACCCTGCCGCGCCTGCGATACAACCACAACTCGTGGTCAAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 79

GAGTCCGGCGCCGCCGCCGCCGCCGATGACACCCCTTTCCTCTTCTGGCTCACCGGCGGCGACCGCTGCTCCGTCTTCAGCGGCCTCGCCTACGAGATCGgtacgccaag ... cgcctcgcagGTCCCATCAGATTCGTCCTGGAACCCTACAACGGCACCCTGCCGCGCCTGCGATACAACCACAACTCGTGGTCAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGTCCGGCGCCGCCGCCGCCGCCGATGACACCCCTTTCCTCTTCTGGCTCACCGGCGGCGACCGCTGCTCCGTCTTCAGCGGCCTCGCCTACGAGATCGgtacgccaagtatttggatgatgcatggagttggagtgagcgattttgatttgccttgtgtgaaaaataagatgctggatgctctctctcgcctcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC