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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGGCACCAGCTCGGCGGCGGCGAAAGCCACCGGCGAGATCGCTAGTACCGCCGCCACCGCATGCAACAGCCCAAGTTCCTGCAATTGgtacgtacgtatgacgattatggcctcacaccataactcacttgttgcttcttgcgcgcttgggagttgctgggagcaatagtggagtacgtagtgtggt...

Basic information

species Zea mays
transcript GRMZM2G123387_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|211492421|gb|FL233183.1|FL233183
EST:     ATCGCTAGTACCGCCGCCACCGCATGCAACAGCCCAAGTTCCTGCAATTG                         GTGGAAGGSCCCGGCGGCGGCAGCAGCGGGGGAGAAAGGAGGACGGATGAA
genomic: ATCGCTAGTACCGCCGCCACCGCATGCAACAGCCCAAGTTCCTGCAATTGgtacgtacgt ... gagcacgcagGTGGAAGGGCCCGGCGGCGGCAGCAGCGGGGGAGAAAGGAGGACGGATGAA
EST: gi|211492418|gb|FL233180.1|FL233180
EST:     ATCGCTAGTACCGCCGCCACCGCATGCAACAGCCCAAGTTCCTGCAATTG                         GTGGAAGGGCCCGGCGGCGGCAGCAGCGGG
genomic: ATCGCTAGTACCGCCGCCACCGCATGCAACAGCCCAAGTTCCTGCAATTGgtacgtacgt ... gagcacgcagGTGGAAGGGCCCGGCGGCGGCAGCAGCGGG
EST: gi|30031986|gb|CB833837.1|CB833837
EST:     ATCGCTAGTACCGCCGCCACCGCATGCAACAGCCCAAGTTCCTGCAATTG                         GTGGAAGGGCCCGGCGGCGGCAGCAGCGGGGGAGAAAGGAGGACGGATGAA
genomic: ATCGCTAGTACCGCCGCCACCGCATGCAACAGCCCAAGTTCCTGCAATTGgtacgtacgt ... gagcacgcagGTGGAAGGGCCCGGCGGCGGCAGCAGCGGGGGAGAAAGGAGGACGGATGAA
EST: gi|71308427|gb|DR790449.1|DR790449
EST:     ATCGCTAGTACCGCCGCCACCGCATGCAACAGCCCAAGTTCCTGCAATTG                         GTGGAAGGGCCCGGCGGCGGCAGCAGCGGGGGAGAAAGGAGGACGGATGAA
genomic: ATCGCTAGTACCGCCGCCACCGCATGCAACAGCCCAAGTTCCTGCAATTGgtacgtacgt ... gagcacgcagGTGGAAGGGCCCGGCGGCGGCAGCAGCGGGGGAGAAAGGAGGACGGATGAA
EST: gi|211492423|gb|FL233185.1|FL233185
EST:     ATCGCTAGTACCGCCGCCACCGCATGCAACAGCCCAAGTKCCTGCAATTG                         GTGGAAGGGCCCGGCGGCGGCAGCAGC
genomic: ATCGCTAGTACCGCCGCCACCGCATGCAACAGCCCAAGTTCCTGCAATTGgtacgtacgt ... gagcacgcagGTGGAAGGGCCCGGCGGCGGCAGCAGC
EST: gi|211492422|gb|FL233184.1|FL233184
EST:     ATCGCTAGTACCGCCGCCACCGCATGCAACAGCCCAAGTTCCTGCAATTG                         GTGGAAGGGCCCGGCGGCGGCAGCAGCGGGGGAGAAAGGAGGACGGATGAA
genomic: ATCGCTAGTACCGCCGCCACCGCATGCAACAGCCCAAGTTCCTGCAATTGgtacgtacgt ... gagcacgcagGTGGAAGGGCCCGGCGGCGGCAGCAGCGGGGGAGAAAGGAGGACGGATGAA
EST: gi|211492419|gb|FL233181.1|FL233181
EST:     ATCGCTAGTACCGCCGCCACCGCATGCAACAGCCCAAGTTCCTGCAATTG                         GTGGAAGGGCCCGGCGGCGGCAGCAGCGGGGGAGAAAGGAGGACGGATGAA
genomic: ATCGCTAGTACCGCCGCCACCGCATGCAACAGCCCAAGTTCCTGCAATTGgtacgtacgt ... gagcacgcagGTGGAAGGGCCCGGCGGCGGCAGCAGCGGGGGAGAAAGGAGGACGGATGAA

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: 41 (upstream exon), 48 (downstream exon)
Score: 13

GCGGGCACCAGCTCGGCGGCGGCGAAAGCCACCGGCGAGATCGCTAGTACCGCCGCCACCGCATGCAACAGCCCAAGTTCCTGCAATTGgtacgtacgt ... gagcacgcagGTGGAAGGGCCCGGCGGCGGCAGCAGCGGGGGAGAAAGGAGGACGGATGAAGGTGAGGAGGAAGATGAGGGAACCGAGGTTCTGCTTCCAGACAAGGAGC


Block sizes: 11 (upstream exon), 39 (downstream exon)
Score: 1

GCGGGCACCAGCTCGGCGGCGGCGAAAGCCACCGGCGAGATCGCTAGTACCGCCGCCACCGCATGCAACAGCCCAAGTTCCTGCAATTGgtacgtacgt ... gagcacgcagGTGGAAGGGCCCGGCGGCGGCAGCAGCGGGGGAGAAAGGAGGACGGATGAAGGTGAGGAGGAAGATGAGGGAACCGAGGTTCTGCTTCCAGACAAGGAGC


Block sizes: 18 (upstream exon), 32 (downstream exon)
Score: 2

GCGGGCACCAGCTCGGCGGCGGCGAAAGCCACCGGCGAGATCGCTAGTACCGCCGCCACCGCATGCAACAGCCCAAGTTCCTGCAATTGgtacgtacgt ... gagcacgcagGTGGAAGGGCCCGGCGGCGGCAGCAGCGGGGGAGAAAGGAGGACGGATGAAGGTGAGGAGGAAGATGAGGGAACCGAGGTTCTGCTTCCAGACAAGGAGC


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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGGGCACCAGCTCGGCGGCGGCGAAAGCCACCGGCGAGATCGCTAGTACCGCCGCCACCGCATGCAACAGCCCAAGTTCCTGCAATTGgtacgtacgtatgacgattatggcctcacaccataactcacttgttgcttcttgcgcgcttgggagttgctgggagcaatagtggagtacgtagtgtggt

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