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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAACCCCTACGACCCCCGTGACCGCCGCCGCCGTCGATGCCTGCGCTCTCCGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGCgtaatggccctccgtctctctcgctctcgcttcggatgtttccacagcttgtttttcaattccaatttttctacaaaataaattttgttgttggttttgcaatatgtcttggttag

Basic information

species Zea mays
transcript GRMZM2G155314_T02
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|94476824|gb|EB705782.1|EB705782
EST:     CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGC                         TGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
genomic: CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGCgtaatggccc ... tcttggttagTGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
EST: gi|78083174|gb|DV511567.1|DV511567
EST:     CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGC                         TGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
genomic: CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGCgtaatggccc ... tcttggttagTGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
EST: gi|74245146|gb|DT653060.1|DT653060
EST:     CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGC                         TGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
genomic: CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGCgtaatggccc ... tcttggttagTGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
EST: gi|211123343|gb|FL425266.1|FL425266
EST:     CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGC                         TGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
genomic: CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGCgtaatggccc ... tcttggttagTGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
EST: gi|91873915|gb|EB403872.1|EB403872
EST:     CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGC                         TGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
genomic: CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGCgtaatggccc ... tcttggttagTGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
EST: gi|71772874|gb|DR970797.1|DR970797
EST:     CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGC                         TGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
genomic: CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGCgtaatggccc ... tcttggttagTGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
EST: gi|78118021|gb|DV536408.1|DV536408
EST:     CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGC                         TGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
genomic: CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGCgtaatggccc ... tcttggttagTGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
EST: gi|91048309|gb|EB158727.1|EB158727
EST:     CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGC                         TGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
genomic: CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGCgtaatggccc ... tcttggttagTGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
EST: gi|76012307|gb|DT939477.1|DT939477
EST:     CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGC                         TGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
genomic: CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGCgtaatggccc ... tcttggttagTGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
EST: gi|78107760|gb|DV526178.1|DV526178
EST:     CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGC                         TGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
genomic: CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGCgtaatggccc ... tcttggttagTGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
EST: gi|211116198|gb|FL414284.1|FL414284
EST:     CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGC                         TGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAANGACGCCGCTGGGCGGA
genomic: CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGCgtaatggccc ... tcttggttagTGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
EST: gi|74242116|gb|DT650030.1|DT650030
EST:     CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGC                         TGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
genomic: CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGCgtaatggccc ... tcttggttagTGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
EST: gi|93283808|gb|EB676072.1|EB676072
EST:     CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGC                         TGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
genomic: CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGCgtaatggccc ... tcttggttagTGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
EST: gi|67031456|gb|CO460205.1|CO460205
EST:     CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGC                         TGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
genomic: CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGCgtaatggccc ... tcttggttagTGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
EST: gi|91870178|gb|EB400743.1|EB400743
EST:     CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGC                         TGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA
genomic: CGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGCgtaatggccc ... tcttggttagTGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGA

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: 40 (upstream exon), 49 (downstream exon)
Score: 45

TAACCCCTACGACCCCCGTGACCGCCGCCGCCGTCGATGCCTGCGCTCTCCGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGCgtaatggccc ... tcttggttagTGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGAACGCGCTCCACCTGGCCGCGGAGATGGGCCGTCTTGAGGTTTGCAGGTT


Block sizes: 37 (upstream exon), 27 (downstream exon)
Score: 2

TAACCCCTACGACCCCCGTGACCGCCGCCGCCGTCGATGCCTGCGCTCTCCGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGCgtaatggccc ... tcttggttagTGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGAACGCGCTCCACCTGGCCGCGGAGATGGGCCGTCTTGAGGTTTGCAGGTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 12

TAACCCCTACGACCCCCGTGACCGCCGCCGCCGTCGATGCCTGCGCTCTCCGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGCgtaatggccc ... tcttggttagTGGTGGCGAGCAAGATGAATCTGCGCGAAGCGAAGGACGCCGCTGGGCGGAACGCGCTCCACCTGGCCGCGGAGATGGGCCGTCTTGAGGTTTGCAGGTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAACCCCTACGACCCCCGTGACCGCCGCCGCCGTCGATGCCTGCGCTCTCCGACGTCGCGCTTCAGGCTGCCATCGCCGGCAACCTCCGCCTCCTGAAGCgtaatggccctccgtctctctcgctctcgcttcggatgtttccacagcttgtttttcaattccaatttttctacaaaataaattttgttgttggttttgcaatatgtcttggttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC