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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAATGCTCATATACCAAGGGAAAATTCTCAAGGATGAAACCACTTTGGAAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAGgtatttggtgctctctgtcttatcccatcagtgatgtgttcaataatctggttcttaactggaaactgtgattggtttgcctgcaagtcgtgccatattt...

Basic information

species Zea mays
transcript GRMZM2G035417_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035417_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g15360.1 (Oryza sativa), 5'ss of exon 2
GCAAATGCTCATATACCAAGGGAAAATTCTCAAGGATGAAACCACTTTGGAAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAGgtatttggtgctctctgtcttatcccatcagtgatgtgttcaataa-tctggttcttaactggaaactgtgattggtttgcctgcaagtcgtgccatattt--
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GCAGATGCTCATACACCAAGGGAAAATTCTCAAGGATGATACAACTTTGGAAGGCAACAAAGTTGCTGAGAACAGCTTCCTTGTTATAATGCTGTCTAAGgtatgtgatgatct-tgtttaatggcatttgattgtttagcagtaactacccttctaaattattatttacagctagacaa--taagggtatttgcagaccaga
















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|60356802|gb|DN223775.1|DN223775
EST:     AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAG                         GCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
genomic: AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAGgtatttggtg ... tttttgctagGCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
EST: gi|29130299|gb|CB381003.1|CB381003
EST:     AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAG                         GCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
genomic: AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAGgtatttggtg ... tttttgctagGCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
EST: gi|71448259|gb|DR829309.1|DR829309
EST:     AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAG                         GCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
genomic: AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAGgtatttggtg ... tttttgctagGCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
EST: gi|78121958|gb|DV540342.1|DV540342
EST:     AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAG                         GCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
genomic: AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAGgtatttggtg ... tttttgctagGCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
EST: gi|78107573|gb|DV525991.1|DV525991
EST:     AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAG                         GCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
genomic: AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAGgtatttggtg ... tttttgctagGCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
EST: gi|9825075|gb|BE575292.1|BE575292
EST:     AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGNTGTCCAAG                         GCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
genomic: AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAGgtatttggtg ... tttttgctagGCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
EST: gi|5566780|gb|AI881646.1|AI881646
EST:     AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAG                         GCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
genomic: AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAGgtatttggtg ... tttttgctagGCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
EST: gi|94472331|gb|EB701289.1|EB701289
EST:     AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAG                         GCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
genomic: AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAGgtatttggtg ... tttttgctagGCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
EST: gi|20803264|gb|BQ294314.1|BQ294314
EST:     AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAG                         GCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
genomic: AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAGgtatttggtg ... tttttgctagGCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
EST: gi|91876714|gb|EB406671.1|EB406671
EST:     AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAG                         GCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
genomic: AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAGgtatttggtg ... tttttgctagGCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
EST: gi|211524983|gb|FL195251.1|FL195251
EST:     AAAGCAACGGAGYKGANN-GAACAGCTTCCTTGTTATAATGTTGTCCAAG                         GCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
genomic: AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAGgtatttggtg ... tttttgctagGCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
EST: gi|74244160|gb|DT652074.1|DT652074
EST:     AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAG                         GCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
genomic: AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAGgtatttggtg ... tttttgctagGCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
EST: gi|76908411|gb|DV162927.1|DV162927
EST:     AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAG                         GCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
genomic: AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAGgtatttggtg ... tttttgctagGCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
EST: gi|89763929|gb|DY690917.1|DY690917
EST:     AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAG                         GCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT
genomic: AAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAGgtatttggtg ... tttttgctagGCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCT

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), 49 (downstream exon)
Score: 259

GCAAATGCTCATATACCAAGGGAAAATTCTCAAGGATGAAACCACTTTGGAAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAGgtatttggtg ... tttttgctagGCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 420

GCAAATGCTCATATACCAAGGGAAAATTCTCAAGGATGAAACCACTTTGGAAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAGgtatttggtg ... tttttgctagGCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 396

GCAAATGCTCATATACCAAGGGAAAATTCTCAAGGATGAAACCACTTTGGAAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAGgtatttggtg ... tttttgctagGCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 334

GCAAATGCTCATATACCAAGGGAAAATTCTCAAGGATGAAACCACTTTGGAAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAGgtatttggtg ... tttttgctagGCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAATGCTCATATACCAAGGGAAAATTCTCAAGGATGAAACCACTTTGGAAAGCAACGGAGTTGCTGAGAACAGCTTCCTTGTTATAATGTTGTCCAAGgtatttggtgctctctgtcttatcccatcagtgatgtgttcaataatctggttcttaactggaaactgtgattggtttgcctgcaagtcgtgccatattt

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