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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAATCCTAAGGGTAGCAGCTGCATAGCTGTAGAGATAAAGgtactttgcaagcttcctcttttattcttattttcatttcttatgtatatttctcctcaaccatttgacttctttttggcatgctttaccttgcag

Basic information

species Zea mays
transcript GRMZM2G067299_T02
intron # 5
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|14244312|gb|BG842305.2|BG842305
EST:     GCAATCCTAAGGGTAGCAGCTGCATAGCTGTAGAGATAAAG                         GCCAAATGTGGGTTTCTGCCATCATCAGAATATATATCAGAAGATAATACT
genomic: GCAATCCTAAGGGTAGCAGCTGCATAGCTGTAGAGATAAAGgtactttgca ... taccttgcagGCCAAATGTGGGTTTCTGCCATCATCAGAATATATATCAGAAGATAATACT
EST: gi|149107346|gb|EE189225.2|EE189225
EST:     GCAATCCTAAGGGTAGCAGCTGCATAGCTGTAGAGATAAAG                         GCCAAATGTGGGTTTCTGCCATCATCAGAATATATATCAGAAGATAATACT
genomic: GCAATCCTAAGGGTAGCAGCTGCATAGCTGTAGAGATAAAGgtactttgca ... taccttgcagGCCAAATGTGGGTTTCTGCCATCATCAGAATATATATCAGAAGATAATACT
EST: gi|78112747|gb|DV531141.1|DV531141
EST:     GCAATCCTAAGGGTAGCAGCTGCATAGCTGTAGAGATAAAG                         GCCAAATGTGGGTTTCTGCCATCATCAGAATATATATCAGAAGATAATACT
genomic: GCAATCCTAAGGGTAGCAGCTGCATAGCTGTAGAGATAAAGgtactttgca ... taccttgcagGCCAAATGTGGGTTTCTGCCATCATCAGAATATATATCAGAAGATAATACT
EST: gi|9952572|gb|BE639260.1|BE639260
EST:     CTGCATAGCTGTAGAGATAAAG                         GCCAAATGTGGGTTTCTGCCATCATCAGAATATATATCAGAAGATAACACT
genomic: CTGCATAGCTGTAGAGATAAAGgtactttgca ... taccttgcagGCCAAATGTGGGTTTCTGCCATCATCAGAATATATATCAGAAGATAATACT
EST: gi|149086246|gb|EE175786.2|EE175786
EST:     GCAATCCTAAGGGTAGCAGCTGCATAGCTGTAGAGATAAAG                         GCCAAATGTGGGTTTCTGCCATCATCAGAATATATATC
genomic: GCAATCCTAAGGGTAGCAGCTGCATAGCTGTAGAGATAAAGgtactttgca ... taccttgcagGCCAAATGTGGGTTTCTGCCATCATCAGAATATATATC
EST: gi|94477323|gb|EB706281.1|EB706281
EST:     GCAATCCTAAGGGTAGCAGCTGCATAGCTGTAGAGATAAAG                         GCCCAATGTGGGTTTCTGC
genomic: GCAATCCTAAGGGTAGCAGCTGCATAGCTGTAGAGATAAAGgtactttgca ... taccttgcagGCCAAATGTGGGTTTCTGC
EST: gi|71772065|gb|DR970002.1|DR970002
EST:     GCAATCCTAAAGGTAGCAGCTGCATAGCTGTAGAGATAAAG                         GCCAAATGTGGGTTTCTGCCATCATCAGAATATATATCAGAAGATAATACT
genomic: GCAATCCTAAGGGTAGCAGCTGCATAGCTGTAGAGATAAAGgtactttgca ... taccttgcagGCCAAATGTGGGTTTCTGCCATCATCAGAATATATATCAGAAGATAATACT

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: 48 (upstream exon), 49 (downstream exon)
Score: 59

GCAATCCTAAGGGTAGCAGCTGCATAGCTGTAGAGATAAAGgtactttgca ... taccttgcagGCCAAATGTGGGTTTCTGCCATCATCAGAATATATATCAGAAGATAATACTATCAAGAAACAAGTAACGAGATATAAGATGCATCAGCACCTCAAATTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72

GCAATCCTAAGGGTAGCAGCTGCATAGCTGTAGAGATAAAGgtactttgca ... taccttgcagGCCAAATGTGGGTTTCTGCCATCATCAGAATATATATCAGAAGATAATACTATCAAGAAACAAGTAACGAGATATAAGATGCATCAGCACCTCAAATTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

GCAATCCTAAGGGTAGCAGCTGCATAGCTGTAGAGATAAAGgtactttgca ... taccttgcagGCCAAATGTGGGTTTCTGCCATCATCAGAATATATATCAGAAGATAATACTATCAAGAAACAAGTAACGAGATATAAGATGCATCAGCACCTCAAATTTT


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 32

GCAATCCTAAGGGTAGCAGCTGCATAGCTGTAGAGATAAAGgtactttgca ... taccttgcagGCCAAATGTGGGTTTCTGCCATCATCAGAATATATATCAGAAGATAATACTATCAAGAAACAAGTAACGAGATATAAGATGCATCAGCACCTCAAATTTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAATCCTAAGGGTAGCAGCTGCATAGCTGTAGAGATAAAGgtactttgcaagcttcctcttttattcttattttcatttcttatgtatatttctcctcaaccatttgacttctttttggcatgctttaccttgcag

- - - - - - -  GCAGCT
- - - - - - - - CAGCTG
- - - - - - - -  AGCTGC