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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGTACTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCATTgtgagttcatttttccttgacttgaaaacgatacttcatatagaagcacacctataataataattggttataatttaggttctaaatttgataaagtgga...

Basic information

species Zea mays
transcript GRMZM2G147882_T01
intron # 4
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|32924156|gb|CF028968.1|CF028968
EST:     GTATTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCGTT                         GAGAGTAGCAAAATCAGTCGCAAGGATCATCGCTCTCGCTCTAGATCTAGA
genomic: GTACTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCATTgtgagttcat ... aaattttcagGATAGTAGCAAAATCAGTCGCAAGGATCATCGCTCTTGCTCTAGATCTAGA
EST: gi|32858736|gb|CD998417.1|CD998417
EST:     GTATTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCGTT                         GAGAGTAGCAAAATCAGTCGCAAGGATCATCGCTCTCGCTCTAGATCTAGA
genomic: GTACTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCATTgtgagttcat ... aaattttcagGATAGTAGCAAAATCAGTCGCAAGGATCATCGCTCTTGCTCTAGATCTAGA
EST: gi|78117759|gb|DV536146.1|DV536146
EST:     GTACTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCATT                         GATAGTAGCAAAATCAGTCGCAAGGATCATCGCTCTTGCTCTAGATCTAGA
genomic: GTACTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCATTgtgagttcat ... aaattttcagGATAGTAGCAAAATCAGTCGCAAGGATCATCGCTCTTGCTCTAGATCTAGA
EST: gi|78078284|gb|DV506699.1|DV506699
EST:     GTACTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCATT                         GATAGTAGCAAAATCAGTCGCAAGGATCATCGCTCTTGCTCTAGATCTAGA
genomic: GTACTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCATTgtgagttcat ... aaattttcagGATAGTAGCAAAATCAGTCGCAAGGATCATCGCTCTTGCTCTAGATCTAGA
EST: gi|88756286|gb|DY540427.1|DY540427
EST:     GTACTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCATT                         GATAGTAGCAAAATCAGTCGCAAGGATCATCGCTCTTGCTCTAGATCT
genomic: GTACTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCATTgtgagttcat ... aaattttcagGATAGTAGCAAAATCAGTCGCAAGGATCATCGCTCTTGCTCTAGATCT
EST: gi|93014970|gb|EB640490.1|EB640490
EST:     GTACTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCATT                         GATAGTAGCAAAATCAGTCGCAAGGATCATCGCTCTTGCTCTAGATCTAGA
genomic: GTACTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCATTgtgagttcat ... aaattttcagGATAGTAGCAAAATCAGTCGCAAGGATCATCGCTCTTGCTCTAGATCTAGA
EST: gi|32924110|gb|CF028922.1|CF028922
EST:     GTATTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCGTT                         GAGAGTAGCAAAATCAGTCGCAAGGATCATCGCTCTCGCTCTAGATCTAGA
genomic: GTACTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCATTgtgagttcat ... aaattttcagGATAGTAGCAAAATCAGTCGCAAGGATCATCGCTCTTGCTCTAGATCTAGA
EST: gi|71299023|gb|DR785502.1|DR785502
EST:     GTACTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCATT                         GATAGTAGCAAAATCAGTCGCAAGGATCATCGCTCTTGCTCTAGATCTAGA
genomic: GTACTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCATTgtgagttcat ... aaattttcagGATAGTAGCAAAATCAGTCGCAAGGATCATCGCTCTTGCTCTAGATCTAGA
EST: gi|71429426|gb|DR810476.1|DR810476
EST:     GTACTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCATT                         GATAGTAGCAAAATCAGTCGCAAGGATCATCGCTCTTGCTCTAGATCTAGA
genomic: GTACTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCATTgtgagttcat ... aaattttcagGATAGTAGCAAAATCAGTCGCAAGGATCATCGCTCTTGCTCTAGATCTAGA
EST: gi|50323931|gb|CO519057.1|CO519057
EST:     GTACTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCATT                         GATAGTAGCAAAATCAGTCGCAAGGATCATCGCTCTTGCTCTAGATCTAGA
genomic: GTACTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCATTgtgagttcat ... aaattttcagGATAGTAGCAAAATCAGTCGCAAGGATCATCGCTCTTGCTCTAGATCTAGA

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: 47 (upstream exon), 49 (downstream exon)
Score: 53

AAGTACTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCATTgtgagttcat ... aaattttcagGATAGTAGCAAAATCAGTCGCAAGGATCATCGCTCTTGCTCTAGATCTAGACGTGGACTTCTTCGATAGACCTGAAATGCTTGGCGAGTCCATAGCCACG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 1266

AAGTACTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCATTgtgagttcat ... aaattttcagGATAGTAGCAAAATCAGTCGCAAGGATCATCGCTCTTGCTCTAGATCTAGACGTGGACTTCTTCGATAGACCTGAAATGCTTGGCGAGTCCATAGCCACG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 1145

AAGTACTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCATTgtgagttcat ... aaattttcagGATAGTAGCAAAATCAGTCGCAAGGATCATCGCTCTTGCTCTAGATCTAGACGTGGACTTCTTCGATAGACCTGAAATGCTTGGCGAGTCCATAGCCACG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 64

AAGTACTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCATTgtgagttcat ... aaattttcagGATAGTAGCAAAATCAGTCGCAAGGATCATCGCTCTTGCTCTAGATCTAGACGTGGACTTCTTCGATAGACCTGAAATGCTTGGCGAGTCCATAGCCACG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGTACTACCAAAATGGAGAGAAGTGATGGAGCAATATCACAGGGAGGCATTgtgagttcatttttccttgacttgaaaacgatacttcatatagaagcacacctataataataattggttataatttaggttctaaatttgataaagtgga

- - - - - - - TGGAGA
- - - - - - - - -  AGAAGT
- - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - GGAGCA