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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTGgtatgtataaactttcaacaggaacttttggtcatcacagtttcattttgtctattagtgtggctaactcatatacag

Basic information

species Zea mays
transcript GRMZM2G003692_T07
intron # 7
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|37376662|gb|CF624883.1|CF624883
EST:     GCCTTCTAGCACCTTACATGCTTGATAGAGGGATGGGCCATTTTGTTGTG                         ATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
genomic: GCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTGgtatgtataa ... tcatatacagATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
EST: gi|14244326|gb|BG842296.2|BG842296
EST:     GCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTG                         ATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
genomic: GCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTGgtatgtataa ... tcatatacagATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
EST: gi|5343223|gb|AI795408.1|AI795408
EST:     GCCTTCTAGCACCTTACATGCTTGATAGAGGGATGGGCCATTTTGTTGTG                         ATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
genomic: GCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTGgtatgtataa ... tcatatacagATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
EST: gi|14208321|gb|BG842006.1|BG842006
EST:     GCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTG                         ATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
genomic: GCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTGgtatgtataa ... tcatatacagATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
EST: gi|37397592|gb|CF636096.1|CF636096
EST:     GCCTTCTAGCACCTTACATGCTTGATAGAGGGATGGGCCATTTTGTTGTG                         ATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
genomic: GCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTGgtatgtataa ... tcatatacagATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
EST: gi|149101270|gb|EE187382.2|EE187382
EST:     GCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTG                         ATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
genomic: GCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTGgtatgtataa ... tcatatacagATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
EST: gi|32856130|gb|CD995811.1|CD995811
EST:     GCCTTCTAGCACCTTACATGCTGGATAGAGGGATGGGCCATTTTGTTGTG                         ATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
genomic: GCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTGgtatgtataa ... tcatatacagATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
EST: gi|32840502|gb|CD980183.1|CD980183
EST:     GCCTTCTAGCACCTTACATGCTGGATAGAGGGATGGGCCATTTTGTTGTG                         ATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
genomic: GCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTGgtatgtataa ... tcatatacagATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
EST: gi|88753506|gb|DY537647.1|DY537647
EST:     GCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTG                         ATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
genomic: GCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTGgtatgtataa ... tcatatacagATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
EST: gi|40337101|gb|CK371171.1|CK371171
EST:     GCCTTCTAGCACCTTACATGCTTGATAGAGGGATGGGCCATTTTGTTGTG                         ATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
genomic: GCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTGgtatgtataa ... tcatatacagATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
EST: gi|67023347|gb|CO452096.1|CO452096
EST:     GCCTTCTAGCACCTTACATGCTTGATAGAGGGATGGGCCATTTTGTTGTG                         ATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
genomic: GCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTGgtatgtataa ... tcatatacagATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
EST: gi|32864069|gb|CF003751.1|CF003751
EST:     GCCTTCTAGCACCTTACATGCTGGATAGAGGGATGGGCCATTTTGTTGTG                         ATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
genomic: GCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTGgtatgtataa ... tcatatacagATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
EST: gi|71759817|gb|DR957754.1|DR957754
EST:     GCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTG                         ATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
genomic: GCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTGgtatgtataa ... tcatatacagATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
EST: gi|6095476|gb|AW120143.1|AW120143
EST:     GCCTTCTAGCACCTTACATGCTTGATAGAGGGATGGGCCATTTTGTTGTG                         ATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
genomic: GCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTGgtatgtataa ... tcatatacagATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
EST: gi|6194694|gb|AW146798.1|AW146798
EST:     GCCTTCTAGCACCTTACATGCTTGATAGAGGGATGGGCCATTTTGTTGTG                         ATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
genomic: GCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTGgtatgtataa ... tcatatacagATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
EST: gi|93015973|gb|EB641493.1|EB641493
EST:     GCCTTCTAGCCCCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTG                         ATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
genomic: GCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTGgtatgtataa ... tcatatacagATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
EST: gi|37387558|gb|CF630976.1|CF630976
EST:     GCCTTCTAGCACCTTACATGCTTGATAGAGGGATGGGCCATTTTGTTGTG                         ATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
genomic: GCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTGgtatgtataa ... tcatatacagATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
EST: gi|71438969|gb|DR820019.1|DR820019
EST:     GCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTG                         ATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT
genomic: GCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTGgtatgtataa ... tcatatacagATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCT

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: 166

GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTGgtatgtataa ... tcatatacagATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCTGCCTCCAAACATGCTCTTAATGGTTACTTTGCTTCTCTGCGATCTGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 477

GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTGgtatgtataa ... tcatatacagATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCTGCCTCCAAACATGCTCTTAATGGTTACTTTGCTTCTCTGCGATCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 455

GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTGgtatgtataa ... tcatatacagATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCTGCCTCCAAACATGCTCTTAATGGTTACTTTGCTTCTCTGCGATCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 476

GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTGgtatgtataa ... tcatatacagATGAGTAGTGCTGCTGGAAAGGTTCCTGCTCCTGGTCAGGCCATTTACTCTGCCTCCAAACATGCTCTTAATGGTTACTTTGCTTCTCTGCGATCTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTGgtatgtataaactttcaacaggaacttttggtcatcacagtttcattttgtctattagtgtggctaactcatatacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG