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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgctccattctgtagaattttcttgggtccaaggagtttctgaggtagagttctgtgtgtatatataatatacgcag

Basic information

species Zea mays
transcript GRMZM2G148176_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G148176_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g46280.3 (Oryza sativa), 5'ss of exon 3
GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgctccatt-----ctgtagaattttctt---------------gggtccaaggagtttctgaggtagagttctgtgtgtatatataatatacgcag
|||||||||||||||||||||||||||||||||||||||||  ||||||||||||||||||| || ||||||||| ||| |||   |   |      ||| || | ||  ||               || ||   ||||||| |||  | ||||| | | |  | || ||          
GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTATAGATTTTCGATCTCTTGGTCAAGAATTTTCCCAAgtatgtggattatgtctgtacctgcagcagttctttttgttgttgttggttggatcagtggagtttgtgatttggagttttctataaaaatttag---------

upper sequence: GRMZM2G148176_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv14s0006g01790.t01 (Vitis vinifera), 5'ss of exon 3
GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgctccattctgtagaattt---------tcttgggtccaaggagtttctgaggtagagttctgtgtgtatatataatatacgcag-----------
|||||| || |||||||||| |   ||   |||||||| ||||||||||| ||||| ||||| ||||||||||| |||| ||    ||  | |    |   ||         || | |||| | |   ||| |    |  |||| ||    | | ||| | |  |   |           
GAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCCATCTCCTGGTCAAGGATTTTCCCTGgtatgtacaatctttgccagtggccttctgtaaacatcattggtcgatgctattttttgaatgaagttatgatgttttgtatga-acccttggttttcatgcag
















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|78107679|gb|DV526097.1|DV526097
EST:     GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG                         ATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
genomic: GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgc ... atatacgcagATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
EST: gi|76291670|gb|DV031238.1|DV031238
EST:     GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG                         ATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
genomic: GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgc ... atatacgcagATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
EST: gi|78078041|gb|DV506456.1|DV506456
EST:     GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG                         ATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
genomic: GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgc ... atatacgcagATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
EST: gi|20300625|gb|BQ163568.1|BQ163568
EST:     GGGCTTTGATGCGTACCGGTTTTCGATCTCTTGGTCGAGGATTTTCCCAG                         ATGGAACTGGCAAGGTGAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
genomic: GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgc ... atatacgcagATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
EST: gi|149013970|gb|EE043477.2|EE043477
EST:     GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG                         ATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
genomic: GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgc ... atatacgcagATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
EST: gi|89248541|gb|DY620327.1|DY620327
EST:     GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG                         ATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
genomic: GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgc ... atatacgcagATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
EST: gi|78082093|gb|DV510505.1|DV510505
EST:     GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG                         ATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
genomic: GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgc ... atatacgcagATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
EST: gi|78090492|gb|DV518866.1|DV518866
EST:     GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG                         ATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
genomic: GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgc ... atatacgcagATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
EST: gi|76018965|gb|DT946135.1|DT946135
EST:     GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG                         ATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
genomic: GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgc ... atatacgcagATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
EST: gi|149072852|gb|EE161103.2|EE161103
EST:     GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG                         ATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
genomic: GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgc ... atatacgcagATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
EST: gi|94476899|gb|EB705857.1|EB705857
EST:     GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG                         ATGGAACTGGGCA-GGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTC
genomic: GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgc ... atatacgcagATGGAACTGG-CAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTC
EST: gi|50339599|gb|CO534725.1|CO534725
EST:     GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG                         ATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
genomic: GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgc ... atatacgcagATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
EST: gi|50338381|gb|CO533507.1|CO533507
EST:     GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG                         ATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
genomic: GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgc ... atatacgcagATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
EST: gi|149089118|gb|EE178296.2|EE178296
EST:     GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG                         ATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
genomic: GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgc ... atatacgcagATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
EST: gi|76932675|gb|DV173111.1|DV173111
EST:     GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG                         ATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
genomic: GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgc ... atatacgcagATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
EST: gi|149070068|gb|EE158468.2|EE158468
EST:     GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG                         ATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
genomic: GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgc ... atatacgcagATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
EST: gi|91049509|gb|EB159927.1|EB159927
EST:     GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG                         ATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
genomic: GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgc ... atatacgcagATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
EST: gi|93012162|gb|EB637682.1|EB637682
EST:     GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG                         ATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
genomic: GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgc ... atatacgcagATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
EST: gi|71333297|gb|DR803704.1|DR803704
EST:     GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG                         ATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
genomic: GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgc ... atatacgcagATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
EST: gi|149073325|gb|EE161620.2|EE161620
EST:     GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAG                         ATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA
genomic: GGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgc ... atatacgcagATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCA

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: 476

GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgc ... atatacgcagATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCATAGATTACATGCTCCAGCAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 267

GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgc ... atatacgcagATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCATAGATTACATGCTCCAGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 119

GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgc ... atatacgcagATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCATAGATTACATGCTCCAGCAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 254

GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgc ... atatacgcagATGGAACTGGCAAGGTAAACCAGGAAGGAGTGGATTACTACAACAGGCTCATAGATTACATGCTCCAGCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGATGTGAACATAATGAAGAACATGGGCTTTGATGCGTACCGATTTTCGATCTCTTGGTCGAGGATTTTCCCAGgtaggtgtgctccattctgtagaattttcttgggtccaaggagtttctgaggtagagttctgtgtgtatatataatatacgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT