Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccatcactcagcacgtgttatcctttattcaacattttccctgtatgtactcttgctctgtttcatataaattcataattatgcattttgttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG

Basic information

species Zea mays
transcript GRMZM2G143462_T06
intron # 2
splice site 3'
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|211491198|gb|FK957019.1|FK957019
EST:     AAGAGAATAAAGTCMATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATC
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATC
EST: gi|211394218|gb|FL229512.1|FL229512
EST:     CAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: CAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|74242202|gb|DT650116.1|DT650116
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|148995692|gb|EE034914.2|EE034914
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|211491201|gb|FK957022.1|FK957022
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|89759371|gb|DY688230.1|DY688230
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|30306905|gb|CD001578.1|CD001578
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|211494075|gb|FK957027.1|FK957027
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTT-CATCTTCCCAG
EST: gi|211488314|gb|FK957004.1|FK957004
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|211491197|gb|FK957018.1|FK957018
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|211491203|gb|FK957024.1|FK957024
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|211491196|gb|FK957017.1|FK957017
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|148947026|gb|EC892323.2|EC892323
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|211491191|gb|FK957012.1|FK957012
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|89758471|gb|DY687642.1|DY687642
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|211488319|gb|FK957009.1|FK957009
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|211488318|gb|FK957008.1|FK957008
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|89761592|gb|DY689541.1|DY689541
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|211491193|gb|FK957014.1|FK957014
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|9731840|gb|BE510592.1|BE510592
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|211491205|gb|FK957026.1|FK957026
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|211394220|gb|FL229514.1|FL229514
EST:     CAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: CAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|211491192|gb|FK957013.1|FK957013
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|78111156|gb|DV529553.1|DV529553
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|148999208|gb|EE036127.2|EE036127
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|211491194|gb|FK957015.1|FK957015
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|37423537|gb|CF649496.1|CF649496
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|93280956|gb|EB673220.1|EB673220
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|211488316|gb|FK957006.1|FK957006
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|149095756|gb|EE181396.2|EE181396
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|71771539|gb|DR969476.1|DR969476
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|32805412|gb|CD957648.1|CD957648
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
EST: gi|76912415|gb|DV164721.1|DV164721
EST:     AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAG                         GGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
genomic: AAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG

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), 39 (downstream exon)
Score: 292

ACAACTGCTGATTTTCAATGGAAAGGTCTTGAAAGATGAAAGTACATTGGAAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 147

ACAACTGCTGATTTTCAATGGAAAGGTCTTGAAAGATGAAAGTACATTGGAAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 101

ACAACTGCTGATTTTCAATGGAAAGGTCTTGAAAGATGAAAGTACATTGGAAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 169

ACAACTGCTGATTTTCAATGGAAAGGTCTTGAAAGATGAAAGTACATTGGAAGAGAATAAAGTCAATGAGGATGGGTTTCTAGTTGTCATGCTTAGTAAGgttgggttct ... ttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtactcttgctctgtttcatataaattcataattatgcattttgttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG
                                        ttttgttttct  CT-rich tract
               tttcatataaattcat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccatcactcagcacgtgttatcctttattcaacattttccctgtatgtactcttgctctgtttcatataaattcataattatgcattttgttttctgcagGGTAAAACATCTGGTTCAACTGGAACTTCATCTTCCCAG

ccatcac
- - - -tcagcac
- - - - - - - - - - - - - - - - - - - - ctgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgcatt