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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgaattttggaccttttatgattattcattagattataaaattgtcttctcacaaatgtgcacatttttttaatattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACAGAGAAGGAAGATCAAATGCAAGAGCAACAACTGTTAAGTGATGAAAAAC

Basic information

species Zea mays
transcript GRMZM2G161337_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161337_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g15780.1 (Oryza sativa), 3'ss of exon 6
gtatatgaattttggaccttttatgattattcattagattataaaattgtcttctcacaaatgtgcacatttttttaatattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACAGAGAAGGAAGATCAAATGCAAGAGCAACAACTGTTAAGTGATGAAAAAC
|||| | || |      ||  ||    |  |  || || || |   || |||| |||  ||  | ||   ||||  |   || |||||| || |||||||| || ||||||||||| ||||||||||||||||||||||||||||||||| |||||||||||||||| ||  |||||||||||||||
gtatgtaaact------ctcctactgatgatagttggaatacattttt-tcttttcattaacattcatccttttaaatctttttcagGGTAAAATTATTAACCGTCCACTTGCTGGGACTGTTCGAAGGGGCAAGACAGAGAAGGAAGATGAAATGCAAGAGCAACAGCTACTAAGTGATGAAAAAC
















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|33099478|gb|CF059438.1|CF059438
EST:     GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG                         GGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
genomic: GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
EST: gi|31364516|gb|CD448871.1|CD448871
EST:     GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG                         GGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
genomic: GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
EST: gi|5901211|gb|AW042311.1|AW042311
EST:     GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG                         GGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
genomic: GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
EST: gi|116816802|gb|EC859574.1|EC859574
EST:     GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG                         GGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
genomic: GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
EST: gi|33093179|gb|CF053173.1|CF053173
EST:     GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG                         GGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
genomic: GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
EST: gi|71448131|gb|DR829181.1|DR829181
EST:     GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG                         GGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
genomic: GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
EST: gi|7238168|gb|AW573390.1|AW573390
EST:     GCTGNGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG                         GGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
genomic: GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
EST: gi|211345789|gb|FL266262.1|FL266262
EST:     GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG                         GGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
genomic: GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
EST: gi|32836931|gb|CD976609.1|CD976609
EST:     GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG                         GGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
genomic: GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
EST: gi|67024314|gb|CO453063.1|CO453063
EST:     GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG                         GGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
genomic: GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
EST: gi|211282582|gb|FL175928.1|FL175928
EST:     GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG                         GGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
genomic: GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA

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), 48 (downstream exon)
Score: 322

GCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACAGAGAAGGAAGATCAAATGCAAGAGCAACAACTGTTAAGTGATGAAAAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1415

GCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACAGAGAAGGAAGATCAAATGCAAGAGCAACAACTGTTAAGTGATGAAAAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1976

GCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACAGAGAAGGAAGATCAAATGCAAGAGCAACAACTGTTAAGTGATGAAAAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 377

GCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACAGAGAAGGAAGATCAAATGCAAGAGCAACAACTGTTAAGTGATGAAAAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attagattataaaattgtcttctcacaaatgtgcacatttttttaatattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACAGAGAAGGAAGATCAAATGCAAGAGCAACAACTGTTAAGTGATGAAAAAC
                                              tattctc  CT-rich tract
                                  acatttttttaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatgaattttggaccttttatgattattcattagattataaaattgtcttctcacaaatgtgcacatttttttaatattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACAGAGAAGGAAGATCAAATGCAAGAGCAACAACTGTTAAGTGATGAAAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA