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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCTTACCTTCAATCTCCACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaacaatattgcgatgttagggaaacatgttgttcttttgtttctataaatgattggtttttcatgtttatatgaaaattaagaactgtttgt...

Basic information

species Zea mays
transcript GRMZM2G055020_T03
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G055020_T03 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os05g32060.1 (Oryza sativa), 5'ss of exon 7
TGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCTTACCTTCAATCTCCACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaacaatattgcgatgttagggaaacatg--ttgttcttttgtttctataaatgattggtttttcatgtttatatgaaaattaagaactgtttgt---
||||||||| || |||||||| ||||||||||||||||| ||||  || ||||| |||||||||||| || | || |||||||||||||| |||||||||||||||||   ||||||    | |||    |  |||  |  | |   |  |  || | |||||||   ||| |  |||| |  ||| |  | | |   ||||   
TGGGAAAATAGGGGAATGGCGGTTTGACAAAAGATCTTATCTTCGTTCACCACCGCCAAGAAATCTTACATTACCTCCTCCAGGAGTTCCCGAAAGTGTGgtatgtgct-taatatt-tagtattatttcagtatgactgatgccacttctcttaaacatgattgaccttt-acatttaca--aaattctaaatcaccttgttga

upper sequence: GRMZM2G055020_T03 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA15G37490.2 (Glycine max), 5'ss of exon 8
TGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCTTACCTTCAATCTCCACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaacaatattgcgatgttagggaaacatgttgttct--tttgtttctataaatgattggtttttcatgtttatatgaaaattaagaactgtttgt
||| ||||| ||||| ||| | ||||| ||||| ||  | || | |   || ||||||| |||  |  |  ||||||| ||||| |||||||||||||||||||||  |  | |       || | |     ||  |  | ||   || ||   ||||    | |      |   ||| | ||| |  |   |  || |   
TGGCAAAATTGGTGAGTGGAGATTTGATAAAAGGTCACATCTACGAGGACCTCCACCAAAAAACTTGCCCTTGCCCCCACCAGGGGTTCCTGAAAGTGTGgtatgtctagaacttgcctattgattgaagtgcacttcatcctatcttattggaataatatctagaaagaactgctttctgtgatacatggaacttgata--

upper sequence: GRMZM2G055020_T03 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA13G26610.1 (Glycine max), 5'ss of exon 8
TGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCTTACCTTCAATCTCCACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaacaatattgcgatgttagggaaacatgttgttct-tttgtttctataaatgattggtttttcatgtttatatgaaaattaagaactgtttgt
||| ||| | ||||||||| | ||||||||||| ||  | || | |   || ||||||| |||  |  | |||||||| ||||| |||||||||||||||||| ||  |  | |       || |     | ||  |  |  | | |  ||  |  |||   | |       || ||  ||  | |    |||||   |  
TGGCAAAGTTGGTGAATGGAGATTTGACAAAAGGTCGCATCTACGAGGACCTCCACCAAAAAACTTGCCCCTGCCCCCACCAGGGGTTCCTGAAAGTGTGgtacgtctagaacttgcctattgatttaagagcacttcatcttatctaattggaataatatctagaaagaactgctttcattgatacatggaacttaata-

upper sequence: GRMZM2G055020_T03 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA02G44810.1 (Glycine max), 5'ss of exon 9
TGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCTTACCTTCAATCTCCACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaacaatattgcgatgttagggaaacatgttgttcttttgtttctataaatgattggtttttcatgtttatat--gaaaattaagaactgtttgt---
|||||| || || ||||||||||||||||| || ||||| |||     ||| ||||| | ||| ||  |  | || ||||||||||||||||||||||||||| ||||    ||  | | |  ||   |   | | ||| | |    ||  ||   |   |    ||     ||| || |  |||| || | |  |         
TGGGAAGATTGGAGAATGGCGTTTTGACAAGAGGTCTTATCTTTTGGGTCCTCCACCCAAAAACCTGCCCTTACCGCCTCCAGGAGTTCCTGAAAGTGTGgtaagtgc----atgcttcaaattttttggttc-tattgctttgaaattattaatcaaagtcatcttgattagttaatgttggaaagttgatatttcccaaacag

upper sequence: GRMZM2G055020_T03 (Zea mays), 5'ss of exon 8
lower sequence: Vv13s0084g00830.t01 (Vitis vinifera), 5'ss of exon 7
TGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCTTACCTTCAATCTCCACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaacaatattgcgatgttagggaaacatgttgttcttttgtttctataaatgattggtttttcatgtttatatgaaaattaagaactgtttgt----
||||||||| || || ||||| |||||||| ||||| ||||| |     || || || ||||| |||||  |||| |||||||| ||||||||||||||||||||| ||     | | |          | | |  ||||||   ||| |         | |     || | ||     |    | |   || ||||| |    
TGGGAAAATTGGAGAGTGGCGATTTGACAAGAGATCATACCTACGTGGACCTCCTCCTAGAAACCTTTCCTTGCCGCCTCCAGGGGTTCCTGAAAGTGTGgtatgttcatggtgactccttcacatttcatatacattgttcccatgtat--gctgtctacttacaattgaagtcagattcc--actggcaattgtttatactg

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|5468725|gb|AI834516.1|AI834516
EST:     CTCCACCAAGAAATCTTTCCCTGCCCCCTCCAGGAGTTCCTGAAAGTGTG                         GTCACCCTTGTGAAGATGGTCAATGAGGCCCCCGCAAACATTCCGGGGTGG
genomic: CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaa ... tctttttcagGTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
EST: gi|71761576|gb|DR959513.1|DR959513
EST:     CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTG                         GTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
genomic: CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaa ... tctttttcagGTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
EST: gi|74237664|gb|DT645578.1|DT645578
EST:     CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTG                         GTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
genomic: CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaa ... tctttttcagGTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
EST: gi|78082143|gb|DV510555.1|DV510555
EST:     CACCCCCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTG                         GTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
genomic: CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaa ... tctttttcagGTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
EST: gi|74237663|gb|DT645577.1|DT645577
EST:     CACCAACAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTG                         GTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
genomic: CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaa ... tctttttcagGTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
EST: gi|76015780|gb|DT942950.1|DT942950
EST:     CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTG                         GTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
genomic: CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaa ... tctttttcagGTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
EST: gi|5686756|gb|AI939849.1|AI939849
EST:     CTCCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTG                         GTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAAC-TTCCGGGGTGG
genomic: CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaa ... tctttttcagGTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
EST: gi|211541009|gb|FL454732.1|FL454732
EST:     CTCCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTG                         GTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
genomic: CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaa ... tctttttcagGTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
EST: gi|76917228|gb|DV166719.1|DV166719
EST:     CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTG                         GTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
genomic: CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaa ... tctttttcagGTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
EST: gi|74245896|gb|DT653810.1|DT653810
EST:     CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTG                         GTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
genomic: CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaa ... tctttttcagGTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
EST: gi|71763634|gb|DR961571.1|DR961571
EST:     CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTG                         GTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
genomic: CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaa ... tctttttcagGTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
EST: gi|60347170|gb|DN214143.1|DN214143
EST:     CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTG                         GTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
genomic: CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaa ... tctttttcagGTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
EST: gi|78023550|gb|DV491937.1|DV491937
EST:     CTCCACCAAGAAATTTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTG                         GTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
genomic: CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaa ... tctttttcagGTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
EST: gi|113702992|gb|EE680496.1|EE680496
EST:     CTCCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTG                         GTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
genomic: CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaa ... tctttttcagGTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
EST: gi|149077162|gb|EE165823.2|EE165823
EST:     GTTCCTGAAAGTGTG                         GTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
genomic: GTTCCTGAAAGTGTGgtatgtgcaa ... tctttttcagGTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
EST: gi|71760330|gb|DR958267.1|DR958267
EST:     CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTG                         GTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
genomic: CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaa ... tctttttcagGTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
EST: gi|60351853|gb|DN218826.1|DN218826
EST:     CTCCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTG                         GTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
genomic: CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaa ... tctttttcagGTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
EST: gi|33094629|gb|CF054623.1|CF054623
EST:     CTCCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTG                         GTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
genomic: CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaa ... tctttttcagGTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
EST: gi|148981075|gb|EE027418.2|EE027418
EST:     CACCACCAAGAAATTTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTG                         GTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
genomic: CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaa ... tctttttcagGTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG
EST: gi|71314168|gb|DR793698.1|DR793698
EST:     CACCACCAAGAAATTTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTG                         GTCACCCTTGTGAAGATGGTCAATGAGGCCCCCGCAAACATTCCGGGGTGG
genomic: CACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaa ... tctttttcagGTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGG

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: 44 (upstream exon), 48 (downstream exon)
Score: 20

TGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCTTACCTTCAATCTCCACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaa ... tctttttcagGTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGGGAGGACGATAGATGATTGATGGTCTGGCTGAGTTGTAGTTTATTCCAGC


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 18

TGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCTTACCTTCAATCTCCACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaa ... tctttttcagGTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGGGAGGACGATAGATGATTGATGGTCTGGCTGAGTTGTAGTTTATTCCAGC


Block sizes: 34 (upstream exon), 48 (downstream exon)
Score: 8

TGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCTTACCTTCAATCTCCACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaa ... tctttttcagGTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGGGAGGACGATAGATGATTGATGGTCTGGCTGAGTTGTAGTTTATTCCAGC


Block sizes: 37 (upstream exon), 48 (downstream exon)
Score: 26

TGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCTTACCTTCAATCTCCACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaa ... tctttttcagGTCACCCTTGTGAAGATGGTCAATGAGGCCACCGCAAACATTCCGGGGTGGGAGGACGATAGATGATTGATGGTCTGGCTGAGTTGTAGTTTATTCCAGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGAAAATCGGTGAATGGCGTTTTGACAAAAGATCTTACCTTCAATCTCCACCACCAAGAAATCTTTCACTGCCCCCTCCAGGAGTTCCTGAAAGTGTGgtatgtgcaacaatattgcgatgttagggaaacatgttgttcttttgtttctataaatgattggtttttcatgtttatatgaaaattaagaactgtttgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA