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'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTTgtatgtatctgaagatagaacttctctctaaacattttttttactatgaactctgtataacacgagaatttgctgatgctttaatgtag

Basic information

species Zea mays
transcript GRMZM2G178822_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178822_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g47220.1 (Oryza sativa), 5'ss of exon 5
ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTTgtatgtatctgaagatagaacttctctc-----taaacatttt----ttttactatgaactctgtataacacgag-aatttgctgatgctttaatgtag------------
||||||  |||||||||||||||| || |||||||| |||||||||||||||||||| |||||||| ||||| ||||||||||||||||||||||| | |            ||  |||||     |||| | |   | ||    | | |  |  || |   ||       |||||              
ATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAAAATGGTGAAGTTgtatgtatctgaagataaatccataggaggaaatatgcatttcatacttttgcaaaatattcccagtgaaataaataactgattgtaagcaaaatgtgcactgatctatag

upper sequence: GRMZM2G178822_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA01G35190.1 (Glycine max), 5'ss of exon 2
ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTTgtatgtatctgaagatagaacttctctctaaacattttttttactatgaactctgtataacacgagaatttgctgatgctttaatgtag---
 | |||||| |||||||||||||| |||||||||||||||||||| ||| | ||||| ||||| || |  || ||||||||| ||||     | |  ||||    |   ||   | | | || |   |  |   | |    | | |   |  | | | | |||  | |   
GTACAAGTTAATTAAGGAAGTTGGTGATGGGACTTTTGGGAGTGTCTGGAGAGCTATTAATAAGCAAACCGGTGAAGTTgtaagtat-----gctttaactgacatgataaaggtatctctatttcaagttggatgttgtcctaaatcctaataa-gttgtaaaattgcag

upper sequence: GRMZM2G178822_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA16G17580.1 (Glycine max), 5'ss of exon 2
ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTTgtatgtatctgaaga-tagaacttctctctaaacattttttttactatgaactctgtataacacgagaatttgctgatgctttaatgtag
 | |||||| |||||||||||||| ||||| || ||||||||||| ||| | || || ||||| || | ||| ||||||||| |||| |  ||| |||||     | | ||     ||   |  | ||   | | | |||   |      | || ||  |  |      
GTACAAGTTAATTAAGGAAGTTGGTGATGGAACATTTGGGAGTGTTTGGAGAGCCATTAATAAGCAAAGTGGTGAAGTTgtaagtatgtttagagtagaatgatacgcgaag----ttacattgtgtgtgttttctctaatttg------tcctaatattacag-----

upper sequence: GRMZM2G178822_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv02s0033g01110.t01 (Vitis vinifera), 5'ss of exon 2
ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTTgtatgtatc-tgaagatagaacttctctctaaacattttttttactatgaactctgtataacacgagaatt-tgctgatgctttaatgtag
 |  | | | || ||||||||||| |||||||||||||| ||||| ||||| || || ||||| |||| ||| ||||||||| | | | ||   ||||   || |  ||    |  |     |  ||  | ||| |||||  |  |  || | ||  || || ||     
GTATACGATAATCAAGGAAGTTGGTGATGGGACTTTTGGAAGTGTTTGGCGAGCAATAAATAAGCAGACTGGTGAAGTTgtaagcagcatgttcatagtttttattgctttgaaactgaaggaa-attgattctatataagtcagggtttgttcttttgtttcaacag--

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|211443458|gb|FL042456.1|FL042456
EST:     GGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTT                         GTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATG
genomic: GGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTTgtatgtatct ... tttaatgtagGTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATG
EST: gi|211443465|gb|FL042463.1|FL042463
EST:     GGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTT                         GTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATG
genomic: GGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTTgtatgtatct ... tttaatgtagGTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATG
EST: gi|60345317|gb|DN212290.1|DN212290
EST:     GGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTT                         GTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATG
genomic: GGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTTgtatgtatct ... tttaatgtagGTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATG
EST: gi|211443464|gb|FL042462.1|FL042462
EST:     GGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGNCGAAGTT                         GTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATG
genomic: GGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTTgtatgtatct ... tttaatgtagGTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATG
EST: gi|211443461|gb|FL042459.1|FL042459
EST:     GGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTT                         GTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATG
genomic: GGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTTgtatgtatct ... tttaatgtagGTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATG
EST: gi|211443466|gb|FL042464.1|FL042464
EST:     GACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAAATGGCGAAGTT                         GTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATG
genomic: GACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAA-TGGCGAAGTTgtatgtatct ... tttaatgtagGTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATG
EST: gi|211443460|gb|FL042458.1|FL042458
EST:     GGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTT                         GTTGCTGTTAANAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATG
genomic: GGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTTgtatgtatct ... tttaatgtagGTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATG
EST: gi|211441339|gb|FL042453.1|FL042453
EST:     GGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTT                         GTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATG
genomic: GGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTTgtatgtatct ... tttaatgtagGTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATG
EST: gi|166575936|gb|EG274034.1|EG274034
EST:     AATAAACAGAATGGCGAAGTT                         GTTGCTGTTAAGAAAATG-AG-AAAAATATTATTCTTTTGAGGAATGTATG
genomic: AATAAACAGAATGGCGAAGTTgtatgtatct ... tttaatgtagGTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATG
EST: gi|211443463|gb|FL042461.1|FL042461
EST:     GGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTT                         GTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATG
genomic: GGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTTgtatgtatct ... tttaatgtagGTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATG

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: 578

ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTTgtatgtatct ... tttaatgtagGTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATGAGTCTACGTGAAGTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 385

ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTTgtatgtatct ... tttaatgtagGTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATGAGTCTACGTGAAGTAAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 228

ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTTgtatgtatct ... tttaatgtagGTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATGAGTCTACGTGAAGTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 677

ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTTgtatgtatct ... tttaatgtagGTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATGAGTCTACGTGAAGTAAAG