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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGCTTGTCGAGGAGAACTTGAGAGGCAAGAATATCTTGTTTCTAGGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacgtgggtcttaaattggcgatagaccgatagtaacaatttgttcatgagtgtcaattgacttcttgtgactgaggcactgagccatatctagcttgg...

Basic information

species Zea mays
transcript GRMZM2G069631_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069631_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 5'ss of exon 3
AATGCTTGTCGAGGAGAACTTGAGAGGCAAGAATATCTTGTTTCTAGGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacgtgggtcttaaattggcgatagaccgatagtaacaatttgttcatgagtgtcaattgacttcttgtgactgaggcactgagccatatctagcttgg---
|  ||  ||||  | ||||||||||| ||||| || |   || | ||||||||||| |||||||||||||| ||||||||||||||||||||||||||| |||   |||||| |||   ||     |  ||  |   | || ||||| |    | |||| | |  |  |||   || |  | | | | ||  || |   
AGCGCCAGTCGGAGTGAACTTGAGAGACAAGATTACCCGATTGCCAGGCATCCTGAATTCCGTTACAAGACTGAATTTCAGAGTCATGAACCTGAGgtatgtgaaacttaaaatggttttaattatagtgtctcccctggtccatgaat-cagagtgacatat-atatctgccacagttggac-tgtataattttgata

upper sequence: GRMZM2G069631_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 3
---AATGCTTGTCGAGGAGAACTTGAGAGGCAAGAATATCTTGTTTCTAGGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacgtgggtcttaaattggcgatagaccgatagtaacaatttgttcatgagtgtcaattgacttcttgtgactgaggcactgagccatatctagcttgg
     ||  |   || | ||  | ||||||   || |||  | ||  |||||||||||||||||||||||| || || |||||||||||||| || ||||||  |     ||   |  |  ||    |   |  | |   | | |||  || ||||||  | || |           || ||   ||            
CATGGTGGATCAAGAAGGGATTTGGAGAGGATGGACTATTCTATTGGTAGGCATCCTGAGTTCCGTTACAAAACAGAGTTTCAGAGTCATGAGCCAGAGgta-atcatcatttggtcagtaatgttgcaccaacatcctatgggtcagaagagtcaat--atttataaatgtatgatcattgtttcag-----------

upper sequence: GRMZM2G069631_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G20830.4 (Glycine max), 5'ss of exon 3
-AATGCTTGTCGAGGAGA-ACTTG-AGAGGCAAGAATATCTTGTTTCTAGGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgta--cgtgggtcttaaattggcgatagaccgatagtaacaatttgttcatgagtgtcaa--ttgacttcttgtgactgaggcactgagccatatctagcttgg
 | |||   || || ||  ||||| |||||   || |||  | ||  ||| ||||||||||||||||| || || || |||||||||||||| |||||||||    |  |||     ||   | |   ||   | |  |   | |  ||  | ||| ||  || |   | ||||| ||  |                      
CATTGCGGATCAAGAAGGGACTTGGAGAGGATGGACTATTCTATTAGTAGACATCCTGAGTTCCGTTATAAAACAGAGTTTCAGAGTCATGAGCCTGAGgtaattttcagtcactggttaatgct--gcctgaaatg-cttgtggagcagaaatgttaacatttatgacatgtgattgttgtttcag----------------

upper sequence: GRMZM2G069631_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA13G42800.1 (Glycine max), 5'ss of exon 3
---AATGCTTGTCGAGGAGAACTTGAGAGGCAAGAATATCTTGTTTCTAGGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacgtgggtcttaaattggcgatagaccgatagtaacaatttgttcatgagtgtcaattgacttcttgtgactgaggcactgagccatatctagcttgg
     ||  |   |  | ||  | ||||||   || |||  | ||  |||||||||||||||||||||||| || || ||||||||||| ||||| ||||||  |     ||   |  |  ||    |   |  | |   | | |||  || ||||||  | || |  ||  |||  || ||   ||            
CATGGTGGATCAAGTAGGGATTTGGAGAGGGTGGACTATTCTATTGGTAGGCATCCTGAGTTCCGTTACAAAACAGAGTTTCAGAGTCACGAACCAGAGgta-atcatcatttggtcagtaatgttgcaccaacatcctatgggtcagaagagtcaat--atttataatgtatgat-cattgtttcag-----------

upper sequence: GRMZM2G069631_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 3
-AATGCTTGTCGAGGAGA-ACTTG-AGAGGCAAGAATATCTTGTTTCTAGGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgta--cgtgggtcttaaattggcgatagaccgatagtaacaatttgttcatgagtgtcaa--ttgacttcttgtgactgaggcactgagccatatctagcttgg
 |   |   || || ||  ||||| |||||   || |||  | ||  ||| ||||||||||||||||| || || || |||||||||||||| |||||||||    |  |||     ||   | | | |||| |    |   | |  ||  | | | ||  || |   ||||||| ||  |                      
CATCACGGATCAAGAAGGGACTTGGAGAGGATGGACTATTCTATTAGTAGACATCCTGAGTTCCGTTATAAAACAGAGTTTCAGAGTCATGAGCCTGAGgtaattttcagtcactggttaatgct-gcccgaaa--tgcttgtggagcagaaatcttaacatttatgacttgtgattgttgtttcag----------------

upper sequence: GRMZM2G069631_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 5
---AATGCTTGTCGAGGAGAACTTGAGAGGCAAGAATATCTTGTTTCTAGGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacgtgggtcttaaattggcgatagaccgatagtaacaatttgttcatgagtgtcaattgacttcttgtgactgaggcactgagccatatctagcttgg
   | ||      || |||| |||||       || ||||   |    |||||||| ||||| ||||| || || || |||||||||||||| |||||||||  ||    || | |  |   |   |  |    | | |||||   ||   | | |  || ||| |  || ||    |  ||      |          
AGCAGTGGAACCAGAAGAGAGCTTGAAGAAGCTGATTATCCACTG---AGGCATCCAGAGTTTCGTTATAAAACAGAGTTTCAGAGTCATGACCCTGAGgtatttga---tttactctgttttcttcttact-cagctatttggctataccttttatctgtcttttcatg-ctctatccttgtttaccag---------

upper sequence: GRMZM2G069631_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 5'ss of exon 3
-AATGCTTGTCGAGGA--GAACTTGAGAGGCAAGAATATCTTGTTTCTAGGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacgtgggtcttaaattggcgatagaccgatagtaacaatttgttcatgagtgtcaattgacttcttgtgactgaggcactgagccatatctagcttgg
 |  |   ||| ||||  || ||||||  |   || || |  |||   |||||||||||||| || || || || |||||||||||||||||||| ||||||| |       || ||  |   |||     | | || | |  ||     ||||   ||||  |  |   | | ||         || ||||   |  |
CATGGAGGGTCCAGGAAGGATCTTGAGCAGACGGATTACCCAGTT---AGGCATCCTGAGTTTCGATATAAAACAGAATTTCAGAGTCATGAACCAGAGgtacattaa----aacttatcaccagattt-cacttacgagtaatt-----gtgttccttgagctactc--aataagcttgcttttca-atctgtttcag

upper sequence: GRMZM2G069631_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 5'ss of exon 3
---AATGCTTGTCGAGGAGAACTTGAGAGGCAAGAATATCTTGTTTCTAGGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacg---tgggtcttaaattggcgatagaccgatagtaacaat-----ttgttcatgagtgtcaattgacttcttgtgactgaggcactgag--ccatatctagcttgg----------
     ||    |||| ||||  | |||| |   || |||         ||||||||||||||||  || || ||||| |||||||| |||||||| |||||      |  |  ||   ||   |     | |||  | || ||     ||  || ||  ||||      | |     ||||  || | | |   |   || ||   ||           
CATGGTGGGAATCGAAGAGATTTAGAGATGGCGGATTATTCACCAAGCAGGCATCCTGAGTTCCACTATAAAACCGAGTTTCAGAGCCATGAACCAGAGgtgtcctttaagaatttcgtttctgggttgctgatgattaccatatccttttatcttgtctgtcttccatccttactggactctggaatttaattctgcatttaatatgtttgaattcag

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|89250814|gb|DY622600.1|DY622600
EST:     GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGA
genomic: GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacgtgggt ... atgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGA
EST: gi|91873992|gb|EB403949.1|EB403949
EST:     GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAG
genomic: GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacgtgggt ... atgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAG
EST: gi|67012325|gb|CO441074.1|CO441074
EST:     GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAG
genomic: GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacgtgggt ... atgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAG
EST: gi|60340196|gb|DN207169.1|DN207169
EST:     GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAG
genomic: GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacgtgggt ... atgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAG
EST: gi|148939774|gb|EC884472.2|EC884472
EST:     GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAG
genomic: GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacgtgggt ... atgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAG
EST: gi|148991720|gb|EE033282.2|EE033282
EST:     GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAG
genomic: GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacgtgggt ... atgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAG
EST: gi|94472892|gb|EB701850.1|EB701850
EST:     GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAG
genomic: GGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacgtgggt ... atgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAG

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: 196

AATGCTTGTCGAGGAGAACTTGAGAGGCAAGAATATCTTGTTTCTAGGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacgtgggt ... atgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAGTGGTGCCAAACAACCAACAATGCACTCTTTCTCTTGTCTACAAATGACA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 148

AATGCTTGTCGAGGAGAACTTGAGAGGCAAGAATATCTTGTTTCTAGGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacgtgggt ... atgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAGTGGTGCCAAACAACCAACAATGCACTCTTTCTCTTGTCTACAAATGACA


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 110

AATGCTTGTCGAGGAGAACTTGAGAGGCAAGAATATCTTGTTTCTAGGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacgtgggt ... atgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAGTGGTGCCAAACAACCAACAATGCACTCTTTCTCTTGTCTACAAATGACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 241

AATGCTTGTCGAGGAGAACTTGAGAGGCAAGAATATCTTGTTTCTAGGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacgtgggt ... atgcatgtagTTTGACTACCTAAAAAGTTTGGAAATAGAAGAGAAGATTAACAAGATCAAGTGGTGCCAAACAACCAACAATGCACTCTTTCTCTTGTCTACAAATGACA