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'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAGgtatgtttaaatcattgtgtgcatcttggacatccttttggtttgaattttttttgtctcctgccaattggcaatagtatttttatatctctaactaagc...

Basic information

species Zea mays
transcript GRMZM5G824405_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g18310.3 (Oryza sativa), 5'ss of exon 10
GTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAGgtatgtttaaatcattgtgtgcatcttggacatccttttgg---tttgaattttttttgtctcctgccaattggcaatagtatttttatatctctaactaagc
|| ||||| || ||||||||||||||||||||||  ||||| || ||||||||||||||||| ||||| || ||||||||||   | ||| | ||||    || | | | |  | ||||   |||||||  ||| | ||||              | | | || |  ||     | ||   
GTAGGTATCTTTGATGCCACAAACAGCACAAGAAACCGGAGAAATATGCTGATGAAAATGGCGGAAGGCAAGTGTAAGgtataactgaataagtgtgcagttcattgcctttttcttggttgtttgaatcatttgtttctcaccattgacattgttggaaattgtccatgcagtaata---

upper sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA11G27410.1 (Glycine max), 5'ss of exon 17
GTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAGgtatgtttaaat--cattgtg-tgcatcttggacatccttttggtttgaattttttttgtctcctgccaattggcaatagtatttttatatctctaactaagc
||||| || || |||||||||||||| |  | |  ||| || ||||||||||||||| |||||||||||| ||| ||||||     | ||  || ||   |   | |  || ||     || |   | ||  |||||    || |  ||      |  | | ||||| | | ||       
GTTGGGATATTTGATGCCACAAACAGTAGCAAAGAACGAAGAAACATGCTGATGAAATTGGCTGAAGGAAGATGCAAGgtagtcaaagatggcactgaaataagtatatgatatgagaatgata-aatttagttttgaactcttctgatccatctttttgtgtttatgt-tgtag------

upper sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA18G06770.1 (Glycine max), 5'ss of exon 13
GTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAGgtatgtttaaat--cattgtg-tgcatcttggacatccttttggtttgaattttttttgtctcctgccaattggcaatagtatttttatatctctaactaagc
||||| || || |||||||||||||| |  |    ||| || ||||||||||||||| |||||||||||| ||| ||||||     | ||  || ||   |   | |  || ||     || |   | ||  |||||    || |  ||      || |  || | |  || ||       
GTTGGGATATTTGATGCCACAAACAGTAGCAAGGAACGAAGAAACATGCTGATGAAATTGGCTGAAGGAAGATGCAAGgtagtcaaagatggcactgaaataagtataagatatgagaatgata-aatttaattttgaactcttctgatccatc-tatttgttcttttgctgtag------

upper sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA11G27870.1 (Glycine max), 5'ss of exon 12
GTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAGgta--tgtttaaatcattgtg-tgcatcttggacatccttttggtttgaattttttttgtctcctgccaattggcaatagtatttttatatctctaactaagc
||||| || || |||||||||||||| |  | |  ||| || ||||||||||||||| |||||||||||| ||| ||||||     | |   || ||   |   | |  || ||     || |   | ||  |||||    || |  ||      |  | | ||||| | |          
GTTGGGATATTTGATGCCACAAACAGTAGCAAAGAACGAAGAAACATGCTGATGAAATTGGCTGAAGGAAGATGCAAGgtagtcaatgatggcactgaaataagtatatgatatgacaatgata-aatttagttttgaactcttctgatccatctttttgtgtttatgttttag-------

upper sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 9
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 5'ss of exon 11
GTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAGgtat----gtttaaatcattgtgtgcatcttggacatccttt--tggtttgaattttttttgtctcctgccaattggcaatagtatttttatatctctaactaagc
||||| || || ||||| || || |||||| || | ||  |||| ||| |||||||||||||||||||||| ||||||||||    | ||  || ||  |||| || |||    || |||  |||   |  | || ||   |      ||        ||| | |||  ||| |  ||  |   
GTTGGAATCTTTGATGCAACTAATAGCACACGAGTTCGACGGAATATGTTGATGAAAATGGCTGAAGGAAAGTGTAAGgtattgaagctttgat-atactgtg-atgttgtttctcatttaatggcacggttattcttctgcggaaagcatgcttggttagcagtttc-tattttcaaaga---

upper sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 9
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 11
GTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAGgta---tgtttaaatcat-tgtgtgcatcttggacatccttttggtttgaattttttttgtctcctgccaattggcaatagtatttttatatctctaactaagc
||||| || ||||||||||||||||| || || | ||| ||||| |||||||||||||||||||| ||||| || ||||||   || | ||  ||  ||    || ||  ||  | | |  |  |  || ||  | ||  |  |     |     |||    ||  |   |   ||| ||  
GTTGGAATATTCGATGCCACAAACAGTACCAGGAAACGAAGGAATATGCTGATGAAAATGGCTGAGGGAAATTGCAAGgtaacatgatcaatgcacatgaagacagctaagaatttcctgagtatgaaaattaatatggatgtt--tggtgaagcatatgtgttccagggcagaaacaaa--

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|84980594|gb|DW530943.1|DW530943
EST:     CAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAG                         ATCATCTTTTTGGAAACATTATGTAATGACCAAGATGTTCTTGAGAGAAAT
genomic: CAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAGgtatgtttaa ... tgctttctagATCATCTTTTTGGAAACATTATGTAATGACCAAGATGTTCTTGAGAGAAAT
EST: gi|19437252|gb|BM953662.1|BM953662
EST:     CAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAG                         ATCATCTTTTTGGAAACATTATGTAATGACCAAGATGTTCTTGAGAGAAAT
genomic: CAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAGgtatgtttaa ... tgctttctagATCATCTTTTTGGAAACATTATGTAATGACCAAGATGTTCTTGAGAGAAAT
EST: gi|22491067|gb|BU050990.1|BU050990
EST:     CAAGAATGCGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAG                         ATCATCTTTTGGGAACCATTATGTAATGCCCAAGATGTTCTTGAGAGAAAT
genomic: CAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAGgtatgtttaa ... tgctttctagATCATCTTTTTGGAAACATTATGTAATGACCAAGATGTTCTTGAGAGAAAT
EST: gi|67010650|gb|CO439399.1|CO439399
EST:     GGAACATGTCTGNATGNAAAATGGGGCTGAAGGGAAAATGTAAG                         ATCATCTTTTTGGAAACATTATGTAATGACCAAGATGTTCTTGAGAGAAAT
genomic: GGAACATG-CTG-ATG-AAAAT--GGCTGAA-GGAAAATGTAAGgtatgtttaa ... tgctttctagATCATCTTTTTGGAAACATTATGTAATGACCAAGATGTTCTTGAGAGAAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGTATTTTCGATGCCACAAACAGCACAAGAATACGGAGGAACATGCTGATGAAAATGGCTGAAGGAAAATGTAAGgtatgtttaaatcattgtgtgcatcttggacatccttttggtttgaattttttttgtctcctgccaattggcaatagtatttttatatctctaactaagc

- - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA