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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttcgtagatatcaaggtgatgcataaaaagtaaggcctaattatgcccttagttttctggttgctctttctagtaatccactggtatatgtttaatagGCTGGAACATACATCAAGGAATTTGTGCATGGTGATCTTGGACGCACGCATCCCAG

Basic information

species Zea mays
transcript GRMZM2G101383_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101383_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os04g47380.1 (Oryza sativa), 3'ss of exon 13
gtttcgtagatatcaaggtga-tgcataaaaagtaaggcc--taattatgcccttagttttctggttgctctttctagt--aatccactggtatatgtttaatagGCTGGAACATACATCAAGGAATTTGTGCATGGTGATCTTGGACGCACGCATCCCAG
    | || ||      |||| | | | | |||  |   |   ||         || | |   | ||||||  ||  ||  |||| ||     | |   ||  ||||||| |||||||| ||||| |||||||| || |||||||||||||| || || ||
----cttaaatgcttttgtgaatccgtcataaggcaattcatcaaaagcatttatattctgtagtttgctccctccggtttaatcaaccttggtgtccata-cagGCTGGGACATACATAAAGGAGTTTGTGCACGGAGATCTTGGACGCACACACCCAAG

upper sequence: GRMZM2G101383_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA14G39890.1 (Glycine max), 3'ss of exon 13
gtttcgtagatatca-aggtgatgcataaaaagtaaggcctaattatgcccttagttttctggt--tgctctttctagtaatccactg-gtatatgttta-atagGCTGGAACATACATCAAGGAATTTGTGCATGGTGATCTTGGACGCACGCATCCCAG
        | ||| | ||  | | | |||    | | |   ||  |   |  || ||    | |  ||    |   |   ||| | |  |  | |  ||  | ||||||| || ||||||||||||||||| ||||| |||||||||||||| ||||| ||
-----aatgttataatagacggtccttaagtcattatgtacaacgaaatctgtaattactagttagtggaagtctgaaagatctaatatgcttgtacttgtacagGCTGGGACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCATCCTAG

upper sequence: GRMZM2G101383_T02 (Zea mays), 3'ss of exon 12
lower sequence: AT1G20410.1 (Arabidopsis thaliana), 3'ss of exon 13
gtttcgtagatatcaaggtgatgcataaaaagtaaggcctaattatgcccttagttttctggttgctctttctag-taatccactggtatatgtttaata-----gGCTGGAACATACATCAAGGAATTTGTGCATGGTGATCTTGGACGCACGCATCCCAG
                               ||     | | || |  |       |  |  |   ||||   || |   | | |  || || || ||||     |||||||||||||||||| || ||||| ||||| |||||||| || ||   ||||||
-------------------------------gttgctacaacttctaactc--acctcattatcattcttgaaagatgggcaagttttaaattttcaataatgcagGCTGGAACATACATCAAAGAGTTTGTTCATGGAGATCTTGGTCGTACCACTCCCAG

upper sequence: GRMZM2G101383_T02 (Zea mays), 3'ss of exon 12
lower sequence: Vv18s0001g00500.t01 (Vitis vinifera), 3'ss of exon 13
--------------------------------------------------------gtttcgtagatatcaaggtgatgcataaaaagtaaggcctaattatgcccttag--ttttctggttgctcttt----ctagtaatccactggtat--atgtttaa----tagGCTGGAACATACATCAAGGAATTTGTGCATGGTGATCTTGGACGCACGCATCCCAG
                                                        ||||  |   ||   |    |       | | ||      | |  |    ||||  |||| || |  || |||     ||||||   |||  |    || || ||     ||||||||||||| |||||||||||||| || ||||||||||||||||| ||||| ||
gtacttaattttgcatctgctttatcaaatatttgctggatactgactattttcgagttttatgcttaaggaaagaacctggctagactact-ttgagtcctatggttagccttttatgttcactttttggaattagtaaaatactaatggtgatattcaaaatgcagGCTGGAACATATATCAAGGAATTTGTTCACGGTGATCTTGGACGCACCCATCCTAG

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|211026724|gb|FL476745.1|FL476745
EST:     AGAAAATCACAGGCAGCTCAAACTACTACTTGCTCCATCTATGCACACAG                         GCTGGAACATACATCAAGGAATTTGTGCATGGTGATCTTGGACGCACGCAT
genomic: AGAAAATCACAGGCAGCTCAAACTACTACTTGCTCCATCTATGCACACAGgttagaattg ... tgtttaatagGCTGGAACATACATCAAGGAATTTGTGCATGGTGATCTTGGACGCACGCAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcccttagttttctggttgctctttctagtaatccactggtatatgtttaatagGCTGGAACATACATCAAGGAATTTGTGCATGGTGATCTTGGACGCACGCATCCCAG
                                         tatatgtttaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttcgtagatatcaaggtgatgcataaaaagtaaggcctaattatgcccttagttttctggttgctctttctagtaatccactggtatatgtttaatagGCTGGAACATACATCAAGGAATTTGTGCATGGTGATCTTGGACGCACGCATCCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA