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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctaaatgatactttcttgtactagagggcagtatatgacatgattgcgtctgaatcagcagctcagttttactgataatggcatgccttgattgtgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTGCAAGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCG

Basic information

species Zea mays
transcript GRMZM2G108829_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g47220.3 (Oryza sativa), 3'ss of exon 3
cctaaatgatactttcttgtactagagggcagtatatgacatgattgcgtctgaatcagcagctcagttttactgataatggca--tgccttgattgtgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTGCAAGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCG
 ||     |      |  |   ||      | || || | ||  || | | ||     | |      || ||   ||      |    |  |  |  ||||||||||||||||||||||||||||||||||||||| || |||||||||||||||||||||||| ||||  |||| ||||| ||||||||||| ||||||||
-ctttgcaaactgaccgagatatactttctaataaat-atatactttcatgtgggattgtattgtgcttatagctatggcactaatcactgtactaatgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTGGCGGACTTTGGTCTTGCAAGGGAAGTTACATCCGTGCCACCATACACAGAATATGTGTCAACTCG
















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|60349468|gb|DN216441.1|DN216441
EST:     TCTTGCTTACATGCATCAGAGGGGCTACTTTCATCGTGACCTCAAACCTG                         AGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTG
genomic: TCTTGCTTACATGCATCAGAGGGGCTACTTTCATCGTGACCTCAAACCTGgtaggtttgc ... gattgtgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTG
EST: gi|211496286|gb|FL041698.1|FL041698
EST:     TCTTGCTTACATGCATCAGAGGGGCTACTTTCATCGTGACCTCAAACCTG                         AGAATCTGTTAGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTG
genomic: TCTTGCTTACATGCATCAGAGGGGCTACTTTCATCGTGACCTCAAACCTGgtaggtttgc ... gattgtgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTG
EST: gi|32871065|gb|CF010747.1|CF010747
EST:     TCTTGCTTACATGCATCAGAGGGGCTACTTTCATCGTGACCTCAAACCTG                         AGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTG
genomic: TCTTGCTTACATGCATCAGAGGGGCTACTTTCATCGTGACCTCAAACCTGgtaggtttgc ... gattgtgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTG
EST: gi|32932540|gb|CF037352.1|CF037352
EST:     TCTTGCTTACATGCATCAGAGGGGCTACTTTCATCGTGACCTCAAACCTG                         AGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTG
genomic: TCTTGCTTACATGCATCAGAGGGGCTACTTTCATCGTGACCTCAAACCTGgtaggtttgc ... gattgtgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTG
EST: gi|31350422|gb|CD434779.1|CD434779
EST:     TCTTGCTTACATGCATCAGAGGGGCTACTTTCTTCTTGACCTCAAACCTG                         AGAATCTGTTAGTGAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTG
genomic: TCTTGCTTACATGCATCAGAGGGGCTACTTTCATCGTGACCTCAAACCTGgtaggtttgc ... gattgtgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTG
EST: gi|32869779|gb|CF009461.1|CF009461
EST:     TCTTGCTTACATGCATCAGAGGGGCTACTTTCATCGTGACCTCAAACCTG                         AGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTG
genomic: TCTTGCTTACATGCATCAGAGGGGCTACTTTCATCGTGACCTCAAACCTGgtaggtttgc ... gattgtgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTG
EST: gi|47961778|gb|CN844487.1|CN844487
EST:     TCTTGCTTACATGCATCAGAGGGGCTACTTTCATCGTGACCTCAAACCTG                         AGAATCTGTTAGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTG
genomic: TCTTGCTTACATGCATCAGAGGGGCTACTTTCATCGTGACCTCAAACCTGgtaggtttgc ... gattgtgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTG
EST: gi|67011156|gb|CO439905.1|CO439905
EST:     TCTTGCTTACATGCATCAGAGGGGCTACTTTCATCGTGACCTCAAACCTG                         AGAATCTGTTAGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTG
genomic: TCTTGCTTACATGCATCAGAGGGGCTACTTTCATCGTGACCTCAAACCTGgtaggtttgc ... gattgtgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTG
EST: gi|211496285|gb|FL041697.1|FL041697
EST:     TCTTGCTTACATGCATCAGAGGGGCTACTTTCATCGTGACCTCAAACCTG                         AGAATCTGTTAGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTG
genomic: TCTTGCTTACATGCATCAGAGGGGCTACTTTCATCGTGACCTCAAACCTGgtaggtttgc ... gattgtgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcgtctgaatcagcagctcagttttactgataatggcatgccttgattgtgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTGCAAGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCG
                    agtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctaaatgatactttcttgtactagagggcagtatatgacatgattgcgtctgaatcagcagctcagttttactgataatggcatgccttgattgtgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTGCAAGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCG

- - - - - - tttcttg
- - - - - - - - - - - - - - - - - - - - -tgattgc
- - - - - - - - - - - - - - - - - - - - - - - - -tctgaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - cagcagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcatgc