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_T01
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

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), 48 (downstream exon)
Score: 431

CCTTTCTCGGAGTCTGAAGTCCGCAACTGGTGCTTTCAGATATTTCAGGCTCTTGCTTACATGCATCAGAGGGGCTACTTTCATCGTGACCTCAAACCTGgtaggtttgc ... gattgtgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTGCAAGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 280

CCTTTCTCGGAGTCTGAAGTCCGCAACTGGTGCTTTCAGATATTTCAGGCTCTTGCTTACATGCATCAGAGGGGCTACTTTCATCGTGACCTCAAACCTGgtaggtttgc ... gattgtgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTGCAAGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 249

CCTTTCTCGGAGTCTGAAGTCCGCAACTGGTGCTTTCAGATATTTCAGGCTCTTGCTTACATGCATCAGAGGGGCTACTTTCATCGTGACCTCAAACCTGgtaggtttgc ... gattgtgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTGCAAGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 386

CCTTTCTCGGAGTCTGAAGTCCGCAACTGGTGCTTTCAGATATTTCAGGCTCTTGCTTACATGCATCAGAGGGGCTACTTTCATCGTGACCTCAAACCTGgtaggtttgc ... gattgtgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTGCAAGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcgtctgaatcagcagctcagttttactgataatggcatgccttgattgtgcagAGAATCTGTTGGTTAGCAAAGATGTCATAAAGCTAGCAGACTTTGGTCTTGCAAGGGAAGTTTCATCTTTGCCGCCATATACAGAATATGTCTCAACTCG
                    agtttta  TA-rich tract