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

gtctctatctctatgtgttatgctgttttatgttctattacgggtgatctggataaattcttacatgatttagttaaacctcaaatgttttctctcccctgtaaaaaacactttaaagGTTAGGGAGAAACCCACAAGTTTAAGGGCTGCTTGGGAGTTGCTGGAGATATTCTATGTTGATAAACGTTTGCAAGGCTGGCTTCCTGAGCGTCTTGTTG

Basic information

species Zea mays
transcript GRMZM2G409430_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G409430_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g54240.2 (Oryza sativa), 3'ss of exon 1
gtctctatctctatgtgttatgctgttttatgttctattacgggtgatctggataaattcttacatgatttagttaaacctcaaatgttttctctcccctgtaaaaaacactttaaagGTTAGGGAGAAACCCACAAGTTTAAGGGCTGCTTGGGAGTTGCTGGAGATATTCTATGTTGATAAACGTTTGCAAGGCTGGCTTCCTGAGCGTCTTGTTG
||  | || ||||||||| |   |||||  |||| | || |      | ||  | || |   |  |  |||  ||     |  || ||  |         ||| |    |  ||  |||| | |||||| || || ||||||| |||||| ||||||||||| |||||||||| |||||||||||  ||||||   |||||||| |||||||||||||
gtgaccatatctatgtgtcacattgtttcctgttttcttgctttgcctttgtttgaagttaaatttactttt-ttgcctatagaaagtaattg-------gtatattttatcttgcagGTCAAGGAGAAGCCTACTAGTTTAAAGGCTGCGTGGGAGTTGCTAGAGATATTCTTTGTTGATAAACAGTTGCAAACTTGGCTTCCAGAGCGTCTTGTTG
















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|18661883|gb|BM501632.1|BM501632
EST:     ACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAG                         GTTAGGGAGAAACCCACAAGTTTAAGGGCTGCTTGGGAGTTGCTGGAGATA
genomic: ACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAGgtctctatct ... cactttaaagGTTAGGGAGAAACCCACAAGTTTAAGGGCTGCTTGGGAGTTGCTGGAGATA
EST: gi|101391554|gb|EB817713.1|EB817713
EST:     ACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAG                         GTTAGGGAGAAACCCACAAGTTTAAGGGCTGCTTGGGAGTTGCTGGAGATA
genomic: ACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAGgtctctatct ... cactttaaagGTTAGGGAGAAACCCACAAGTTTAAGGGCTGCTTGGGAGTTGCTGGAGATA
EST: gi|71423081|gb|DR805945.1|DR805945
EST:     ACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAG                         GTTAGGGAGAAACCCACAAGTTTAAGGGCTGCTTGGGAGTTGCTGGAGATA
genomic: ACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAGgtctctatct ... cactttaaagGTTAGGGAGAAACCCACAAGTTTAAGGGCTGCTTGGGAGTTGCTGGAGATA
EST: gi|149010019|gb|EE041829.2|EE041829
EST:     ACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAG                         GTTAGGGAGAAACCCACAAGTTTAAGGGCTGCTTGGGAGTTGCTGGAGATA
genomic: ACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAGgtctctatct ... cactttaaagGTTAGGGAGAAACCCACAAGTTTAAGGGCTGCTTGGGAGTTGCTGGAGATA
EST: gi|101401938|gb|EB822595.1|EB822595
EST:     ACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAG                         GTTAGGGAGAAACCCACAAGTTTAAGGGCTGCTTGGGAGTTGCTGGAGATA
genomic: ACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAGgtctctatct ... cactttaaagGTTAGGGAGAAACCCACAAGTTTAAGGGCTGCTTGGGAGTTGCTGGAGATA
EST: gi|71449560|gb|DR830610.1|DR830610
EST:     ACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAG                         GTTAGGGAGAAACCCACAAGTTTAAGGGCTGCTTGGGAGTTGCTGGAGATA
genomic: ACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAGgtctctatct ... cactttaaagGTTAGGGAGAAACCCACAAGTTTAAGGGCTGCTTGGGAGTTGCTGGAGATA
EST: gi|149015081|gb|EE044836.2|EE044836
EST:     ACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAG                         GTTAGGGAGAAACCCACAAGTTTAAGGGCTGCTTGGGAGTTGCTGGAGATA
genomic: ACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAGgtctctatct ... cactttaaagGTTAGGGAGAAACCCACAAGTTTAAGGGCTGCTTGGGAGTTGCTGGAGATA
EST: gi|78113107|gb|DV531501.1|DV531501
EST:     ACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAG                         GTTAGGGAGAAACCCACAAGTTTAAGGGCTGCTTGGGAGTTGCTGGAGATA
genomic: ACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAGgtctctatct ... cactttaaagGTTAGGGAGAAACCCACAAGTTTAAGGGCTGCTTGGGAGTTGCTGGAGATA
EST: gi|18963165|gb|BM660276.1|BM660276
EST:     ACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAG                         GCTAGGGAGAAACCCACAAGTTTAAGGGCTGCTTGGGAGTTGCTGGAGATA
genomic: ACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAGgtctctatct ... cactttaaagGTTAGGGAGAAACCCACAAGTTTAAGGGCTGCTTGGGAGTTGCTGGAGATA

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: 104

GTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAGgtctctatct ... cactttaaagGTTAGGGAGAAACCCACAAGTTTAAGGGCTGCTTGGGAGTTGCTGGAGATATTCTATGTTGATAAACGTTTGCAAGGCTGGCTTCCTGAGCGTCTTGTTG


Block sizes: 49 (upstream exon), 33 (downstream exon)
Score: 19

GTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAGgtctctatct ... cactttaaagGTTAGGGAGAAACCCACAAGTTTAAGGGCTGCTTGGGAGTTGCTGGAGATATTCTATGTTGATAAACGTTTGCAAGGCTGGCTTCCTGAGCGTCTTGTTG


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 38

GTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAGgtctctatct ... cactttaaagGTTAGGGAGAAACCCACAAGTTTAAGGGCTGCTTGGGAGTTGCTGGAGATATTCTATGTTGATAAACGTTTGCAAGGCTGGCTTCCTGAGCGTCTTGTTG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 32

GTGGCAATATGTGCTTGAATACAGCAAAACCATTGGCAGTCTCCTTGGGAACCCAGACCCTTCTGGTTTCATGATTGAAGAACCCAAGACAATTCTTAAGgtctctatct ... cactttaaagGTTAGGGAGAAACCCACAAGTTTAAGGGCTGCTTGGGAGTTGCTGGAGATATTCTATGTTGATAAACGTTTGCAAGGCTGGCTTCCTGAGCGTCTTGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgatttagttaaacctcaaatgttttctctcccctgtaaaaaacactttaaagGTTAGGGAGAAACCCACAAGTTTAAGGGCTGCTTGGGAGTTGCTGGAGATATTCTATGTTGATAAACGTTTGCAAGGCTGGCTTCCTGAGCGTCTTGTTG
                                      taaaaaacactttaaa  TA-rich tract