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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgactgttttcagtttttgaccatacgattgtttacattgttcaattctctatttatgttatttgttgagcttgaataaatgacattattcagAGTGTGCAAGATGTAACTGGTTCAGAATTTGAACTATTCATGGGGTTTCTGCGAAGCTTGAGCATATTTGGGGATTCTGCTCCTAGAGAGTCCTTTCAAG

Basic information

species Zea mays
transcript GRMZM2G014577_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014577_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g20930.1 (Oryza sativa), 3'ss of exon 6
gtatgttgac-tgttttcagtttttgaccatacgattgtttac---attgttcaattctctatttatgttatttgttgagcttgaataaa---tgacattattcagAGTGTGCAAGATGTAACTGGTTCAGAATTTGAACTATTCATGGGGTTTCTGCGAAGCTTGAGCATATTTGGGGATTCTGCTCCTAGAGAGTCCTTTCAAG
||||| | | |||||||||||| | | |||| ||| | || || | || || || || | || ||| ||| | || || || ||||||||||||| ||||||||| || | |||||| || ||||||||| || ||||| || | || |||||||||||||| |||||| ||||||| || || |
gtatgccttcattatttcagtttttggctgtctgatttttttttcagtgatttaagtttccatgtacattgtgtgatgacctttgacaatggctgttataattcagAGTGTGCTAGATGTAACCGGGTTGGAATTTAAATTATTCATGGATTTCCTGCGGAGTCTCAGTATATTTGGGGATTCCGCTCCTCGAGAGTCGTTCCAGG

upper sequence: GRMZM2G014577_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv19s0014g01790.t01 (Vitis vinifera), 3'ss of exon 6
gtatgttgactgttttcagtttttgaccatacgattgtttacattgttca--att--ctctatttatgttatttgttgagcttgaataaatgacattattcagAGTGTGCAAGATGTAACTGGTTCAGAATTTGAACTATTCATGGGGTTTCTGCGAAGCTTGAGCATATTTGGGGATTCTGCTCCTAGAGAGTCCTTTCAAG
| | |||||| | | || || ||| | || ||| || | | | ||| | ||| ||| || | | | |||||| |||||||||||||||| |||||||| |||| ||||||| || || ||||||||||| | ||||| | |||||| |||| | ||||
--ctctcctatgttttagtcatgatagtatcagagtgtcagctgtgatcatggttgccacaagttactgaaagtgtgacaattggatttg-aatgtactccagAGTTTGCAAGATGTAACTGGGGCAGAATTTAAACTGTTCATGGACTTCTTGAGAAGCTTGAGCTTGTTTGGACAGAAGGCTCCTGCAGAGCGTGTACAAG
















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|74234428|gb|DT642342.1|DT642342
EST:     TGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGGTAAAGAAA                         AGTGTGCAAGATGTAACTGGTTCAGAATTTGAACTATTCATGGGGTTTCTG
genomic: TGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGGTAAAGAAAgtatgttgac ... cattattcagAGTGTGCAAGATGTAACTGGTTCAGAATTTGAACTATTCATGGGGTTTCTG




















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), 46 (downstream exon)
Score: 131

GTTTTTCCTCTTAAAGCAGAGCTACTGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGGTAAAGAAAgtatgttgac ... cattattcagAGTGTGCAAGATGTAACTGGTTCAGAATTTGAACTATTCATGGGGTTTCTGCGAAGCTTGAGCATATTTGGGGATTCTGCTCCTAGAGAGTCCTTTCAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 96

GTTTTTCCTCTTAAAGCAGAGCTACTGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGGTAAAGAAAgtatgttgac ... cattattcagAGTGTGCAAGATGTAACTGGTTCAGAATTTGAACTATTCATGGGGTTTCTGCGAAGCTTGAGCATATTTGGGGATTCTGCTCCTAGAGAGTCCTTTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 76

GTTTTTCCTCTTAAAGCAGAGCTACTGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGGTAAAGAAAgtatgttgac ... cattattcagAGTGTGCAAGATGTAACTGGTTCAGAATTTGAACTATTCATGGGGTTTCTGCGAAGCTTGAGCATATTTGGGGATTCTGCTCCTAGAGAGTCCTTTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 104

GTTTTTCCTCTTAAAGCAGAGCTACTGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGGTAAAGAAAgtatgttgac ... cattattcagAGTGTGCAAGATGTAACTGGTTCAGAATTTGAACTATTCATGGGGTTTCTGCGAAGCTTGAGCATATTTGGGGATTCTGCTCCTAGAGAGTCCTTTCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttcaattctctatttatgttatttgttgagcttgaataaatgacattattcagAGTGTGCAAGATGTAACTGGTTCAGAATTTGAACTATTCATGGGGTTTCTGCGAAGCTTGAGCATATTTGGGGATTCTGCTCCTAGAGAGTCCTTTCAAG
     aattctctatttatgt  TA-rich tract