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

TGTCATAACAGCATCCACTTTTCTGGTGCTGCTTTACTTTTTTATGTCATCATGGTTTGTTTGGGTGCTGATTGTACTCTTTTGCATCGGTGGTGTTGAGgtaatatagtttttccatattattcctcatttatttttgttgctgaaattagaacatattgcatactattggataatttgggaggaaaggagttaaagag...

Basic information

species Vitis vinifera
transcript Vv05s0062g01250.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G082330_T03 (Zea mays), 5'ss of exon 6
TGTCATAACAGCATCCACTTTTCTGGTGCTGCTTTACTTTTTTATGTCATCATGGTTTGTTTGGGTGCTGATTGTACTCTTTTGCATCGGTGGTGTTGAGgtaatatagtttttc---catattattcctcatttatttttgttgctgaaattagaacatat---tgcatactattggataatttgggaggaaaggagttaaagag
| | |||  ||| ||   ||| ||  | || || | ||  || |||||||| ||||| ||||||||||| |||||||| || ||||| |||||| |||||||| |      ||||   || | || | ||  | | || |  | |   | |||   |  |||   | | |  | ||||  | ||    || |  |  |||||    
TATTATAGTAGCTTCAGTTTTCCTCCTCCTCCTGTTCTACTTCATGTCATCTTGGTTCGTTTGGGTGCTAATTGTACTATTCTGCATTGGTGGTATTGAGgtattccctcctttcgggcacagtaattcttctatcttgtactagtgcatattgatatgtatttttcccttttgttggggagttc---agcactgaggttaat---

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G082330_T01 (Zea mays), 5'ss of exon 6
TGTCATAACAGCATCCACTTTTCTGGTGCTGCTTTACTTTTTTATGTCATCATGGTTTGTTTGGGTGCTGATTGTACTCTTTTGCATCGGTGGTGTTGAGgtaatatagtttttc---catattattcctcatttatttttgttgctgaaattagaacatatt---gcatactattggataatttgggaggaaaggagttaaagag------------
| | |||  ||| ||   ||| ||  | || || | ||  || |||||||| ||||| ||||||||||| |||||||| || ||||| |||||| |||||||| |      ||||   || | || | ||  | | || |  | |   | |||   |  ||||    | |  | ||||  | ||  | |   | |    |   ||             
TATTATAGTAGCTTCAGTTTTCCTCCTCCTCCTGTTCTACTTCATGTCATCTTGGTTCGTTTGGGTGCTAATTGTACTATTCTGCATTGGTGGTATTGAGgtattccctcctttcgggcacagtaattcttctatcttgtactagtgcatattgatatgtatttttcccttttgttggggagttcagcactgaggttaatggtgatattatcttgcag

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA08G47600.1 (Glycine max), 5'ss of exon 5
TGTCATAACAGCATCCACTTTTCTGGTGCTGCTTTACTTTTTTATGTCATCATGGTTTGTTTGGGTGCTGATTGTACTCTTTTGCATCGGTGGTGTTGAGgtaatatagttt-ttccatattattcctcatttatttttgttgctgaaat-----tag--aacatattgcatactattggataatttgggaggaaaggagttaaagag
||||||| |||| || || ||||| |||||  | | ||| ||||||||||| |||||||| ||||||||||||||||| || ||||| |||||| |||||||||| ||| |  || | |   |||    ||||| || |  |   | | |     ||   |||| |    ||  ||||  ||  | ||  | ||| || ||       
TGTCATAGCAGCGTCTACCTTTCTTGTGCTATTGTTCTTCTTTATGTCATCTTGGTTTGTCTGGGTGCTGATTGTACTTTTCTGCATTGGTGGTATTGAGgtaatgtagctcatttccttggatttggaatttacttctactctagtactccttctaattaacaaaaaaaatcatatttcatggtgtgc-atgaagggggt-------

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA18G53880.1 (Glycine max), 5'ss of exon 5
TGTCATAACAGCATCCACTTTTCTGGTGCTGCTTTACTTTTTTATGTCATCATGGTTTGTTTGGGTGCTGATTGTACTCTTTTGCATCGGTGGTGTTGAGgtaatatagttt-ttccatattattcctcatttatttttgttgctgaaat---tagaacatattgcatactat--tggataatttgggaggaaaggagttaaagag
||||||| |||| || || ||||| |||||  | | ||| || |||||| | |||||||| ||||||||||||||||| || ||||| |||||| |||||||||| ||| |  || | |   |||    ||||| || |  |   | | |   |  ||   | |  |||  ||  |  ||  | ||   | |  ||  ||      
TGTCATAGCAGCGTCTACCTTTCTTGTGCTATTGTTCTTCTTCATGTCAACTTGGTTTGTCTGGGTGCTGATTGTACTTTTCTGCATTGGTGGTATTGAGgtaatgtagctcatttccttggatttgaaatttacttctactctggtactctttctaattaactaaatatcatgtttcatggtgtgcatgaaggggtatt------

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA20G39260.1 (Glycine max), 5'ss of exon 5
TGTCATAACAGCATCCACTTTTCTGGTGCTGCTTTACTTTTTTATGTCATCATGGTTTGTTTGGGTGCTGATTGTACTCTTTTGCATCGGTGGTGTTGAGgtaatatagtttttc---catattattcctcatttatttttgttgctgaaattagaacatattgcatactattggataatttgggaggaaaggagttaaagag
 ||||| || ||||| |||||||| ||||| || | ||| || ||||| || |||||| | |||||||||||| |||| || ||||| |||||| ||||||| |  ||  |||||    || ||| |||| |  |  | |  ||     || || | | |||| |||  | | |   ||  ||   |      | |       
CGTCATTACGGCATCTACTTTTCTTGTGCTACTGTTCTTCTTCATGTCGTCTTGGTTTATCTGGGTGCTGATTATACTTTTCTGCATTGGTGGTATTGAGgtgaggtacattttcgtggattttactcctaacct--tctaattaaaataactatatcttatttcatgatgt-gcccaaggtgtcggttccttattcttgttc

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA10G44490.1 (Glycine max), 5'ss of exon 6
TGTCATAACAGCATCCACTTTTCTGGTGCTGCTTTACTTTTTTATGTCATCATGGTTTGTTTGGGTGCTGATTGTACTCTTTTGCATCGGTGGTGTTGAGgtaatatagtttttccatattattcctcatttatttttgttgctgaaattagaacatattgcatactattggataatttgggaggaaagg-agttaaagag-----
 ||||| || ||||| |||||||| || || || | ||| || ||||| || |||||| | |||||||||||| |||| || ||||| |||||| ||||||| |  ||| |  |     |   |     |||  |  |     |  ||||| |||| ||   ||  ||||  || || ||     |  |   | |    |      
CGTCATCACTGCATCTACTTTTCTTGTACTACTGTTCTTCTTCATGTCGTCTTGGTTTATCTGGGTGCTGATTATACTTTTCTGCATTGGTGGTATTGAGgtgaggtagctcattttcgtggat-----tttgctcctaaccttccaattaaaacaaat-atatcttatttcatgatgtgcccaaagtgttggctccttattcttg

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|110383722|gb|EC948114.1|EC948114
EST:     CATGGTTTGTTTGGGTGCTGATTGTACTCTTTTGCATCGGTGGTGTTGAG                         GGAATGCATGCTTGTATAGTTAACTCTGATACTAAG
genomic: CATGGTTTGTTTGGGTGCTGATTGTACTCTTTTGCATCGGTGGTGTTGAGgtaatatagt ... ttcctttcagGGAATGCATGCTTGTATAGTTA-CTCTGATACTAAG
EST: gi|294965259|gb|GW838946.1|GW838946
EST:     CATGGTTTGTTTGGGTGCTGATTGTACTCTTTTGCATCGGTGGTGTTGAG                         GGAATGCATGCTTGTATAGTTACTCTGATACTAAG
genomic: CATGGTTTGTTTGGGTGCTGATTGTACTCTTTTGCATCGGTGGTGTTGAGgtaatatagt ... ttcctttcagGGAATGCATGCTTGTATAGTTACTCTGATACTAAG
EST: gi|110731688|gb|EE106318.1|EE106318
EST:     TGATTGTACTCTTTTGCATCGGTGGTGTTGAG                         GGAATGCATGCTTGTATAGTTACTCTGATACTAAG
genomic: TGATTGTACTCTTTTGCATCGGTGGTGTTGAGgtaatatagt ... ttcctttcagGGAATGCATGCTTGTATAGTTACTCTGATACTAAG
EST: gi|110687402|gb|EE064779.1|EE064779
EST:     CATGGTTTGTTTGGGTGCTGATTGTACTCTTTTGCATCGGTGGTGTTGAG                         GGAATGCATGCTTGTATAGTTACTCTGATACTAAG
genomic: CATGGTTTGTTTGGGTGCTGATTGTACTCTTTTGCATCGGTGGTGTTGAGgtaatatagt ... ttcctttcagGGAATGCATGCTTGTATAGTTACTCTGATACTAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTCATAACAGCATCCACTTTTCTGGTGCTGCTTTACTTTTTTATGTCATCATGGTTTGTTTGGGTGCTGATTGTACTCTTTTGCATCGGTGGTGTTGAGgtaatatagtttttccatattattcctcatttatttttgttgctgaaattagaacatattgcatactattggataatttgggaggaaaggagttaaagag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaacata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggaaag