Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggattttctcacttcccctgtactgggtgtcttggcttcttacctgtcgtccatctttaccttccaatttgttcgatcacccaccattttttagatgggtcgatgagctctaaccataaggtctatacatatctgattgttgttgctgcagTTCAGGAAACTCTTTCCACCGACGAGGTGGGCTGCAGAGTTCAATGCTGCGTTCACAGTGCCTTTCTTCGCCTGGTTGGTTGGGCCTTCTGAG

Basic information

species Vitis vinifera
transcript Vv02s0025g02640.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g02640.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G10340.1 (Glycine max), 3'ss of exon 2
gtgggattttctcact--tcccctgtactgggtgtcttggcttcttacctgtc---gtccatctttaccttccaatttgtt----------cgatcacccacc-----------attttttagatgggtcgatgagctctaaccataaggt-----ctatacatatctgattgt--------tgttgctgcagTTCAGGAAACTCTTTCCACCGACGAGGTGGGCTGCAGAGTTCAATGCTGCGTTCACAGTGCCTTTCTTCGCCTGGTTGGTTGGGCCTTCTGAG
||||    || |||||  ||   ||         | ||   |||| |  | |    ||| ||  |||      ||  || |           |||  |  ||            | | | || |||  |  ||  |     |   | ||       ||  |  |||   ||||         ||||  |||||||| ||||| | ||||| || || |  |||||||||||||| |||||||| || |||||||||||||||| |||||| |||||||| ||||||
gtggatcattttcactgatctattgcgtcactgcttttaatttctaatttatgatggtcaatagttaatagtgaaaatgataaagatgagttgatggctaacttgtgaacacatagtatatacatgcctgtatctgtgtgcaatttgagtcttttactgcatgtattgaattgaattagctatgttattgcagTTCCGGAAATTGTTTCCGCCAACAAAATGGGCTGCAGAGTTTAATGCTGCATTGACAGTGCCTTTCTTCGACTGGTTAGTTGGGCCATCTGAG

upper sequence: Vv02s0025g02640.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G09680.1 (Glycine max), 3'ss of exon 2
------------------gtgggattttctcacttc------ccctgtactgggtgtcttggcttcttacctgtcgtccatctt--taccttccaatttgt--tcgatcacccaccattttttagatgggtcgat-gag-ctctaaccataaggtctatacatatctgattgttgttgctgcagTTCAGGAAACTCTTTCCACCGACGAGGTGGGCTGCAGAGTTCAATGCTGCGTTCACAGTGCCTTTCTTCGCCTGGTTGGTTGGGCCTTCTGAG
                   ||    || |   |||       |    || ||    |  |      | |  || || | | |||   | | |  ||| | |    |    | |       | ||  || |    | ||| |||| |||  | |   |  |   |  |   | | |||  |||||||| ||||| | ||||| || || |  |||||||||||||| |||||||| || |||||||||||||||| |||||| |||||||| ||||||
gtggatggttcattttcactgttgcttccctgcttttaaatacttaatagtgaaaatgataaaga-tgagttgacggctaacttgtgaacatataatatatagatgcctgctcttgggcctgtatgtgtgcaatttgagtctcttaccgcatgtattgaattgaattagctat-gttattgcagTTCCGGAAATTATTTCCGCCAACAAAATGGGCTGCAGAGTTTAATGCTGCTTTGACAGTGCCTTTCTTCGACTGGTTAGTTGGGCCATCTGAG
















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|18459168|gb|BM437446.1|BM437446
EST:     TGGTTAGAGAGGTCCTCTTGTCCATGCTCCCTCCTGGCGCCCCTGATCAG                         TTCAGGAAACTCTTTCCACCGACGAGGTGGGCTGCAGAGTTCAATGCTGCG
genomic: TGGTTAGAGAGGTCCTCTTGTCCATGCTCCCTCCTGGCGCCCCTGATCAGgtgggatttt ... gttgctgcagTTCAGGAAACTCTTTCCACCGACGAGGTGGGCTGCAGAGTTCAATGCTGCG
EST: gi|110384986|gb|EC949461.1|EC949461
EST:     TGGTTAGAGAGGTCCTCTTGTCCATGCTCCCTCCTGGCGCCCCTGATCAG                         TTCAGGAAACTCTTTCCACCGACGAGGTGGGCTGCAGAGTTCAATGCTGCG
genomic: TGGTTAGAGAGGTCCTCTTGTCCATGCTCCCTCCTGGCGCCCCTGATCAGgtgggatttt ... gttgctgcagTTCAGGAAACTCTTTCCACCGACGAGGTGGGCTGCAGAGTTCAATGCTGCG
EST: gi|27580835|gb|CB003530.1|CB003530
EST:     TGGTTAGAGAGGTCCTCTTGTCCATGCTCCCTCCTGGCGCCCCTGATCAG                         GTCAGGAAACTCTTTCCACCGACGAG
genomic: TGGTTAGAGAGGTCCTCTTGTCCATGCTCCCTCCTGGCGCCCCTGATCAGgtgggatttt ... gttgctgcagTTCAGGAAACTCTTTCCACCGACGAG
EST: gi|110374326|gb|EC939496.1|EC939496
EST:     TGGTTAGAGAGGTCCTCTTGTCCATGCTCCCTCCTGGCGCCCCTGATCAG                         TTCAGGAAACTCTTTCCACCGACGAGGTGGGCTGCAGAGTTCAATGCTGCG
genomic: TGGTTAGAGAGGTCCTCTTGTCCATGCTCCCTCCTGGCGCCCCTGATCAGgtgggatttt ... gttgctgcagTTCAGGAAACTCTTTCCACCGACGAGGTGGGCTGCAGAGTTCAATGCTGCG
EST: gi|110379290|gb|EC944475.1|EC944475
EST:     TGGTTAGAGAGGTCCTCTTGTCCATGCTCCCTCCTGGCGCCCCTGATCAG                         TTCAGGAAACTCTTTCCACCGACGAGGTGGGCTGCAGAGTTCAATGCTGCG
genomic: TGGTTAGAGAGGTCCTCTTGTCCATGCTCCCTCCTGGCGCCCCTGATCAGgtgggatttt ... gttgctgcagTTCAGGAAACTCTTTCCACCGACGAGGTGGGCTGCAGAGTTCAATGCTGCG
EST: gi|110376860|gb|EC941936.1|EC941936
EST:     TGGTTAGAGAGGTCCTCTTGTCCATGCTCCCTCCTGGCGCCCCTGATCAG                         TTCAGGAAACTCTTTCCACCGACGAGGTGGGCTGCAGAGTTCAATGCTGCG
genomic: TGGTTAGAGAGGTCCTCTTGTCCATGCTCCCTCCTGGCGCCCCTGATCAGgtgggatttt ... gttgctgcagTTCAGGAAACTCTTTCCACCGACGAGGTGGGCTGCAGAGTTCAATGCTGCG
EST: gi|110372636|gb|EC936820.1|EC936820
EST:     TGGTTAGAGAGGTCCTCTTGTCCATGCTCCCTCCTGGCGCCCCTGATCAG                         TTCAGGAAACTCTTTCCACCGACGAGGTGGGCTGCAGAGTTCAATGCTGCG
genomic: TGGTTAGAGAGGTCCTCTTGTCCATGCTCCCTCCTGGCGCCCCTGATCAGgtgggatttt ... gttgctgcagTTCAGGAAACTCTTTCCACCGACGAGGTGGGCTGCAGAGTTCAATGCTGCG
EST: gi|27755371|gb|CB036126.1|CB036126
EST:     TGGTTAGAGAGGTCCTCTTGTCCATGCTCCCTCCTGGCGCCCCTGATCAG                         TTCAGGAAACTCTTTCCACCGACGAGGTGGGCTGCAGAGTTCAATGCTGCG
genomic: TGGTTAGAGAGGTCCTCTTGTCCATGCTCCCTCCTGGCGCCCCTGATCAGgtgggatttt ... gttgctgcagTTCAGGAAACTCTTTCCACCGACGAGGTGGGCTGCAGAGTTCAATGCTGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggtcgatgagctctaaccataaggtctatacatatctgattgttgttgctgcagTTCAGGAAACTCTTTCCACCGACGAGGTGGGCTGCAGAGTTCAATGCTGCGTTCACAGTGCCTTTCTTCGCCTGGTTGGTTGGGCCTTCTGAG
                           tatacatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggattttctcacttcccctgtactgggtgtcttggcttcttacctgtcgtccatctttaccttccaatttgttcgatcacccaccattttttagatgggtcgatgagctctaaccataaggtctatacatatctgattgttgttgctgcagTTCAGGAAACTCTTTCCACCGACGAGGTGGGCTGCAGAGTTCAATGCTGCGTTCACAGTGCCTTTCTTCGCCTGGTTGGTTGGGCCTTCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC