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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccgttcatttctgtcctaccctttgtccacttctgttttatatttttcttttatctgattaaaatatgtaattctcatattatttgccttgagtttatagGATGAGGTAGAGGACAATTTCGCCATCGTCTTTGCTGCTATGGGAGTAAACATGGAAACAGCACAATTTTTTAAGCGTGATTTTGAGGAAAATGGATCCA

Basic information

species Vitis vinifera
transcript Vv18s0001g01020.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 7
-ccgttcatttctgtcctaccc-tttgtccacttctgttttatatttttcttttatctgattaaaatatgtaattctcatattatttgccttgagtttatagGATGAGGTAGAGGACAATTTCGCCATCGTCTTTGCTGCTATGGGAGTAAACATGGAAACAGCACAATTTTTTAAGCGTGATTTTGAGGAAAATGGATCCA
   ||    |   |  | |      ||| || || | |            ||||   |   | ||  |  |  || |  |  |  || | || | | |  ||| ||  | ||| ||||| || || ||||| ||||||||||||||||| || ||||||||||| ||||| || || ||||||||||| || || || || |
atggtatgctgtagagcaatttacctgttcatttttttccatggagacatttttgcatcgctgaatcac-tgcttatt-tgctgattacttttaatctccagGGTGGTGAAGATGACAACTTTGCTATCGTGTTTGCTGCTATGGGAGTGAATATGGAAACAGCCCAATTCTTCAAACGTGATTTTGAAGAGAACGGGTCAA

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 7
ccgttcatttctgtcctaccctttgtccacttctgttttatatttttcttttatctgattaaa-atatgtaattctcatattatttgccttg-agtttatagGATGAGGTAGAGGACAATTTCGCCATCGTCTTTGCTGCTATGGGAGTAAACATGGAAACAGCACAATTTTTTAAGCGTGATTTTGAGGAAAATGGATCCA
   |  |       | | |   | |  || || ||| ||| || | |  ||||  ||  |||| ||   | | || |   || |     ||| |   |  ||| ||  | ||| ||||| || || || || ||||||||||||||||| |||||||||||||| ||||| || || ||||||||||| || ||||| ||||
tactgtaaggtcaacattcatatggagca-ttgtgtatta-atgtatgctttacatgtctaaatatggcttaatcactgcttctgatttttgtaacctgcagGGTGGTGAAGATGACAACTTTGCTATTGTGTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAATGGTTCCA

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 7
ccgttcatttctgtcctaccctt---tgtccacttctgt-tttatatttttcttttatctgattaaaatatgtaatt-ctcatattatttgccttgagtttatagGATGAGGTAGAGGACAATTTCGCCATCGTCTTTGCTGCTATGGGAGTAAACATGGAAACAGCACAATTTTTTAAGCGTGATTTTGAGGAAAATGGATCCA
   ||| | |  |  | ||  ||   ||     || ||| || || | |   ||  || |  | | ||    || |  ||  |  |  ||   ||     |  ||| ||  | ||| ||||| || || || || ||||||||||||||||| |||||||||||||| ||||| || || ||||||||||| || || || ||||
---ttcctgtgaggtcaacatttatatggaggattgtgtattcatgtatgctttacatgtcttaataaggcttagtcactggttctgattttatta--cctgcagGGTGGTGAAGATGACAACTTTGCTATTGTGTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAACGGTTCCA

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 7
ccgttcatttctgtcctaccctttgtccacttctgttttatatttttcttttatctgattaaaatatgtaattctcatattatttgccttgagtttat--agGATGAGGTAGAGGACAATTTCGCCATCGTCTTTGCTGCTATGGGAGTAAACATGGAAACAGCACAATTTTTTAAGCGTGATTTTGAGGAAAATGGATCCA
   |  | |||| |         | |     || || |   | ||    | ||  |   |    | |||||    |||  ||||  | ||| |||| |  ||||| | | |||||||||||| || || || ||||| |||||||| ||||||||||| ||||| || ||||| |||||||||||||| ||||||||||| |
tactcaacttctatgaagattgatatagcagtcagtctctcaattcctgtgtagttttgtttgctttgtaaactccat--tattaacattgtgtttttccagGATCATGGAGAGGACAATTTTGCAATTGTTTTTGCAGCTATGGGTGTAAACATGGAGACAGCTCAGTTTTTCAAGCGTGATTTTGAAGAAAATGGATCGA

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 7
-----ccgttcatttctgtcctaccctttgtccacttctgttttatatttttcttttatctgattaaaatatgtaattctcatattatttgccttgagtttatagGATGAGGTAGAGGACAATTTCGCCATCGTCTTTGCTGCTATGGGAGTAAACATGGAAACAGCACAATTTTTTAAGCGTGATTTTGAGGAAAATGGATCCA
       ||  |  |      |    |||||  || |   | ||  |  ||   |   ||| || | |  | | | |  |  |  |  |||  ||   |||  ||||| | | |||||||||||| || || || ||||| |||||||| || |||||||| ||||| || || || ||||| |||||||| ||||||||||| |
agttgttgtcaaaattgaatttcttgtttgtagacattcctcttcaacgttggct--gtctcataatatcaaggattctttctcattcttgtgtt---tttccagGATCATGGAGAGGACAATTTTGCAATTGTGTTTGCAGCTATGGGTGTGAACATGGAGACAGCTCAGTTCTTCAAGCGAGATTTTGAAGAAAATGGATCAA

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 6
ccgttcatttctgtcctaccctttgtccacttctgttttatatttttcttttatctg--attaaaatatgtaattctcatattatttgccttgagtttatagGATGAGGTAGAGGACAATTTCGCCATCGTCTTTGCTGCTATGGGAGTAAACATGGAAACAGCACAATTTTTTAAGCGTGATTTTGAGGAAAATGGATCCA
                            ||   ||||||   ||| |||| | ||||   || | |    | | | |            |||  || |  ||  ||| || || ||||| || || ||||||||||| |||||||| || |||||||| || ||||| ||||| ||  | |||||||||||||||||||| |
--------------------------gtacaattgttttccgtttatcttctgtctgttgttgagactgatgagttt------------ctttcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGA

upper sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 6
ccgttcatttctgtcctaccctttgtccacttctgttttatatttttcttttatctg--attaaaatatgtaattctcatattatttgccttgagtttatagGATGAGGTAGAGGACAATTTCGCCATCGTCTTTGCTGCTATGGGAGTAAACATGGAAACAGCACAATTTTTTAAGCGTGATTTTGAGGAAAATGGATCCA
                            |||| ||||||   ||| |||| | ||||   || | |    | | | |            |||  || |  ||  ||| || || ||||| || || ||||||||||| |||||||| || |||||||| || ||||| ||||| ||  | |||||||||||||||||||| |
--------------------------gtacttttgttttccgtttatcttctgtctgttgttgagactgatgagttt------------ctttcgtatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGAGATTTTGAGGAAAATGGATCGA

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|33402236|gb|CF207863.1|CF207863
EST:     GTCAGGCTGGTCTTGTAAAGCGGTTGGAAAAAGCTGGAAATCTCCTAGAG                         GATGAGGTAGAGGACAATTTCGCCATCGTCTTTGCTGCTATGGGAGTAAAC
genomic: GTCAGGCTGGTCTTGTAAAGCGGTTGGAAAAATCTGGAAATCTCCTAGAGgtactagttt ... gagtttatagGATGAGGTAGAGGACAATTTCGCCATCGTCTTTGCTGCTATGGGAGTAAAC
EST: gi|110706083|gb|EE083673.1|EE083673
EST:     GTCAGGCTGGTCTTGTAAAGCGGTTGGAAAAAGCTGGAAATCTCCTAGAG                         GATGAGGAAGAGGACAATTTCGCCATCGTCTTTGCTGCTATGGGAGTAAAC
genomic: GTCAGGCTGGTCTTGTAAAGCGGTTGGAAAAATCTGGAAATCTCCTAGAGgtactagttt ... gagtttatagGATGAGGTAGAGGACAATTTCGCCATCGTCTTTGCTGCTATGGGAGTAAAC
EST: gi|161715538|gb|FC069467.1|FC069467
EST:     GTCAGGCTGGTCTTGTAAAGCGGTTGGAAAAAGCTGGAAATCTCCTAGAG                         GATGAGGTAGAGGACAATTTCGCCATCGTCTTTGCTGCTATGGGAGTAAAC
genomic: GTCAGGCTGGTCTTGTAAAGCGGTTGGAAAAATCTGGAAATCTCCTAGAGgtactagttt ... gagtttatagGATGAGGTAGAGGACAATTTCGCCATCGTCTTTGCTGCTATGGGAGTAAAC
EST: gi|161717869|gb|FC068184.1|FC068184
EST:     GTCAGGCTGGTCTTGTAAAGCGGTTGGAAAAATCTGGAAATCTCCTAGAG                         GATGAGGTAGAGGACAATTTCGCCATCGTCTTTGCTGCTATGGGAGTAAAC
genomic: GTCAGGCTGGTCTTGTAAAGCGGTTGGAAAAATCTGGAAATCTCCTAGAGgtactagttt ... gagtttatagGATGAGGTAGAGGACAATTTCGCCATCGTCTTTGCTGCTATGGGAGTAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttttatctgattaaaatatgtaattctcatattatttgccttgagtttatagGATGAGGTAGAGGACAATTTCGCCATCGTCTTTGCTGCTATGGGAGTAAACATGGAAACAGCACAATTTTTTAAGCGTGATTTTGAGGAAAATGGATCCA
       atctgat  putative branch site (score: 4)
     ttatctgattaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccgttcatttctgtcctaccctttgtccacttctgttttatatttttcttttatctgattaaaatatgtaattctcatattatttgccttgagtttatagGATGAGGTAGAGGACAATTTCGCCATCGTCTTTGCTGCTATGGGAGTAAACATGGAAACAGCACAATTTTTTAAGCGTGATTTTGAGGAAAATGGATCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - cctaccc
- - - - - - - - - - - - - ccacttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -attaaaa