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'   
18  
 5'  3'   
19  
 5'  3'   
20  
 5'  3'   
21  
 5'  3'   
22  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtcaacatcatgaatgtttgttagcaacttgtttgattacattaattagtagttcaagttgtgtgatattttctatgtttatgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA

Basic information

species Vitis vinifera
transcript Vv04s0044g02020.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 18
gcaag-tcaacatcatgaatgtttgttagca-acttgt-ttgattacattaattagtagttcaagttgtgtgatattttctatgtttatgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA
| | | | | | | || ||| || || ||| | |||| |||| || | | | |||| | | | ||| |||| ||||||| | ||||||||||| || |||||||||||||| || |||||||| ||||| || |||||||||||||| || || ||||||||||| ||||| |
gtgaccttttttttaacacttctttttaacatacatgtgctcattagattatttgcaattggactccatgtgtttatcatgaattttgtgat-gcagTATCTAGTTCAATCGGCCGTTGATGGATATAATGTTTGTATATTTGCTTATGGGCAAACTGGTTCTGGAAAAACTTTTACAATTTATGGATCTGAAAACA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 17
---------gcaagtcaacatcatgaatgtt-----tgttagcaacttg--tttgattacattaattagtagttcaag---ttgtgtgatattttctatgtttatgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA
||| | ||| | |||| | || || | ||| ||| | | | | | | | | | |||| | || || | | |||| |||||| |||| ||||| ||||| ||||||||||| || |||||||||||||||||||| ||||||||||||||||| ||||| ||||||||||| ||| |
gtgaatatttcaaat-gctatcttttgtgttgatgccatcagtaatataaattttatttctaggactgttcactgagggtttcatatgatgtgttgaatttatgtgat-gcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATATGGTCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGATAACA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 17
----------------------------------------gcaagtcaacatc---atgaatgtttgttagca--acttgtttgattacattaattagtagttcaagttgtgtgatattttctatgtttatg-attgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA
| || ||| | | | | ||||| || | || | || ||| || | || ||| | || | | |||||| |||||||| |||| ||||| ||||| |||||||||||||| || |||||||| ||||| || ||||||||||||||||| ||||| ||||||||||| || |
gtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttgaatttatgttcattttgggtttcatatgatctgttgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 22
gcaagtcaacatcatgaatgtttgttagcaacttgtttgattacattaattagtagttcaagttgtgtgatattttctatgtttatgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA
|||||||| | | | ||| || ||| | | | || || | | | || || | | | | ||| || |||||||||||| ||||| ||||||||||| |||||||| ||||||||||| |||||||| ||||| |||||||||||||| ||||| ||||| || || |
gcaagtca---taaattgtatttatttcttgcttatggaaacatat--ataacttacactcattac-caatttctcgtgtatttgcaat-gcagTATTTGGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTATGGTCAAACTGGATCTGGAAAGACATTTACAATCTATGGATCGGACATCA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 19
------------gcaagtcaacatcatgaatgtttgttagcaacttgttt--gattacattaattagtagttcaagttgtgtgatattttctatgtttatgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA
||| | |||| || | || ||||||| | |||| || | | | || | || | | | ||| || |||||||||||| || || ||||||||||| |||||||| ||||||||||| |||||||| ||||| |||||||||||||| ||||| ||||| ||||| |
gtatttgaggatacaaaggcaagtcatttat-catatttatttcttgtttatgggaacatatataacttacactcattat-caatttctcgtggatttgcaat-gcagTATTTGGTGCAGTCTGCTGTAGATGGTTATAATGTTTGCATATTTGCCTATGGTCAAACTGGCTCTGGAAAGACATTTACAATCTATGGATCTGACAACA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 19
-----------gcaagtca-acatcatgaatgtttgtt------agca-acttgtttgattacattaattagtagttcaagttgt--gtgatattttctatgt-----ttatgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA-------
||| | | | ||||| | |||| | |||| | || | | ||| | || | || | | | || |||| | | || | ||||||| || || ||||| ||||| ||||| |||||||| ||||||||||| |||||||| ||||||||||||||||| || ||||| ||||| ||| |
gtcttagtataacaaattatagatcatagttttttgctttagatagcatatacattgaaatggatttaatattttttatactcattaccaatgtttttcttttggaaatttgcaatgcagtacttagTGCAATCTGCTGTGGATGGTTATAATGTTTGCATATTTGCTTATGGTCAAACTGGTTCTGGAAAGACTTTTACAATCTATGGAGTTGAAAACAATCCTGG

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 19
---------------gcaagtcaac-atcatgaatgtttgtt---agcaacttgt----ttgattacattaattagtagttcaagttgtgtgatattttctatgtttatgat--------tgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA
||| | || ||| | | |||| | || ||| | | || ||| | || | | | | | || | | | | ||| || ||||||| || || ||||| ||||||||||| |||||||| ||||||||||| || ||||| ||||||||||| ||||| || ||||| ||||| |||| |
gcaagtcttagtataacaaattaaagatcctagttttttgctttagataatatgtacattgaaatagatttaatatttttctatactcattactaatgtttttcttttggacatttgcaatgcagTACTTAGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTACGGTCAAACTGGTTCTGGGAAGACTTTTACAATCTATGGAGCTGAAAACA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 16
gcaagtcaacatcatgaatgtttgttagcaacttgtttgattacattaattagtagttcaagttgtgtgatattttctatgtttatgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA
|| || || | | | || || ||| || || || || | || || | || | | ||||||||||| || |||||||||||||| ||||| || ||||| |||||||||||||| |||||||||||||| || ||||| || ||||| ||| | |
--------gtattattgatatgtaactgtgttcatttacctttcatcctttgttattttcttgtggttactaacatc-gttttccttttaacagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: EFJ06058 (Selaginella moellendorffii), 3'ss of exon 18
gcaagtcaacatcatgaatgtttgttagcaacttgtttgattacattaattagtagttcaagttgtgtgatattttctatgtt-tatgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA
| | || | || | ||| | | | | ||||| ||| || ||||||||||| |||||||| || || ||||| || |||||||| || || |||||||| ||||| || || || ||||| ||||| |||||| | || ||
------------------------------------------gtaatgatgtctctttgacgttattttgttactaacatgttctatcatc-cagTATTTGGTGCAATCGGCAGTCGACGGATACAACGTGTGCATTTTCGCTTATGGTCAAACTGGGTCCGGCAAAACATTTACAATATATGGTCCGGAAAATA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: EFJ30174 (Selaginella moellendorffii), 3'ss of exon 18
gcaagtcaacatcatgaatgtttgttagcaacttgtttgattacattaattagtagttcaagttgtgtgatattttctatgtttatgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA
| | || || || | ||| | | | | ||||| | ||||||||||| |||||||| || || ||||| || |||||||| || || |||||||| ||||| || || || ||||| ||||| |||||| | || ||
------------------------------------------gtaatgatgtctatttgacgttattttgttactaacatgttctgtcatccagTATTTGGTGCAATCGGCAGTCGACGGATACAACGTGTGCATTTTCGCTTATGGTCAAACTGGGTCCGGCAAAACATTTACAATATATGGTCCGGAAAATA

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|351015272|gb|FQ445556.1|FQ445556
EST:     ATGTGTTTGGTGGTAGTGCCACTCAAGAAGATGTGTTTGAGGATACAAGG                         TATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATAT
genomic: ATGTGTTTGGTGGTAGTGCCACTCAAGAAGATGTGTTTGAGGATACAAGGgcaagtcaac ... atgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATAT
EST: gi|351043062|gb|FQ443904.1|FQ443904
EST:     ATGTGTTTGGTGGTAGTGCCACTCAAGAAGATGTGTTTGAGGATACAAGG                         TATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATAT
genomic: ATGTGTTTGGTGGTAGTGCCACTCAAGAAGATGTGTTTGAGGATACAAGGgcaagtcaac ... atgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATAT
EST: gi|351026499|gb|FQ428511.1|FQ428511
EST:     ATGTGTTTGGTGGTAGTGCCACTCAAGAAGATGTGTTTGAGGATACAAGG                         TATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATAT
genomic: ATGTGTTTGGTGGTAGTGCCACTCAAGAAGATGTGTTTGAGGATACAAGGgcaagtcaac ... atgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attacattaattagtagttcaagttgtgtgatattttctatgtttatgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA
    cattaat  putative branch site (score: 3)
 atattttctatgttta  TA-rich tract