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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgtttgccatcagagagggttttcattttctacttctgcttcataagtttgaatgctatgaatcttgctgaggtcaaagtcttctgctgtttatgcagATTCAAATATTTGAGCCATTTAGCATTCTTGGATTAGAATCTGGAGCTTCAGATTCAGAAATAAAGAAGGCATACAGGAGACTCTCGATTCAATACCATC

Basic information

species Vitis vinifera
transcript Vv16s0050g01460.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g01460.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G20400.1 (Glycine max), 3'ss of exon 3
--------------------------------------cttgtttgccatcagagagggttttc-----attttctacttctgcttcataagtttgaat----gctatgaatcttgctgagg-----tcaaagtcttctgctgt-----ttatgcagATTCAAATATTTGAGCCATTTAGCATTCTTGGATTAGAATCTGGAGCTTCAGATTCAGAAATAAAGAAGGCATACAGGAGACTCTCGATTCAATACCATC
                                        || |||   |  || |    | ||     || || |  || || |  |  | |||   |    |||  || |    | |  |     ||  | | || |  |||     ||||||||||| |||| || || |||||||  ||||| ||||||||  |||||||  | || || |||||||||||    || |||||||| || |||||||||||||
gtaaacaattagaaagttcaaatgaattcagctattccagtgcttgggttatgaaattagtatcgagggatcttgtgtttgtggtataacattttacttattggctgagagttccaccggtgcatgttctgaattttttcttgtaaattttatgcagATTGAAATTTTCGATCCATTTAATATTCTAGGATTAGAGCCTGGAGCGGCTGAGTCTGAAATAAAGAAAAAGTATAGGAGACTTTCTATTCAATACCATC

upper sequence: Vv16s0050g01460.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G08830.1 (Glycine max), 3'ss of exon 3
---------------------------------------cttgtttgccatcagagagggtttt----cattttctacttctgcttcataagtt--tgaatg-ctatgaatcttgctgagg-------tcaaagtcttctgctg---tttatgcagATTCAAATATTTGAGCCATTTAGCATTCTTGGATTAGAATCTGGAGCTTCAGATTCAGAAATAAAGAAGGCATACAGGAGACTCTCGATTCAATACCATC
                                       ||| ||     |   |    || ||     || || || || || || | |  ||  | | || ||  || |    |||  |       | ||| | ||||  |    |||||||||||| |||| ||||| || ||||  ||||| ||||||||  |||||||  |||| || |||||||||||    || ||| |||| || |||||||||||||
gtaaacaattagaaagttaaaatgaattcagctattccacttcttgagatttgaaattagtattgagggatcttgtatttgtgtttaacattttactaattggctgagacttccactggtgcacgttctgaaatttttcttttaaattttatgcagATTGAAATTTTTGATCCGTTTAATATTCTAGGATTAGAGCCTGGAGCGGCAGAGTCTGAAATAAAGAAAAAGTATAGGCGACTTTCTATTCAATACCATC

upper sequence: Vv16s0050g01460.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G21180.1 (Arabidopsis thaliana), 3'ss of exon 3
cttgtttgccatcagagagggttttcattttctacttctgcttcataagtttgaatgctatgaatcttgctgaggtcaaagtcttctgctgtttatgcagATTCAAATATTTGAGCCATTTAGCATTCTTGGATTAGAATCTGGAGCTTCAGATTCAGAAATAAAGAAGGCATACAGGAGACTCTCGATTCAATACCATC
               |     |  | ||| |||  |   ||||  |      || ||||       ||||| |  |||   ||||  |    |  |  ||| |||| | |||||||||||  | || || || || ||| |||| ||||||||||||||||| ||||| ||||| || |||||||| |||||||||||||
-------------gtaataactaataattatctcttcaagcttagtccaa--gattgcttca---tttgcttat-tcattatcttgggtaaatattatagAGTCAACTCTTTGAGCCATTCGGTATACTCGGTTTGGAACCTGGTGCTTCAGATTCAGAAATCAAGAAAGCATATAGAAGACTCTCTATTCAATACCATC

upper sequence: Vv16s0050g01460.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G79940.3 (Arabidopsis thaliana), 3'ss of exon 3
cttgtttgccatcagagagggttttcattttctactt--ctgcttcataagtttgaatgctatgaatcttgctgaggtcaaagtcttctgctgtttatgcagATTCAAATATTTGAGCCATTTAGCATTCTTGGATTAGAATCTGGAGCTTCAGATTCAGAAATAAAGAAGGCATACAGGAGACTCTCGATTCAATACCATC
       |  |||  |  |    ||  | ||  ||||   |||  |      ||  || | |  |||  | ||    |      |||||  ||| | | |||  |||| | ||||| ||||| || || |||||| | ||| |||||| | ||||||||||||||||||| ||||| || || || ||||||||||||||||
-------gtaatcccattg---cttgctgttgaacttgaatgcaccgctgacttatat-caactaattctacttgcttatttaccttcttttgtgt-tacagGCTCAAGTTTTTGACCCATTCAGTATACTTGGACTGGAACCTGGAGTTACAGATTCAGAAATAAAGAAAGCATATAGAAGGCTGTCGATTCAATACCATC

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|351014635|gb|FQ437637.1|FQ437637
EST:     TAAACACATAAGCCAAGAG                         ATTCAAATATTTGAGCCATTTAGCATTCTTGGATTAGAATCTGGAGCTTCA
genomic: TAAACACATAAGCCAAGAGgtaatgacct ... gtttatgcagATTCAAATATTTGAGCCATTTAGCATTCTTGGATTAGAATCTGGAGCTTCA
EST: gi|351040685|gb|FQ438229.1|FQ438229
EST:     TAAACACATAAGCCAAGAG                         ATTCAAATATTTGAGCCATTTAGCATTCTTGGATTAGAATCTGGAGCTTCA
genomic: TAAACACATAAGCCAAGAGgtaatgacct ... gtttatgcagATTCAAATATTTGAGCCATTTAGCATTCTTGGATTAGAATCTGGAGCTTCA
EST: gi|351023901|gb|FQ423324.1|FQ423324
EST:     TAAACACATAAGCGAAGAG                         ATTCAAATATTTGAGCCATTTAGCATTCTTGGATTAGAATCTGGAGCTTCA
genomic: TAAACACATAAGCCAAGAGgtaatgacct ... gtttatgcagATTCAAATATTTGAGCCATTTAGCATTCTTGGATTAGAATCTGGAGCTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagtttgaatgctatgaatcttgctgaggtcaaagtcttctgctgtttatgcagATTCAAATATTTGAGCCATTTAGCATTCTTGGATTAGAATCTGGAGCTTCAGATTCAGAAATAAAGAAGGCATACAGGAGACTCTCGATTCAATACCATC
             tatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgtttgccatcagagagggttttcattttctacttctgcttcataagtttgaatgctatgaatcttgctgaggtcaaagtcttctgctgtttatgcagATTCAAATATTTGAGCCATTTAGCATTCTTGGATTAGAATCTGGAGCTTCAGATTCAGAAATAAAGAAGGCATACAGGAGACTCTCGATTCAATACCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - -gccatca
- - - - - - - - - - - - - - - - - - -ctgcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - gaatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgctg