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

...gattggtttctcaaattgtttaggtttacatgctgtagatacttgtattatttgtttatatacttctagtttctaaaattttggcttttgaaattcacagGGATACTGCTGGCCAAGAAAGATTTAGGAGTCTTATACCAAGCTACATAAGAGATTCTTCAGTTGCTGTGATTGTTTATGATGTTGGAA

Basic information

species Vitis vinifera
transcript Vv00s0665g00040.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G128771_T01 (Zea mays), 3'ss of exon 2
gattggtttctcaaattgtttaggtttacatgctgtagatacttgtattatttgtttatatacttctagt-ttctaaaattttggcttttgaaattcacagGGATACTGCTGGCCAAGAAAGATTTAGGAGTCTTATACCAAGCTACATAAGAGATTCTTCAGTTGCTGTGATTGTTTATGATGTTGGAA
                     |  ||   ||        |  | |  || || ||| || | |||  ||     | |   |||   | ||     |  |||||||||||| || || || || |||||||||||||| ||||||||||| || || ||||| ||||| ||| |||||||||||||    |
-nnnnnnnnnnnnnnnnnnncacattactatttgagttttggtagctttgttagttcattttcttggagaacagttagcatttcattgttcttgctgtcagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA

upper sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G14390.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------gattggtttctca--aattgtttaggtttacatgctgtagatacttgtattatttgtt-tatatacttctagtttctaaaattttggcttttgaaattcacagGGATACTGCTGGCCAAGAAAGATTTAGGAGTCTTATACCAAGCTACATAAGAGATTCTTCAGTTGCTGTGATTGTTTATGATGTTGGAA
                                                          ||  ||| |||  |||| | |  |  | ||   ||  | ||    || ||    || | |||  ||  | ||||| |  ||      | | || |||||||||||||||| || |||||||||||||| ||||| || ||||||||||||||||||||||| ||||| || || || ||||||||||  |
gtaggatgaattcctcttcaaatcatatatacaagctcagtctttttatatttgtttgtttatttttcaacaattatattagagtgcacattgctggtatgcctagtaggcattgtttatttttacaatttctgagcttagtatatgttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTATAGTATATGATGTTGCTA

upper sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G31200.1 (Glycine max), 3'ss of exon 2
----------------------------------------------------gattggtttctcaa--attgtttaggtttacatgctgtagatac-ttgtattatttgtttatatacttctagtttctaaaattttggcttttgaaattcacagGGATACTGCTGGCCAAGAAAGATTTAGGAGTCTTATACCAAGCTACATAAGAGATTCTTCAGTTGCTGTGATTGTTTATGATGTTGGAA
                                                    | ||  ||| ||||  ||| | |  |  ||||   ||  | |||    |||      | | ||| |||  | ||||| |  ||      | | || |||||||||||||||| || |||||||||||||| ||||| || ||||||||||||||||||||||| ||||| || || || ||||||||||  |
gtaggatgactcctcttcaaatcataaatacaagctcagtctatttatatttgttttatttttcaacaattatattagagtacacattgctggtacgccttataggcactctttattcttacaatttctgagcttagtatatgttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCGGTTATAGTATATGATGTTGCTA

upper sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G38110.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------gattggtttctcaaa--ttgtttaggtttacatgctgtagatacttgtattatttgtttatatacttctagtttctaaaat-tttggcttttgaaattcacagGGATACTGCTGGCCAAGAAAGATTTAGGAGTCTTATACCAAGCTACATAAGAGATTCTTCAGTTGCTGTGATTGTTTATGATGTTGGAA
                                                     || || | | |||  || | |  | || ||   |||  ||    | | | ||| ||    | |||    | |  ||| | | | |  ||| || |||||||||||||||| || |||||||| ||||| ||||| || ||||||||||||||||||||||| ||||| || ||||| |||||||| |  |
gtaggccatattcctcttcaactcataccacaagatctatttatatttgtttttttgtattttaaaagttatattagatttcacattgtt-atgtaggcaattttttttaccgttctttgtatgttaaaagtgtgtcgtattttaacttcacagGGATACTGCAGGGCAAGAAAGGTTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTATTGTATATGATGTAGCCA

upper sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G02040.1 (Glycine max), 3'ss of exon 2
-------------------------------------------gattggtttctc---aaattgtttaggtttacatgctgtagatacttgtattatttgtttatatacttctagttt-ctaaaatt--ttggcttttgaaattcacagGGATACTGCTGGCCAAGAAAGATTTAGGAGTCTTATACCAAGCTACATAAGAGATTCTTCAGTTGCTGTGATTGTTTATGATGTTGGAA
                                            |||  ||| ||   || || | |  | || ||   ||| | |    | | | ||| || |   | |  | || |  |||||||  ||    ||| || |||||||||||||||| || |||||||||||||| ||||| || ||||||||||||||||||||||| ||||| ||  |||| || ||||| |  |
gtaggccatattcctctttaactcatgccacaagacctatttatatttttttttctaaaagttatattagatttcacattgttg-tgtaggcacttttt-ttaacccattctttgtatgttaaaattgtttcatattttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTGATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTGTTGTATACGATGTAGCCA

upper sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G22290.1 (Arabidopsis thaliana), 3'ss of exon 2
gattggtttctcaaattgtttaggtttacatgctgtagatacttgtattatt-tgtttatatacttctagtttctaaaattttggcttttgaaattcacagGGATACTGCTGGCCAAGAAAGATTTAGGAGTCTTATACCAAGCTACATAAGAGATTCTTCAGTTGCTGTGATTGTTTATGATGTTGGAA-----------
            ||    |   | |||   | ||   | | || | | | |  | ||   |    |   |   |||| | | ||  ||||    ||   |||||||| ||||| ||||||||||| |||||| | |||||||| ||||||||||||||||| ||||| ||  ||||||||||||| |  |           
----------gtaagaaatgctgtttt---ttctagggcttctcgcaatgtaatattcgcaa---tgaggaagctaataatgtgaattttcg--tttttagGGATACAGCTGGACAAGAAAGATTCAGGAGTTTAATACCAAGTTACATAAGAGATTCTTCTGTTGCAGTTGTTGTTTATGATGTAGCCAATAGACTCTCA

upper sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G39890.1 (Arabidopsis thaliana), 3'ss of exon 2
gattggtttctcaaattgtttaggtttacatgctgtagatacttgtattatttgtttatatacttctagtttctaaaattttggcttttgaaattcacagGGATACTGCTGGCCAAGAAAGATTTAGGAGTCTTATACCAAGCTACATAAGAGATTCTTCAGTTGCTGTGATTGTTTATGATGTTGGAA
          | | |    |     ||     || ||  ||      | |  |||| ||    |   |     ||| |       ||||||  || | |||||||||||||| ||||||||||| |||||||| || ||||| ||||| ||||||||||| |||||  |  |||| || |||||    |
---------gtgagaacaatgttacttttgctctttacctaaaaac-taacatgttaat---ttcaaaagcaataacaaaacaagttttga--ttgaaagGGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCA

upper sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G10260.1 (Arabidopsis thaliana), 3'ss of exon 2
-gattggtttctcaaattgtttaggtttacatgctgtagatacttgtattatttgtttatatacttctagtt-tctaaaattttggcttttgaaatt-cacagGGATACTGCTGGCCAAGAAAGATTTAGGAGTCTTATACCAAGCTACATAAGAGATTCTTCAGTTGCTGTGATTGTTTATGATGTTGGAA
 || |||    ||||| |||  | |   | || ||    ||   ||||| |    | |  || ||| ||||| | |   ||||||  |  |   | |   |||||||||||| || || || |||||| | ||||| |||||||| || || ||||||||||| |||||||| ||||| |||||||||| ||
tgaatggaacatcaaaatgtccatgg--aaattctcagcat-tgtgtatcaaccatgttcattcttttagttatatgtcattttgaatcatattactgtgcagGGATACTGCAGGACAGGAGAGATTTCGAAGTCTAATACCAAGTTATATCAGAGATTCTTCTGTTGCTGTAATTGTCTATGATGTTGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattatttgtttatatacttctagtttctaaaattttggcttttgaaattcacagGGATACTGCTGGCCAAGAAAGATTTAGGAGTCTTATACCAAGCTACATAAGAGATTCTTCAGTTGCTGTGATTGTTTATGATGTTGGAA
                         ttctaaa  putative branch site (score: 2)
         tttatatacttctagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattggtttctcaaattgtttaggtttacatgctgtagatacttgtattatttgtttatatacttctagtttctaaaattttggcttttgaaattcacagGGATACTGCTGGCCAAGAAAGATTTAGGAGTCTTATACCAAGCTACATAAGAGATTCTTCAGTTGCTGTGATTGTTTATGATGTTGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - -acatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttctag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggcttt