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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagaccctttctctggcattctcctcttccttgcaattatcaattgtttcatgtttcttataatgagagagcttgtaggatttttcaaatctgtagtagaagcttataagggcaaatccccatagcattgatccatctttttctcaaaccagGCCAAGACAACCAAGAAGATTGTGCTGAGGCTTCAATGCCAGGGTTGCAAACATGTATCGCAACACCCAATCAAG

Basic information

species Vitis vinifera
transcript Vv01s0011g02090.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 2
gtaaagaccctttctctggcattctcctcttccttgcaattatcaattgtttcatgtttcttataatgagagagcttgtaggatttttcaaatctgtagtagaagcttataagggcaaatccccatagcattgatccatctttttctcaaac---cagGCCAAGACAACCAAGAAGATTGTGCTGAGGCTTCAATGCCAGGGTTGCAAACATGTATCGCAACACCCAATCAAG
           |  |    |||  ||   ||  ||| | ||||   ||  |   | ||  |  ||    ||  |  |  |    | | | |||    | |    | | |  ||   || |    |||  |   ||     | | |    | |   ||||||||||| |||||||||||||| |||| ||| || |||||| | ||||| ||    || || ||| | ||||||
----------gtaatgcaacata-tctatttgattgtacttatacctttgtctgttttgatggtagcatgaatgtctagaaatatctgcgaattctaaatgcctgttga-gagaataatttgggatatgacaaatgtgattgtattaatacctttcagGCCAAGACCACCAAGAAGATTGTTCTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCCATCAAG

upper sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G125527_T02 (Zea mays), 3'ss of exon 2
gtaaag-accctttctctggcattctcctctt--ccttgcaattatcaattgtttcatgtttcttataatgagagagcttgtaggatttttcaaatctgtagtagaagcttataagggcaaatccccatagcattgatccatctttttctcaaaccagGCCAAGACAACCAAGAAGATTGTGCTGAGGCTTCAATGCCAGGGTTGCAAACATGTATCGCAACACCCAATCAAG
|||| | | | | ||| |   ||| | ||  |  | |||    | |  ||  |  ||||  | |     ||| |     ||  | ||| |  |   ||||   ||    | ||  |||  |   |  ||   ||||    || | |  ||     ||||||||||| |||||||||||||| |||| ||| || |||||| | ||||| ||    || || ||| | ||||||
gtaatgcagcatatctatttgattgtacttatacctttgtctgttttgatgctagcatgaatgtc----tgaaaatatctgc-gaattctaaatgcctgtt-cagtgattaatgtgggatatgacaaatgagattg---tatttatacctt---tcagGCCAAGACCACCAAGAAGATTGTTCTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCCATCAAG

upper sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G19320.1 (Glycine max), 3'ss of exon 2
gtaaagaccctttctctggcattctcctcttccttgcaattatcaattgtttcatgtttcttataatgagagagcttgtaggatttttcaaatctgtagtagaagcttataagggcaaatccccatagcattgatccatctttttctca--aaccagGCCAAGACAACCAAGAAGATTGTGCTGAGGCTTCAATGCCAGGGTTGCAAACATGTATCGCAACACCCAATCAAG
                                                                             |||   | |    || ||  |||  |     || |||     |   | |  ||   |    | | ||| | |   |  |||| ||||| |||||||||||||| |||||| | ||||||||||||||||| ||||| || |||||| | || |||
-----------------------------------------------------------------------------gtaacctctcgttaaccta-agtgcataggaattaggagtttttttcctgacaaaaacatttttatttttaattgattagGCTAAGACCACCAAGAAGATTGTTCTGAGGTTGCAATGCCAGGGTTGCAAGCATGTCTCCCAACACGCTATTAAG

upper sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G05670.1 (Glycine max), 3'ss of exon 2
gtaaagaccctttctctggcattctcctcttccttgcaattatcaattgtttcatgtttc-ttataatgagagagcttgtaggatttttcaaatctgtagtagaagcttataagggcaaatccccatagcattgatccatctttttctcaaaccagGCCAAGACAACCAAGAAGATTGTGCTGAGGCTTCAATGCCAGGGTTGCAAACATGTATCGCAACACCCAATCAAG
                                          ||  | |||  || |||| ||||||    | ||    |||||| |||    | |         ||| | ||    | ||                    ||||  | |||  |||| || || |||||||||||||| |||||| | ||||||||||||||||| ||||| || |||||| | || |||
----------------------------------------gttcgttggttaaatatttcgttataagtgcataggaattaggatcttttttttttt--------gctgacaaaaatatat--------------------ttttatttaaaatagGCTAAAACCACCAAGAAGATTGTTCTGAGGTTGCAATGCCAGGGTTGCAAGCATGTCTCCCAACACGCTATTAAG

upper sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G05670.2 (Glycine max), 3'ss of exon 2
gtaaagaccctttctctggcattctcctcttccttgcaattatcaattgtttcatgtttc-ttataatgagagagcttgtaggatttttcaaatctgtagtagaagcttataagggcaaatccccatagcattgatccatctttttctcaaaccagGCCAAGACAACCAAGAAGATTGTGCTGAGGCTTCAATGCCAGGGTTGCAAACATGTATCGCAACACCCAATCAAG----
                                          ||  | |||  || |||| ||||||    | ||    |||||| |||    | |         ||| | ||    | ||                    ||||  | |||  |||| || || |||||||||||||| |||||| | ||||||||||||||||| ||||| || |||||| | || |||    
----------------------------------------gttcgttggttaaatatttcgttataagtgcataggaattaggatcttttttttttt--------gctgacaaaaatatat--------------------ttttatttaaaatagGCTAAAACCACCAAGAAGATTGTTCTGAGGTTGCAATGCCAGGGTTGCAAGCATGTCTCCCAACACGCTATTAAGGTTA

upper sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G14320.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaaagaccctttctctggcattctc-ctcttccttgcaattatcaattgtttcatgtttcttataatgagagagcttgtaggatttt----tcaaatctgtagtagaag-cttataagggcaaatcccca--tagcattgatccat------ctttttctcaaaccagGCCAAGACAACCAAGAAGATTGTGCTGAGGCTTCAATGCCAGGGTTGCAAACATGTATCGCAACACCCAATCAAG
                  | || ||| || |||||||   | |||  |  || | ||| |  |||  |||||     | ||||||||     |  | |||||   | | | |||||| |    | |    |  | |   |    |||        |||  |   | ||||| |||||||| |||||||||||||||||||||||||||||  | ||||| ||| | ||||||| ||| || |||
------------------gtatactcgcttttccttgtcttgatctctaattac-tgtcttctatg-tgagaaccaatttaggatttcagaattgactctgtgaaatatgtcttataggaatgatttgttaattggaccttgctcattatttgtctttctttggaacagGCTAAGACAACTAAGAAGATTGTGCTGAGGCTTCAATGCCAAAGCTGCAAGCATTTCTCGCAACGCCCGATTAAG

upper sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S22_326V6.2 (Physcomitrella patens), 3'ss of exon 3
gtaaagaccctttctctggcattctcctcttccttgcaattatcaattgtttcatgtttcttataatgagagagcttgtaggatttttcaaatctgtagtagaagcttataagggcaaatccccatagcattgatccatctttttctcaaaccagGCCAAGACAACCAAGAAGATTGTGCTGAGGCTTCAATGCCAGGGTTGCAAACATGTATCGCAACACCCAATCAAG
                                                                                    |  ||   ||||   |    | |            |   | |  | |   | | | ||| | | |   ||||| ||||| |||||||||||||| |||||| | || ||||||| |||||| || ||  | ||||| || ||||||
------------------------------------------------------------------------------------tcatcttctctgcgatttttgtt-----------gttttcttttcttc--ttcttttttattttacctcaggctaagactaccaagaagattgtactgaggttacagtgccagGCTTGCAAGCACGTGACACAACATCCTATCAAG

upper sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S22_326V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaaagaccctttctctggcattctcctcttccttgcaattatcaattgtttcatgtttcttataatgagagagcttgtaggatttttcaaatctgtagtagaagcttataagggcaaatccccatagcattgatccatctttttctcaaaccagGCCAAGACAACCAAGAAGATTGTGCTGAGGCTTCAATGCCAGGGTTGCAAACATGTATCGCAACACCCAATCAAG
                                       |  |  |||||      |||||  || | | | |      |||| |     |   | |    ||   || |         |   | |  | |   | | | ||| | | |   ||||| ||||| |||||||||||||| |||||| | || ||||||| |||||| || ||  | ||||| || ||||||
---------------------------------------tcgt--attgtcaatgatttctggtagtaaaaaa-----caggactaagtcatcttctctgcgatttttgttg-------ttttcttttcttc--ttcttttttattttacctcagGCTAAGACTACCAAGAAGATTGTACTGAGGTTACAGTGCCAGGCTTGCAAGCACGTGACACAACATCCTATCAAG

upper sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S2_415V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaaagaccctttctctggcattctcctcttccttgcaattatcaattgtttcatgtttcttataatgagagagcttgtaggatttttcaaat-ctgtagtaga-agcttataagggcaaatccccatagcattgatccatctttttctcaaacc--agGCCAAGACAACCAAGAAGATTGTGCTGAGGCTTCAATGCCAGGGTTGCAAACATGTATCGCAACACCCAATCAAG
                                                          || |  | |    | | ||  |   |    |||||  |||  ||    |  |||     |   |  |  |   |  |||  || || |  |  || |  |||| ||||| ||||||||||||||||||||| | || || |||| |||||| || ||  | ||||| || || |||
----------------------------------------------------------tcctggagtttcggggtttcaaatgtggggcaaatgttgttatatttggactatgctttcgtgtatct-ttttaccgatttatgttgtcttggaatctcagGCTAAGACTACCAAGAAGATTGTGCTGAGGTTGCAGTGTCAGGCTTGCAAGCACGTGACACAACATCCCATTAAG

upper sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S74_73V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaaagaccctttctctggcattctcctcttccttgcaattatcaattgtttcatgtttcttataatgagagagcttgtaggatttttcaaatctgtagtagaagcttataagggcaaatccccatagcattgatccatctttttctcaaaccagGCCAAGACAACCAAGAAGATTGTGCTGAGGCTTCAATGCCAGGGTTGCAAACATGTATCGCAACACCCAATCAAG
                                              |  ||||||      | | |    |   | | |  | ||| ||      |||      ||   |       |      | ||   || |  || ||||  ||    ||||||||||| || |||||||||||||| ||| | ||||| |||| |||||| |||||  | ||||| || ||||||
---------------------------------------------gtgatttcataacaaatttga--gaaccccctcttcgctttgtctcgctggtatcgatggcacgtggcactgag-----aaagtcctgtttgatattttgttc---tcagGCCAAGACCACAAAGAAGATTGTGCTTAGGTTGCAATGTCAGGCTTGCAAGCATGTGACTCAACATCCCATCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaagcttataagggcaaatccccatagcattgatccatctttttctcaaaccagGCCAAGACAACCAAGAAGATTGTGCTGAGGCTTCAATGCCAGGGTTGCAAACATGTATCGCAACACCCAATCAAG
                            cattgat  putative branch site (score: 4)
                                  tccatctttttctc  CT-rich tract
                                     atcttttt  TA-rich tract