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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgctacgtgttggttggaaatttcttcaatttggggttcgtgttgtgaaatttagttaacctagttggcttgtgtgcttttgaagTATTTTTGGGCCAGTTCAAGATGTGAGGATTCCATACCAGCAGAAGAGGATGTTCGGATTCGTCACTTTCGTCTACCCCGAGACTGTGAAGCTCATTTTA

Basic information

species Vitis vinifera
transcript Vv06s0061g00150.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0061g00150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os07g48410.2 (Oryza sativa), 3'ss of exon 2
gtaattgctacgtgttggttggaaatttcttcaatttggggttcgtgttgtgaaatttagttaacctagttggcttgtgtgcttttgaagTATTTTTGGGCCAGTTCAAGATGTGAGGATTCCATACCAGCAGAAGAGGATGTTCGGATTCGTCACTTTCGTCTACCCCGAGACTGTGAAGCTCATTTTA
           ||  |       |||  |  |        ||    |   ||  ||    |||| ||  |       | | |  |||||| || |  || || || || || ||  | || || |||||||||||| | |||||||| |||||||| ||||||||||| ||||| |||||||| ||| | 
-----------gtagtatactataatcccaccg-cccaccgtcaccgccatgccatagctttaatctgatgatgccctct-caattgaagCATCTACGGCCCCGTCCACGACGTTCGCATCCCGTACCAGCAGAAGCGCATGTTCGGCTTCGTCACCTTCGTCTACCCGGAGACGGTGAAGCTGATTCTC

upper sequence: Vv06s0061g00150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g21160.1 (Oryza sativa), 3'ss of exon 2
----gtaat----tgctacg-tgttggttggaaatttcttcaatttggggttcgtgttgtgaaatttagttaacctagttggcttg-tgtgctt--------------ttgaagTATTTTTGGGCCAGTTCAAGATGTGAGGATTCCATACCAGCAGAAGAGGATGTTCGGATTCGTCACTTTCGTCTACCCCGAGACTGTGAAGCTCATTTTA
     ||||    || | |  || || ||     ||  ||||    ||| |  ||     |  || |  ||  | |  |||  ||| ||| |||               || || || |  ||||| || || || ||| | || || |||||||||||| | |||||||| |||||||| ||||| ||||| ||||| |||||||| || || 
gtatataatgcgatgttgcaatgatgcttcttccttctttcatggcgggctcggtaggacgcgatctgattggcatttttgcattgctgttcttggcaacgcgccgcgctgcagCATCTACGGGCCGGTGCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTTTACCCGGAGACGGTGAAGCTGATCTTG

upper sequence: Vv06s0061g00150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g21140.1 (Oryza sativa), 3'ss of exon 2
gta-attgctacgtgttggt--tggaaatttcttcaatttggggttcgtgttgtgaaatttagttaacctagttgg----cttg----tgtgctt---ttgaagTATTTTTGGGCCAGTTCAAGATGTGAGGATTCCATACCAGCAGAAGAGGATGTTCGGATTCGTCACTTTCGTCTACCCCGAGACTGTGAAGCTCATTTTA
||| | ||| | ||     |  ||    ||  ||||    ||  |  ||     |  || |  ||  | |  |||     ||||    || ||      || || || |  || || || || || ||| | || || |||||||||||| | |||||||| |||||||| ||||| ||||| ||||| |||||||| || || 
gtataatgcgatgttgcaatgatgtttcttctttcatggcggactcggtagaacgcgatctgattggcatgtttgctgttcttggcaatgcgcccgcgctgcagCATCTACGGTCCGGTGCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCTGAGACGGTGAAGCTGATCTTG

upper sequence: Vv06s0061g00150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G086614_T01 (Zea mays), 3'ss of exon 2
-------gtaattgc-tacgtgttggt-tggaaatttcttcaatttggggttcgtgttgtgaaatttagttaacctagttggcttgtgtgctttt------------gaagTATTTTTGGGCCAGTTCAAGATGTGAGGATTCCATACCAGCAGAAGAGGATGTTCGGATTCGTCACTTTCGTCTACCCCGAGACTGTGAAGCTCATTTTA
        |   |||  || ||||  | ||     | || |||| |  | |||| || |   ||    |||    | |||| |    | |||| |            | || || |  || |||||||| || ||| | ||||| |||||||||||| | |||||||| |||||||| ||||| ||||| ||||| |||||||||||  | 
gtatgctatgcatgcacacatgttaatgtgattgatgctgcaatctttgcttcg-gtagaagaaccccgtttggttggttgaccctcgcgcttcttggcaatgcggcgcagCATCTACGGTCCAGTTCACGACGTGCGCATTCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCAGAGACGGTGAAGCTCATCCTG

upper sequence: Vv06s0061g00150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G003424_T01 (Zea mays), 3'ss of exon 2
----------gta-attgctacgtgttggttggaaatttcttcaatttggggttcgt---gttgtgaaatttagttaacctagttggcttgtgtgcttt----tgaagTATTTTTGGGCCAGTTCAAGATGTGAGGATTCCATACCAGCAGAAGAGGATGTTCGGATTCGTCACTTTCGTCTACCCCGAGACTGTGAAGCTCATTTTA
            | |  |  | ||| || |   |  |||  |    | |     |||   ||||    | ||    | |    ||  |||||  ||  |    || || || |  || |||||||| || ||| | || || |||||||||||| | |||||||| |||||||| ||||||||||| ||||| |||||||||||  | 
gtatgcatgcacacacggtaatgtgatgctccaatctttgcttccgtagaaccccgtttggttggctgacttgaccatcgcgctt--cttgttggcaatgcggtgcagCATCTACGGTCCAGTTCACGACGTGCGCATCCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTCTACCCAGAGACGGTGAAGCTCATCCTG

upper sequence: Vv06s0061g00150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM5G819035_T01 (Zea mays), 3'ss of exon 3
--gtaattgc-tacgtgttggttggaaatttcttcaat-ttggggttcgtgttgtgaaatttagttaacctagttggcttgtgtgcttttga------------agTATTTTTGGGCCAGTTCAAGATGTGAGGATTCCATACCAGCAGAAGAGGATGTTCGGATTCGTCACTTTCGTCTACCCCGAGACTGTGAAGCTCATTTTA
   |   |||  ||  | |  |  ||   | || |||| || | || |||         ||| |||     | ||| |    | |||| | |            || || |  || |||||||| || ||| | || || |||||||||||| | |||||||| |||||||| |||||||| || ||||| |||||||||||  | 
gtatgcatgcacacacggtaatgtga---tgctccaatctttgcgtccgtagaaacccgtttggttgcgtgacttgaccctcgcgcttcttagcaatgcggtgtagCATCTACGGTCCAGTTCACGACGTGCGCATCCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTCTATCCAGAGACCGTGAAGCTCATCCTG

upper sequence: Vv06s0061g00150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G044004_T03 (Zea mays), 3'ss of exon 2
-----------------------------------------------------------------------gtaattgctacgtgttggttggaaatttcttcaatttggggttcgtgttgtgaaatttagttaacctagttggcttgtgtgcttttgaagTATTTTTGGGCCAGTTCAAGATGTGAGGATTCCATACCAGCAGAAGAGGATGTTCGGATTCGTCACTTTCGTCTACCCCGAGACTGTGAAGCTCATTTTA
                                                                       ||||  |   || |         ||        |||   |  |||  | | ||     |     ||    || ||      |||| | || || |  ||||| || || || ||| | || || |||||||||||| | |||||||| |||||||| ||||||||| ||||||| |||||| ||||  | 
gtaccgggcacgccgccattattggggtttctcctctctctctctctctcctagtagcccagcccagtccagtaaacgg-gcgagcgaaaaaagaaaccgactgattgatgcatcg-atcgcgacgcgcacgcgccccgtctgtctct----ctttggcagCATGTACGGGCCGGTGCAGGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGCTTCGTCACCTTCGTCTACGCCGAGACGGTGAAGATCATCCTC

upper sequence: Vv06s0061g00150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G311665_T01 (Zea mays), 3'ss of exon 2
gtaattgctacgt--gttggttggaaatttcttcaatttggggttcgtgttgtgaaatttagttaacctagttggctt--gtgtgcttttgaagTATTTTTGGGCCAGTTCAAGATGTGAGGATTCCATACCAGCAGAAGAGGATGTTCGGATTCGTCACTTTCGTCTACCCCGAGACTGTGAAGCTCATTTTA
|||| || | |    ||  |  |       |||| | |    |     | |  |   | |             ||||   | | |    || || || |  || || || || || ||| | || || |||||||||||| | |||||||| |||||||| ||||| ||||| ||||| |||||||| ||  | 
gtaactgttcctctagtctgccgtgctccacttccactaccagccgccgctccggcctctgacgcgtgcgccgggctccggcgaggcactgcagCATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCGGAGACGGTGAAGCTGATCCTG

upper sequence: Vv06s0061g00150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G346113_T01 (Zea mays), 3'ss of exon 2
---------gtaattgctacgtgttggttggaaatttcttcaatttggggttcgtgttgtgaaatttagttaaccta----gttggcttgtgtgcttttga------agTATTTTTGGGCCAGTTCAAGATGTGAGGATTCCATACCAGCAGAAGAGGATGTTCGGATTCGTCACTTTCGTCTACCCCGAGACTGTGAAGCTCATTTTA
         | |   ||  |   ||  | |      ||| |       | | ||| | ||      |||    || |    |||| | ||    |  | ||      || || |||||||| || || |||||| | || || |||||||||||| | |||||||| |||||||| ||||| ||| ||||||| ||||||  |||  | 
gtacccagagcacacgccgc-cattattggcccccctctgctccgctcgttccgtttcgtttccactagccgtccaataatgttgccctgccatcgatggaccgagcagCATGTTTGGGCCGGTGCAGGATGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACGCCGAGACGGTGAAGGCCATCCTG

upper sequence: Vv06s0061g00150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G156656_T01 (Zea mays), 3'ss of exon 10
------------------gtaattgctacgtgttggttggaaatttcttcaatttggggttcgt--gttgtgaaatttagttaacctagttggcttgtgtgcttttgaagTATTTTTGGGCCAGTTCAAGATGTGAGGATTCCATACCAGCAGAAGAGGATGTTCGGATTCGTCACTTTCGTCTACCCCGAGACTGTGAAGCTCATTTTA
                  |  |||  |  |      | |     |  |||  ||| |  | |    | |||  |||   |||  ||        | |   |    || || || || ||||| || || || ||| | || || ||||||||||||   |||||||| |||||||| ||||| ||| ||||||| |||||| ||||   |
gtacccagagcacacgctgccattattg-gcacccctggtccgctcgttccgtttcgtttccactagctgtccaataatgttgccccgcca---tcgatggaccgtgcagCATGTTCGGGCCGGTGCAGGACGTGCGCATCCCGTACCAGCAGAAGCACATGTTCGGCTTCGTCACCTTCGTGTACGCCGAGACGGTGAAGGTCATCCCA

upper sequence: Vv06s0061g00150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G535911_T03 (Zea mays), 3'ss of exon 7
gtaattgctacgtgttggttggaaatttcttcaatttggggttcgt--gttgtgaaatttagttaacctagttggcttgtgtgcttttgaagTATTTTTGGGCCAGTTCAAGATGTGAGGATTCCATACCAGCAGAAGAGGATGTTCGGATTCGTCACTTTCGTCTACCCCGAGACTGTGAAGCTCATTTTA-------------------
         ||  |    ||      |  |||  ||| |  | |    |   |  |||   |||  ||           ||| |    |||| || || ||||| || || || ||| | || || |||||||||||| | |||||||| |||||||| ||| | ||| ||||||| ||||||  |||  ||                   
-------aaacccgccc-ttctccgctcgttccgtttcgtttccactagccatccaataatgttgccccgcc--atcgatgtaccga-gaagcatattcgggccggtgcagGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGCTTCGTCACCTTCATGTACGCCGAGACGGTGAAGGCCATCCTAAGCAAGGCAACCCGCACTT

upper sequence: Vv06s0061g00150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G21100.1 (Arabidopsis thaliana), 3'ss of exon 1
---------------------gtaattgctacgtgttggttggaaatttcttcaatttggggttcgtgttgtgaaatttagttaacctagttg---------------gcttgt-gtgcttttgaagTATTTTTGGGCCAGTTCAAGATGTGAGGATTCCATACCAGCAGAAGAGGATGTTCGGATTCGTCACTTTCGTCTACCCCGAGACTGTGAAGCTCATTTTA
                       |  || || ||||| ||| | |   |    | ||||| |   || |  | |  |||   |  |   |||                | |||| ||  | ||| || | |||||| ||||| |||||||| ||||||||||||||||||||  ||||||| || || ||||||||  || || | || |||||||   |||| || 
gtaatcttttacaattgtatcaaagctgttatgtgtttgtttgcatcattaaaagtttggtggatgtctactaatgtttgcctggctctgttattgtagactgattatgtttgttgttttcttgtagCAATTTTGGACCAGTGCAAGATGTTAGGATTCCATACCAGCAGAAACGGATGTTTGGGTTTGTCACTTTTCTCCACTCTGAAACTGTGAGAATCATATTG

upper sequence: Vv06s0061g00150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ13340 (Selaginella moellendorffii), 3'ss of exon 3
gtaattgctacgtgttggttggaaatttcttcaatttggggttcgtgttgtgaaatttagttaacctagttggcttgtgtgcttt-tgaagTATTTTTGGGCCAGTTCAAGATGTGAGGATTCCATACCAGCAGAAGAGGATGTTCGGATTCGTCACTTTCGTCTACCCCGAGACTGTGAAGCTCATTTTA
                        || |  |  |   |    |||  |  |    |||  ||  | |  ||   || | | | ||    |||  ||| ||||| || ||||| ||||||||||| |||||||| ||||| ||||| || |||||||| ||    ||| | ||||| ||   |   ||  | 
----------------------gtatgtgattgagaagaaaatcgcatcattg--ttttatt--catgattcttttcttttcattgctcagTTCTTTCGGGCCCGTACAAGACGTGAGGATTCCTTACCAGCAAAAGAGAATGTTTGGCTTCGTCACCTTTACGTACTCGGAGACCGTACGGACAATCCTG

upper sequence: Vv06s0061g00150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ24679 (Selaginella moellendorffii), 3'ss of exon 3
gtaattgctacgtgttggttggaaatttcttcaatttggggttcgtgttgtgaaatttagttaacctagttggcttgtgtgcttttgaagTATTTTTGGGCCAGTTCAAGATGTGAGGATTCCATACCAGCAGAAGAGGATGTTCGGATTCGTCACTTTCGTCTACCCCGAGACTGTGAAGCTCATTTTA
                        || |  |  |   |    |||  | |     ||| ||| |  | |||   ||   ||||     |||  ||| ||||| || ||||| ||||||||||| |||||||| ||||| ||||| || |||||||| ||    ||| | ||||| ||   |   ||  | 
----------------------gtatgtgattgagaagaaaatcgcatggcattgttttgttta--tggttcttttcgttgctc----agTTCTTTCGGGCCCGTACAAGACGTGAGGATTCCTTACCAGCAAAAGAGAATGTTTGGCTTCGTCACCTTTACGTACTCGGAGACCGTACGGACGATCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggggttcgtgttgtgaaatttagttaacctagttggcttgtgtgcttttgaagTATTTTTGGGCCAGTTCAAGATGTGAGGATTCCATACCAGCAGAAGAGGATGTTCGGATTCGTCACTTTCGTCTACCCCGAGACTGTGAAGCTCATTTTA
                       agttaac  putative branch site (score: 3)
                                            tgctttt  putative PPT
               tgaaatttagttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgctacgtgttggttggaaatttcttcaatttggggttcgtgttgtgaaatttagttaacctagttggcttgtgtgcttttgaagTATTTTTGGGCCAGTTCAAGATGTGAGGATTCCATACCAGCAGAAGAGGATGTTCGGATTCGTCACTTTCGTCTACCCCGAGACTGTGAAGCTCATTTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA