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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaggtggctttaagattctggatgtccaggcctaaatgcctgggtctactgtctagtgattttttttttatgtttttcttttttcatcttcccatctagGGGCATGATATTCTCATGGCTACAATGCTTAATGGAGCGGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAATGAAAGCTGTCCACAGCCGCAAA

Basic information

species Vitis vinifera
transcript Vv10s0042g01220.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os12g41400.1 (Oryza sativa), 3'ss of exon 5
gaaggtggctttaagattctggatgtccaggcctaaatgcctgggtctactgtctagtgattttttttttatgtttttcttttttcatcttcccatctagGGGCATGATATTCTCATGGCTACAATGCTTAATGGAGCGGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAATGAAAGCTGTCCACAGCCGCAAA
     ||| |    |  | | | | |  |    |  ||  || |   |      |    |  | ||   |||||  | | |   |  |  | |     |||||||||| ||||||||||||||||||||||||||||| || || |||||||| ||||| ||| | ||||| |||||||||||||| ||||| || ||||
ttttatgggtcactgcatattgttttttattttttgatctctcgaagtcaataatgagaaaatattacatatgtaatacatacctatttcttcttaacagGGGCATGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCATTGCTTTTGATAGCAGCCAATGAAAGCTGCCCACAACCCCAAA

upper sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os12g07740.1 (Oryza sativa), 3'ss of exon 5
-gaaggtggctttaagatt--ctggatgtccaggcctaaatgcctgggt-ctactgtctagtgattttttttttatgtttttcttttttcatcttcccatctagGGGCATGATATTCTCATGGCTACAATGCTTAATGGAGCGGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAATGAAAGCTGTCCACAGCCGCAAA
 | |    ||| | |  |   ||   | |   ||||   | | || |||  |  | |  | |  ||      | |    || | | |||| ||||  ||    ||| || ||||||||||||||||| |||||||||||||| || || |||||||| ||||| ||||| ||||| || |||||||| || ||||| || || |
tgtaaaatgctatcatttcaacttcttttatgggccactaagactaggtattggtttacatttgttgaagcctgagaaattacctatttcctcttaaca----gGGACACGATATTCTCATGGCTACGATGCTTAATGGAGCTGCTATCATGGATGGAGCATTGCTTCTGATAGCAGCAAATGAAAGTTGCCCACAACCCCAGA

upper sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 5
--gaaggtggctttaagattctggatgtccaggcctaaatgcctgggtctactgtctagtgattttttttttatgtttttcttttttcatcttcccatctagGGGCATGATATTCTCATGGCTACAATGCTTAATGGAGCGGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAATGAAAGCTGTCCACAGCCGCAAA
   | |||    ||||  |  | ||  |        | ||   |   | ||   | |||  | |  || | | | ||   |  |    |||| |     ||||| || || ||||||||||||||||||||||||||||| || || |||||||| ||  | ||| | || || || |||||||| ||||||||||| || |
aaaatggttatcttaatttctttgacatttcatttgatattgatcaat-tatgatatagaaaataattgtatgt-ttcaacaatacctatctccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCTCAGA

upper sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G107654_T01 (Zea mays), 3'ss of exon 5
gaaggtggctttaagattctg-gatgtccaggcctaaatgcctgggtctact-gtctagt-gattttttttttatgtttttcttttttcatcttcccatctagGGGCATGATATTCTCATGGCTACAATGCTTAATGGAGCGGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAATGAAAGCTGTCCACAGCCGCAAA
     |   | || | |||    |   | |   |          | |  | | |||||   |    |  || |||||||  |  |    || | |     ||||| || || ||||||||||||||||||||||||||||| || || |||||||| ||  | ||| | || || || |||||||| ||||||||||| || |
--gaataattgtatgtttcaacaacacctatctccttgaatagagatgaatttgtctaacaggaaataattgtatgtttaacaatacctat-tccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCCCAGA

upper sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G18240.1 (Glycine max), 3'ss of exon 5
gaaggtggctttaagattctggatgtc-caggcctaaatgcctgggtctactgtctagtgatt--ttttttttatgtttttcttttttcatcttcccatctagGGGCATGATATTCTCATGGCTACAATGCTTAATGGAGCGGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAATGAAAGCTGTCCACAGCCGCAAA
     |   |||| || | |   | |   | ||    |      ||||| |  || | || |   |  ||| | |||||||  |||| ||  |||   | ||||| ||||||||||| ||||||||||||||||||||||| ||||| |||||||| || || || || |||||||| ||||||||||| ||||| || ||||
ttccatatttttatgagtatcctttttataagcaggtaattacaggtctccaatcaaatgctaaatcatttgtttgtttttacttttccaatttc---tgtagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCGTTGCTACTCATAGCTGCTAATGAAAGCTGCCCACAACCACAAA

upper sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 5
--gaaggtggctttaagattctggatgtccaggc-ctaaatgcctgggtctactgtctagtgattttttt--tttatgtttttcttttttcatcttcccatctagGGGCATGATATTCTCATGGCTACAATGCTTAATGGAGCGGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAATGAAAGCTGTCCACAGCCGCAAA
   |     | | |   ||     |||   |  |  | ||    |   | |  ||| | |  || | | |  | | |||||||  |||| ||  |||   |  |||| ||||||||||| ||||||||||||||||||||||| ||||| |||||||| || || || || || ||||||||||||||||| ||||| || ||||
ataattacaggtcttcaatc--aaatgctaaatcattgaacatatattttttttgttttgacatctgtgtgatatttgtttttacttttccaatttc---tgcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCTTTGCTACTCATTGCTGCCAATGAAAGCTGCCCACAACCACAAA

upper sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 5
gaaggtggctttaagattctggatgtccaggcctaaatgcctgggtctactg-tctagtgattttttttttatgtttttc-----ttttttcatcttcccatctagGGGCATGATATTCTCATGGCTACAATGCTTAATGGAGCGGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAATGAAAGCTGTCCACAGCCGCAAA
      |  |    | |  ||||     |  | |  |||  |   |||  || | |  | || | |  || ||  || |      | || |  |  |    |  |||| || |||||||||||||| ||||||||||||||||| || || |||||||| ||| ||||| | || ||||| |||||||  |||||||| || ||||
------gagtgagggttgatggagaagtattcattgatgtttccatcttttgcttttcttatctctacttcattcttgttgaatgtattcttgttctattcttcagGGTCACGATATTCTCATGGCAACAATGCTTAATGGAGCAGCCATCATGGATGGTGCACTACTTTTAATCGCTGCAAATGAAACTTGTCCACAACCACAAA

upper sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G18330.1 (Arabidopsis thaliana), 3'ss of exon 4
gaaggtggctttaagattctggatgtccaggcctaaatgcctgggtctactgtctagtgattttttttttatgtttttcttttttcatcttcccatctagGGGCATGATATTCTCATGGCTACAATGCTTAATGGAGCGGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAATGAAAGCTGTCCACAGCCGCAAA
                |  |             || |    ||  |||     ||||     ||   | |||||   |   || |  | |   |||| |||| ||||||||||| ||||| |||||||| |||||||| |||||  ||||||| || |||||||| || ||||| || || || |||||||| || ||||
---------------gtattaatgagtttaatttacac-tttgtctctcaaaactagaaccattggctatatgtaactgagttgttttttattcatc-agGGACATGATATTCTTATGGCGACAATGCTCAATGGAGCAGCAATCGTGGATGGTGCTTTACTTCTAATTGCTGCTAACGAGAGTTGTCCACAACCACAAA

upper sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G18720.1 (Arabidopsis thaliana), 3'ss of exon 3
gaaggtggctttaagattctggatgtccaggcctaaatgcctgggtctactgtctagtgattttttttttatgtttttcttttttcatcttcccatctagGGGCATGATATTCTCATGGCTACAATGCTTAATGGAGCGGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAATGAAAGCTGTCCACAGCCGCAAA
         | ||| ||   |  | |  |  |    ||  ||   |||  |||  |   ||||| | | | |   |    | |||  | |    || ||||| || ||||| || ||||| |||||||| |||||||| || ||||||||||| || |||||  | || ||||| ||||| |  |||||||| || ||||
--------gtataaaat---gagttttaacact---atttctaaatcttttgt--aaccattttctatatgttaatgaggtgttttgtgtgttgat-tagGGACACGATATCCTAATGGCGACAATGCTGAATGGAGCAGCGATTATGGATGGTGCTTTACTAATCATTGCTGCGAATGAGACATGTCCACAACCACAAA

upper sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S207_94V6.1 (Physcomitrella patens), 3'ss of exon 4
gaaggtggctttaagattctggatgtccaggcctaaatgcctgggtctactgtctagtgattttttttt-tatgtttttcttttttcatcttcccatctagGGGCATGATATTCTCATGGCTACAATGCTTAATGGAGCGGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAATGAAAGCTGTCCACAGCCGCAAA
 ||   | ||  |    ||      ||   |     |||    |   |||| ||  ||  || |||||  |  |  ||    | ||  | ||    |  |||| || ||||||||||||||||| |||||||||||||| || ||||||||||| || |||||| | || ||   |||||| || || || ||||| ||||
-aattcgactacacacatcacttaatctgagggcttatgggaagcggtactttcgtgttcttgtttttaatccggattgaaatgtttgtgtttgtttgcagGGACACGATATTCTCATGGCTACTATGCTTAATGGAGCTGCTATTATGGATGGTGCTTTACTTTTGATTGCCAGCAATGAGAGTTGCCCCCAGCCCCAAA

upper sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ14781 (Selaginella moellendorffii), 3'ss of exon 3
gaaggtggctttaagattctggatgtccaggcctaaatgcctgggtctactgtctagtgattttttttttatgtttttcttttttcatcttcccatctagGGGCATGATATTCTCATGGCTACAATGCTTAATGGAGCGGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAATGAAAGCTGTCCACAGCCGCAAA
                                                | |   | ||  ||||  |||| | | |  || || | |      | |  |||| |||||||||||||||||||| ||||||||||| || || || ||||| || || || ||| | || ||   ||| |||||||| || ||||||||||
---------------------------------------------gtaagttcgtcgtagttttcgttttct-tctagctgttcttacgaagactttcagGGACATGATATTCTCATGGCTACGATGCTTAATGGTGCTGCGATCATGGACGGCGCTTTGCTTTTGATTGCCAGCAACGAAAGCTGCCCGCAGCCGCAAA

upper sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ26525 (Selaginella moellendorffii), 3'ss of exon 3
gaaggtggctttaagattctggatgtccaggcctaaatgcctgggtctactgtctagtgattttttttttatgtttttcttttttcatcttcccatctagGGGCATGATATTCTCATGGCTACAATGCTTAATGGAGCGGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAATGAAAGCTGTCCACAGCCGCAAA
                                                | |   | ||  ||||  |||| | | |  ||||| | |      | |  |||| |||||||||||||||||||| ||||||||||| || || || ||||| || || || ||| | || ||   ||| ||||||||||| ||||||||||
---------------------------------------------gtaagttcttcgtagttttcgttttct-tctagcttttcttacgaagactttcagGGACATGATATTCTCATGGCTACGATGCTTAATGGTGCTGCGATCATGGACGGCGCTTTGCTTTTGATTGCCAGCAACGAAAGCTGTCCGCAGCCGCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctactgtctagtgattttttttttatgtttttcttttttcatcttcccatctagGGGCATGATATTCTCATGGCTACAATGCTTAATGGAGCGGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAATGAAAGCTGTCCACAGCCGCAAA
               ttttttttttatgttt  CT-rich tract
         tagtgatttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaggtggctttaagattctggatgtccaggcctaaatgcctgggtctactgtctagtgattttttttttatgtttttcttttttcatcttcccatctagGGGCATGATATTCTCATGGCTACAATGCTTAATGGAGCGGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAATGAAAGCTGTCCACAGCCGCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - -tggcttt
- - - - - - - - - ctggatg
- - - - - - - - - - - - - ccaggcc
- - - - - - - - - - - - - - - - - aaatgcc
- - - - - - - - - - - - - - - - - - - - - - - -tactgtc