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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATGAAGAAGGCGCTTCCCGCGAATGGAAAGATCGCTAAGGATGCGAAAGAGATCATGCAAGAATGCGTCTCGGAGTTCATCAGTTTCATCACTAGCGAgtatggctgatgcattttttctttttaattttaggcggtgcgtgattgatggtgttgttggttttgtttttcaattggatgcctag

Basic information

species Vitis vinifera
transcript Vv08s0040g03260.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g03260.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os01g61810.3 (Oryza sativa), 5'ss of exon 2
TCATGAAGAAGGCGCTTCCCGCGAATGGAAAGATCGCTAAGGATGCGAAAGAGATCATGCAAGAATGCGTCTCGGAGTTCATCAGTTTCATCACTAGCGAgtatggctg----------atgc----attttttctttttaa-----ttttaggcggtgcgtgattgatggtgttgttg-gttttgtttttcaattggatgcctag---------------
|||||||||||||  | || ||||| || |||||||| ||||| || || |||| | |||| || ||||||||||||||||||   ||| |||| |||||||  | |||           | |    ||  |  | |    |     | ||  | | ||  || || | |||||  ||  | |||| |||    || |     | |               
TCATGAAGAAGGCCGTCCCGGCGAACGGCAAGATCGCCAAGGACGCCAAGGAGACCCTGCAGGAGTGCGTCTCGGAGTTCATCTCCTTCGTCACCAGCGAgtgagtctgcgcgggctcggtaccgtgatcctgccctccccacaccttcttttgtgatggttggtttagggtgtgattttgctttgctttgtggtttgggcggtggtgcgggatgggacag

upper sequence: Vv08s0040g03260.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G064426_T02 (Zea mays), 5'ss of exon 2
TCATGAAGAAGGCGCTTCCCGCGAATGGAAAGATCGCTAAGGATGCGAAAGAGATCATGCAAGAATGCGTCTCGGAGTTCATCAGTTTCATCACTAGCGAgtatggctgatg-cattttttctttttaattttaggcggtgcgtgattgat--ggtgttgttggttttgtttttcaattggatgcctag-----------------------------------------------------------
|||||||||||||  | || || || || |||||||| ||||| || || |||| | |||| || ||||||||||||||||||   ||||||||||||||||| | |    | |      |   | | | | |      ||| ||     |  ||  ||    ||   ||||  |||   |     |||                                                           
TCATGAAGAAGGCCATCCCGGCTAACGGGAAGATCGCCAAGGACGCTAAGGAGACCGTGCAGGAGTGCGTCTCGGAGTTCATCTCCTTCATCACTAGCGAgtaagtccctcggccgcggctgactctgactcttctgtttgcttggcatgttgggaattcagagtggcgtttcgcaaaccgcactttagcttaggtggggttttgtgttgacttgtctacgtccacgttccttgtctgctgtttgcag

upper sequence: Vv08s0040g03260.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM5G804893_T01 (Zea mays), 5'ss of exon 2
TCATGAAGAAGGCGCTTCCCGCGAATGGAAAGATCGCTAAGGATGCGAAAGAGATCATGCAAGAATGCGTCTCGGAGTTCATCAGTTTCATCACTAGCGAgta--tggctgatgcattttttctttttaattttaggcggtgcgt----gattgatggtgttgtt--ggttttgtttttcaattggatgcctag------------------------------------------
|||||||||||||  | || || || || |||||||| ||||| || || |||| | |||| || |||||||| |||||||||   |||||||||||||||||  || || |        |   | ||| ||||    ||   ||     |||    |||  |||  ||  ||    ||   | || |     |                                          
TCATGAAGAAGGCCATCCCGGCTAACGGGAAGATCGCCAAGGACGCTAAGGAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgcctcagctgcggctgactcttacttttgcttggcttgttgggaatttggagtggcgttcagggctttagcttggctggggttttgtgttgacttgtccatgtccacgtttttttgtccgctctttgcag

upper sequence: Vv08s0040g03260.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA03G33490.1 (Glycine max), 5'ss of exon 2
TCATGAAGAAGGCGCTTCCCGCGAATGGAAAGATCGCTAAGGATGCGAAAGAGATCATGCAAGAATGCGTCTCGGAGTTCATCAGTTTCATCACTAGCGAgtatggctgatgcattttttctttttaattttaggcggtgcgtgattgatggtgttgttggttttgtttttcaattggatgcctag----------
||||||||||||| ||||| || || || || ||||| ||||| || ||||||| | | || ||||||||||| ||||||||||| |||||||| ||||||| | |    |   ||||||||| | | | ||      | |||  ||  |  |  |  | |  |  ||||    |   || ||| |          
TCATGAAGAAGGCACTTCCTGCCAACGGTAAAATCGCAAAGGACGCCAAAGAGACCGTTCAGGAATGCGTCTCCGAGTTCATCAGCTTCATCACCAGCGAgt-tagtgtgttttttttttcttctgattcttttctcctccgtttttcttatttatcatcgcctgcttttaatttaaaattccttgaattctgtag

upper sequence: Vv08s0040g03260.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA19G36220.1 (Glycine max), 5'ss of exon 2
TCATGAAGAAGGCGCTTCCCGCGAATGGAAAGATCGCTAAGGATGCGAAAGAGATCATGCAAGAATGCGTCTCGGAGTTCATCAGTTTCATCACTAGCGAgt--atggctgatgcattttttcttttta--attttaggcggtgcgtgattgatggtgttgt-tggttttgtttttcaattggatgcctag------------
||||||||||||| || || ||||| || || ||||| ||||| || ||||||| | | || |||||||| || |||||||||||||||||||| |||||||   || ||  | | ||| || || |||  |||        | |||  ||  |  | || | |  |   ||  || ||||      |               
TCATGAAGAAGGCACTACCTGCGAACGGTAAAATCGCCAAGGACGCCAAAGAGACCGTTCAGGAATGCGTATCCGAGTTCATCAGTTTCATCACCAGCGAgttagtgtctttttcttttctttttcttatgattcattctcttccgttttttctcttattatatcatcccgtgctttaatttcgaatccgtttaatcgtgtag

upper sequence: Vv08s0040g03260.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT2G37060.3 (Arabidopsis thaliana), 5'ss of exon 2
TCATGAAGAAGGCGCTTCCCGCGAATGGAAAGATCGCTAAGGATGCGAAAGAGATCATGCAAGAATGCGTCTCGGAGTTCATCAGTTTCATCACTAGCGAgtatggctgatgcattttttctttttaattttaggcggtgcgtgat--tgatgg-tgttgttggttttgtttttcaattggatgcctag-------------
||||||| |  |  ||||| || ||||| || |||||||| ||||| || |||||  |||| ||||| ||||| || |||||||||||| |||| |||||||||| ||  |  |   |||  |   |||  || |  |||  || |  || ||  ||||    |  ||| |    | || ||    |||             
TCATGAAAAGAGGTCTTCCTGCTAATGGGAAAATCGCTAAAGATGCTAAGGAGATTGTGCAGGAATGTGTCTCTGAATTCATCAGTTTCGTCACCAGCGAgtatgtcttttttaaccttt--taacaatgctatgttgtgtttgctcttgctgaatgtttagaggcttgataggaactttgagttttagtttcaagtcttaa

upper sequence: Vv08s0040g03260.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S25_10V6.1 (Physcomitrella patens), 5'ss of exon 1
----TCATGAAGAAGGCGCTTCCCGCGAATGGAAAGATCGCTAAGGATGCGAAAGAGATCATGCAAGAATGCGTCTCGGAGTTCATCAGTTTCATCACTAGCGAgtatggctgatgcattttttctttttaattttaggcggtgcgtgattgatggtgttgttggttttgtttttcaattggatgcctag-----------
    |||||||||||||| | || || ||||  ||||| || || |||||||| ||||   | || || || || || || |||||||||||||||||||||||||||   |  | ||     |||   ||||| | | |  |     || |||   | ||      |  |   ||   |       |||           
CGCATCATGAAGAAGGCGTTGCCTGCTAATGCTAAGATTGCCAAAGATGCGAAGGAGACTGTTCAGGAGTGTGTTTCAGAATTCATCAGTTTCATCACTAgcgagtatccgtttttcacaacgtctaaataattct-gacatttttgcatagatcccgctgccctcatcttacctctgctaatcttgtagttgatccatgc

upper sequence: Vv08s0040g03260.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EFJ15374 (Selaginella moellendorffii), 5'ss of exon 1
TCATGAAGAAGGCGCTTCCCGCGAATGGAAAGATCGCTAAGGATGCGAAAGAGATCATGCAAGAATGCGTCTCGGAGTTCATCAGTTTCATCACTAGCGAgtatg-gctgatgcattttttctttttaattttaggcggtgcgtgattgatggtgttgttggttttgtttttcaattggatgcctag
| |||||||||||||| || ||||||| ||||||||| |||||||| || ||||   |||||||||||||||||||||||||||| ||||||||||||||||| |   || | |  |  ||  |  | || |||       | |  |  |   ||| |                             
TAATGAAGAAGGCGCTGCCGGCGAATGCAAAGATCGCCAAGGATGCCAAGGAGACGGTGCAAGAATGCGTCTCGGAGTTCATCAGCTTCATCACTAGCGAgtaagtattgcttcgatcctttgtggtgatgttaacta--tcttcttctactttgtag-----------------------------

upper sequence: Vv08s0040g03260.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EFJ24973 (Selaginella moellendorffii), 5'ss of exon 1
TCATGAAGAAGGCGCTTCCCGCGAATGGAAAGATCGCTAAGGATGCGAAAGAGATCATGCAAGAATGCGTCTCGGAGTTCATCAGTTTCATCACTAGCGAgtatggctgatgcattttttctttttaattttaggcggtgcgtgattgatggtgttgttggttttgtttttcaattggatgcctag
| |||||||||||||| || ||||||| ||||||||| |||||||| || ||||   |||||||||||||||| ||||||||||| ||||||||||||||||| |  |  |||      |  |||  ||  |  | ||||        ||  | |  |   || |  ||| ||             
TAATGAAGAAGGCGCTGCCGGCGAATGCAAAGATCGCCAAGGATGCCAAGGAGACGGTGCAAGAATGCGTCTCAGAGTTCATCAGCTTCATCACTAGCGAgtaag--tattgctggaagttctttcgatcctttgtggtg--------atactatcttc--ttctactttgcag------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATGAAGAAGGCGCTTCCCGCGAATGGAAAGATCGCTAAGGATGCGAAAGAGATCATGCAAGAATGCGTCTCGGAGTTCATCAGTTTCATCACTAGCGAgtatggctgatgcattttttctttttaattttaggcggtgcgtgattgatggtgttgttggttttgtttttcaattggatgcctag

- - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA