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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACAACTACACCTTGAGGTTGTTCTGCATTGCATTCACTAAGAAGCGTGTAAACCAGAACAAGAAGACTTGTTACGCACAATCCAGCCAAATTCGACAGgtattgttaatatgcaagtcctgattttgtgatttcattctttttacaatttcactccctttttcttataaattttattctttaaataaagaaatgtttg...

Basic information

species Vitis vinifera
transcript Vv05s0020g03900.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g03900.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: PP1S174_49V6.1 (Physcomitrella patens), 5'ss of exon 4
TGACAACTACACCTTGAGGTTGTTCTGCATTGCATTCACTAAGAAGCGTGTAAACCAGAACAAGAAGACTTGTTACGCACAATCCAGCCAAATTCGACAGgtattgttaatatgcaagtcctgattttgtgatttcattctttttacaatttcactccctttttcttataaattttattctttaaataaagaaatgtttg----
 ||||| |||    |  |  | ||||||||||||| ||| |||||| |    ||||||| |||||||||||| ||||||||   |||||||||||| ||||| |||  ||   | |  ||    || | |||||   || | || |  |||  || |  | || ||   | | |  | |  |    |     | |         
GGACAATTACCAGCTTCGCATTTTCTGCATTGCATCCACGAAGAAGAGGCCGAACCAGATCAAGAAGACTTGCTACGCACAGAGCAGCCAAATTCGTCAGgt-ttg--aaaccgtacatcgattttatttgattggcttgtattcagcattg-accctgtattactcgaagagtgcaattctagcttgcgctactaacctaagt

upper sequence: Vv05s0020g03900.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: PP1S179_15V6.1 (Physcomitrella patens), 5'ss of exon 4
TGACAACTACACCTTGAGGTTGTTCTGCATTGCATTCACTAAGAAGCGTGTAAACCAGAACAAGAAGACTTGTTACGCACAATCCAGCCAAATTCGACAGgtattgttaatatgcaa-gtcctgattttgtgatttcattctttttacaatttcactccctttttcttataaattttattctttaaataaagaaatgtttg
 |||||||||    |  |  | || |||||||||||||| ||||||||   |||||||| |||||| ||||| || || |||   ||||||||||| ||||| ||||   |  ||||  |    |    |    |   |   || |  ||||| |  |  | | | |   | |  | ||     | ||       |  || 
AGACAACTACCAGCTTCGCATTTTTTGCATTGCATTCACGAAGAAGCGGCCAAACCAGATCAAGAAAACTTGCTATGCTCAAAGTAGCCAAATTCGCCAGgt-ttgtgtcttcgcaacattgctacaccgctgctgactcacttgtttaatttaagactgtatctgtccaagacatcatataacacatgggattctacttt

upper sequence: Vv05s0020g03900.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: PP1S46_147V6.1 (Physcomitrella patens), 5'ss of exon 4
TGACAACTACACCTTGAGGTTGTTCTGCATTGCATTCACTAAGAAGCGTGTAAACCAGAACAAGAAGACTTGTTACGCACAATCCAGCCAAATTCGACAGgtat-tgtta----atatgcaagtcctgattttgtgatttcattctttttacaatttcactccctttttcttataaattttattctttaaataaagaaatgtttg
||||||||||    |  |  ||||||||||||||||||| |||||| |   |||||||| |||||| ||||| ||||| ||||| ||||| |||||||||||   |||||    |     || |  | | | |   |   | | |   | ||   |        ||   |  |||   ||| || ||||  |||      |    
TGACAACTACCAGATCCGCATGTTCTGCATTGCATTCACCAAGAAGAGGCCAAACCAGATCAAGAAAACTTGCTACGCGCAATCGAGCCAGATTCGACAGgtgcgtgttaggtgacgcttaaattgtcaatgtcacaacacgtccacctaacttctgtgaaggattcggcacatagcatttgtttttta--taattttgcgc---

upper sequence: Vv05s0020g03900.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: EFJ09804 (Selaginella moellendorffii), 5'ss of exon 5
TGACAACTACACCTTGAGGTTGTTCTGCATTGCATTCACTAAGAAGCGTGTAAACCAGAACAAGAAGACTTGTTACGCACAATCCAGCCAAATTCGACAGgtattgttaatatgcaagtcctgattttgtgatttcattctttttacaatttcactccctttttcttataaattttattctttaaataaagaaatgtttg
||||||||||||||||||| | |||||||||| |||||| ||   | |    ||||||   |||| |||||| ||||| || || || || || || |||||||  || | | | |||   ||    |      |||||      | | | || | |                                           
TGACAACTACACCTTGAGGCTCTTCTGCATTGGATTCACCAAACGGAGGCCCAACCAGGTGAAGAGGACTTGCTACGCTCAGTCAAGTCAGATCCGCCAGgtatacttgaaaagaaagagttggccgt------tcattacaaacatactctcgcacag-----------------------------------------

upper sequence: Vv05s0020g03900.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: EFJ11647 (Selaginella moellendorffii), 5'ss of exon 5
TGACAACTACACCTTGAGGTTGTTCTGCATTGCATTCACTAAGAAGCGTGTAAACCAGAACAAGAAGACTTGTTACGCACAATCCAGCCAAATTCGACAGgtattgttaatatgcaagtcctgattttgtgatttcattctttttacaatttcactccctttttcttataaattttattctttaaataaagaaatgtttg
||||||||||||||||||| | |||||||||| |||||| ||   | |    ||||||   |||| |||||| ||||| || || || || || || |||||||  || | | | |||   || |  | | ||| ||  | |  |    | ||||                                             
TGACAACTACACCTTGAGGCTCTTCTGCATTGGATTCACCAAACGGAGGCCCAACCAGGTGAAGAGGACTTGCTACGCTCAGTCAAGTCAGATCCGCCAGgtatacttgaaaagaaagagttggtcgt-tcattacaaacatcctc---tctcacag-------------------------------------------

upper sequence: Vv05s0020g03900.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: EFJ11589 (Selaginella moellendorffii), 5'ss of exon 5
TGACAACTACACCTTGAGGTTGTTCTGCATTGCATTCACTAAGAAGCGTGTAAACCAGAACAAGAAGACTTGTTACGCACAATCCAGCCAAATTCGACAGgtattgttaatatgcaagtcctgattttgtgatttcattctttttacaatttcactccctttttcttataaattttattctttaaataaagaaatgtttg
||||||||||||||||||| |||||||||| | |||||| |||  | |    ||||||   |||| |||||| ||||| || || || || || || ||||||   || | | | |||   ||  | |      ||||     | ||||   ||||| | |                                       
TGACAACTACACCTTGAGGCTGTTCTGCATCGGATTCACCAAGCGGAGGCCCAACCAGGTGAAGAGGACTTGCTACGCTCAGTCGAGTCAGATCCGCCAGgtacacttgaaaagaaagagttggctgt------tcat-----taacaaacacactctcgtgcag-----------------------------------

upper sequence: Vv05s0020g03900.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: EFJ09763 (Selaginella moellendorffii), 5'ss of exon 5
TGACAACTACACCTTGAGGTTGTTCTGCATTGCATTCACTAAGAAGCGTGTAAACCAGAACAAGAAGACTTGTTACGCACAATCCAGCCAAATTCGACAGgtattgttaatatgcaagtcctgattttgtgatttcattctttttacaatttcactccctttttcttataaattttattctttaaataaagaaatgtttg
||||||||||||||||||| | |||||||||| |||||| |||  | |    ||||||   |||| |||||| ||||| || || || || || || ||||||   || | | | |||   |   | |    |  ||  | |  |    |                                                  
TGACAACTACACCTTGAGGCTCTTCTGCATTGGATTCACCAAGCGGAGGCCCAACCAGGTGAAGAGGACTTGCTACGCTCAGTCGAGTCAGATCCGCCAGgtacacttgaaaagaaagagtttgctgttcattaacaaacatgctctcgtacag----------------------------------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|71871064|gb|DT020119.1|DT020119
EST:     TAAACCAGAACAAGAAGACTTGTTACGCACAATCCAGCCAAATTCAACAG                         ATTCGACGGAAGATGAGAGAAATCATGACAAACATGGCAACATCTTGTGAT
genomic: TAAACCAGAACAAGAAGACTTGTTACGCACAATCCAGCCAAATTCGACAGgtattgttaa ... gttttgacagATTCGACGGAAGATGAGAGAAATCATGACAAACATGGCAACATCTTGTGAT
EST: gi|77585608|gb|DV221898.1|DV221898
EST:     TAAACCAGAACAAGAAGACTTGTTACGCACAATCCAGCCAAATTCGACAG                         ATTCGACGGAAGATGAGAGAAATCATGACAAACATGGCAACATCTTGTGAT
genomic: TAAACCAGAACAAGAAGACTTGTTACGCACAATCCAGCCAAATTCGACAGgtattgttaa ... gttttgacagATTCGACGGAAGATGAGAGAAATCATGACAAACATGGCAACATCTTGTGAT
EST: gi|71890772|gb|DT039827.1|DT039827
EST:     TAAACCAGAACAAGAAGACTTGTTACGCACAATCCAGCCAAATTCAACAG                         ATTCGACGGAAGATGAGAGAAATCATGACAAACATGGCAACATCTTGTGAT
genomic: TAAACCAGAACAAGAAGACTTGTTACGCACAATCCAGCCAAATTCGACAGgtattgttaa ... gttttgacagATTCGACGGAAGATGAGAGAAATCATGACAAACATGGCAACATCTTGTGAT
EST: gi|77580898|gb|DV219373.1|DV219373
EST:     TAAACCAGAACAAGAAGACTTGTTACGCACAATCCAGCCAAATTCGACAG                         ATTCGACGGAAGATGAGAGAAATCATGACAAACATGGCAACATCTTGTGAT
genomic: TAAACCAGAACAAGAAGACTTGTTACGCACAATCCAGCCAAATTCGACAGgtattgttaa ... gttttgacagATTCGACGGAAGATGAGAGAAATCATGACAAACATGGCAACATCTTGTGAT
EST: gi|71868214|gb|DT017269.1|DT017269
EST:     TAAACCAGAACAAGAAGACTTGTTACGCACAATCCAGCCAAATTCAACAG                         ATTCGACGGAAGATGAGAGAAATCATGACAAACATGGCAACATCTTGTGAT
genomic: TAAACCAGAACAAGAAGACTTGTTACGCACAATCCAGCCAAATTCGACAGgtattgttaa ... gttttgacagATTCGACGGAAGATGAGAGAAATCATGACAAACATGGCAACATCTTGTGAT
EST: gi|71873149|gb|DT022204.1|DT022204
EST:     TAAACCAGAACAAGAAGACTTGTTACGCACAATCCAGCCAAATTCAACAG                         ATTCGACGGAAGATGAGAGAAATCATGACAAACATGGGCA-CATCTTGTGA
genomic: TAAACCAGAACAAGAAGACTTGTTACGCACAATCCAGCCAAATTCGACAGgtattgttaa ... gttttgacagATTCGACGGAAGATGAGAGAAATCATGACAAACATGG-CAACATCTTGTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACAACTACACCTTGAGGTTGTTCTGCATTGCATTCACTAAGAAGCGTGTAAACCAGAACAAGAAGACTTGTTACGCACAATCCAGCCAAATTCGACAGgtattgttaatatgcaagtcctgattttgtgatttcattctttttacaatttcactccctttttcttataaattttattctttaaataaagaaatgtttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagaaa