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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAGgtattttgttcttatggtcacagattaggaaaaaaagggctgaattatgtaatttgttctttgacttattccccccaaaagaagaattgacatggcttaa...

Basic information

species Vitis vinifera
transcript Vv01s0026g01640.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g01640.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA02G02540.2 (Glycine max), 5'ss of exon 4
GCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAGgtattttgttcttatggtcacagattaggaaaaaaagggctgaattatgtaatttgttctttgacttattccccccaaaagaagaattgacatggcttaa--
|| |||||||||||||| |  ||||||||||| || |||||||||||||| || ||||||||||||||||| ||||| ||||||||||| ||||| ||||| || |    ||| |||    || |    |        || ||||  |  ||    ||| |   |||      ||   ||   ||    | | ||    
GCTATGTCAGCTTATGGGTATGAGATAGTTCAGACGCTTATTGTGGATATTGAGCCAGATGAGCATGTGAAGAGAGCCATGAATGAGATTAATGCTGgtatgttttctagatgttcatgtttttgcttcagttata--gagttattcatatttccatttcaagcattgaaaaaaatttaaatgttagtttagtttggtg

upper sequence: Vv01s0026g01640.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA02G02500.1 (Glycine max), 5'ss of exon 5
GCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAGgtattttgttcttatggtca----cagattaggaaaaaaagggctgaattatgtaatttgttctttgacttattccccccaaaagaagaattgacatggcttaa
|| |||||||||||||| | |||||||||||| || |||||||||||||| || |||||||||| |||||| ||||| ||||||||||| || || ||||| || |    ||| |||    ||  ||        |      || | ||  | ||| | ||||       | |   ||||| ||   ||    |       
GCCATGTCAGCTTATGGGTACGAGATAGTTCAGACTCTTATTGTGGATATTGAGCCAGATGAGCGTGTGAAGAGAGCCATGAATGAGATCAACGCTGgtatgttttcaaaatgttcatgttcatgttcttgcttcagttatagagtcattcattttttccttttcaagcatgctatcaaaataaatgttagtttaat----

upper sequence: Vv01s0026g01640.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA18G16270.1 (Glycine max), 5'ss of exon 5
GCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAGgtattttgttcttatggtcacagattagga--aaaaaagggctgaattatgtaatttgttctttgacttattccccccaaaagaagaattgacatggcttaa
 ||||||| |||||||| |  |||||||| || || |||||||||||||| ||||| ||||||| |||||| ||||| ||||| ||||||||||| |||||  | |    || |  | ||  ||            |    |||||  |  |||  |||||   |  | |     || ||||| | |    |  |   |
-CAATGTCTGCTTATGGGTATGAGATAGTCCAGACTCTTATTGTGGATATTGAACCGGATGAGCGTGTGAAGAGAGCCATGAACGAGATAAATGCTGGtatgctttatgcattgggatagtatattttttggctgtgctcaaattactttctttcatctttt-ttcgtacatgtaaatagaaggaattcatttacagga

upper sequence: Vv01s0026g01640.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA02G02550.1 (Glycine max), 5'ss of exon 5
GCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAGgtattttgttcttatggtcacagattaggaaaaaaagggctgaattatgtaatttgttctttgacttattccccccaaaagaagaattgacatggcttaa--------
|| |||||||| ||||| | |||||||||||| || |||||||||||||| |  || |||||||||||||| | ||| ||||||||||| ||||| ||||| ||  || ||  ||   |  ||        ||    ||| |||| |  | | | ||||   |||  |   | || | || || ||  |    |||         
GCTATGTCAGCATATGGGTACGAGATAGTTCAGACTCTTATTGTGGATATTGTGCCGGATGAGCATGTGAAGAAAGCCATGAATGAGATTAATGCTGgtatgtt--tcctacagttttatgttcttgcttcaat--ttgagttat-tcgtatttccttt---ttaagcatgctaacaaaataaatgctagaatttagtgtggtgt

upper sequence: Vv01s0026g01640.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA01G04950.1 (Glycine max), 5'ss of exon 4
GCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAGgtattttgttcttatggtcacagattaggaaaaaaagggctgaattatgta-atttgttctttgacttattccccccaaaagaag---aattgacatggcttaa
|| |||||||| ||||| |  ||||||||||| || |||||||||||||| || |||||||||| |||||| || || |||||||| || ||||| ||||| || |    ||| |||    ||   |    ||     || | ||  | ||||  | ||  |  |||       ||    ||   ||| || | |  ||  
GCTATGTCAGCATATGGGTATGAGATAGTTCAGACTCTTATTGTGGATATTGAGCCAGATGAGCGTGTGAAGAGGGCCATGAATGAAATTAATGCTGgtatgttttcaagatgttcatgtgttt--acttcaattatagagtcattcatatttccttttcaagctatcaaaataaatgttagtttaatggagaggtttt--

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|161721397|gb|FC070773.1|FC070773
EST:     TATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAG                         CTTCTAGAAATGAGGTTGGCTGCTACTGAGAAGGC
genomic: TATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAGgtattttgtt ... tgtaaaatagCTTCAAGAA-TGAGGTTGGCTGCTACTGAGAAGGC
EST: gi|26262182|gb|CA813245.1|CA813245
EST:     TATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAG                         CTTCTAGAATGAGGTTGGCTGCTACTGAGAAGGCCGAAGCTGAGAAGATAT
genomic: TATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAGgtattttgtt ... tgtaaaatagCTTCAAGAATGAGGTTGGCTGCTACTGAGAAGGCCGAAGCTGAGAAGATAT
EST: gi|110400525|gb|EC967091.1|EC967091
EST:     TATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAG                         CTTCTAGAATGAGGTTGGCTGCTACTGAGAAGGCCGAAGCTGAGAAGATAT
genomic: TATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAGgtattttgtt ... tgtaaaatagCTTCAAGAATGAGGTTGGCTGCTACTGAGAAGGCCGAAGCTGAGAAGATAT
EST: gi|110724693|gb|EE100742.1|EE100742
EST:     TATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAG                         CTTCAAGAATGAGGTTGGCTGCTACTGAGAAGGCCGAAGCTGAGAAGATAT
genomic: TATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAGgtattttgtt ... tgtaaaatagCTTCAAGAATGAGGTTGGCTGCTACTGAGAAGGCCGAAGCTGAGAAGATAT
EST: gi|110423580|gb|EC989927.1|EC989927
EST:     TATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAG                         CTTCAAGAATGAGGTTGGCTGCTACTGAGAAGGCCGAAGCTGAGAAGATAT
genomic: TATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAGgtattttgtt ... tgtaaaatagCTTCAAGAATGAGGTTGGCTGCTACTGAGAAGGCCGAAGCTGAGAAGATAT
EST: gi|110425409|gb|EC991794.1|EC991794
EST:     TATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAG                         CTTCAAGAATGAGGTTGGCTGCTACTGAGAAGGCCGAAGCTGAGAAGATAT
genomic: TATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAGgtattttgtt ... tgtaaaatagCTTCAAGAATGAGGTTGGCTGCTACTGAGAAGGCCGAAGCTGAGAAGATAT
EST: gi|32250322|gb|CD716141.1|CD716141
EST:     GAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAG                         CTTCAAGAATGAGGTTGGCTGCTACTGAGAAGGCCGAAGCTGAGAAGATAT
genomic: GAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAGgtattttgtt ... tgtaaaatagCTTCAAGAATGAGGTTGGCTGCTACTGAGAAGGCCGAAGCTGAGAAGATAT
EST: gi|110697820|gb|EE075232.1|EE075232
EST:     TATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAG                         CTTCTAGAATGAGGTTGGCTGCTACTGAGAAGGCCGAAGCTGAGAAGATAT
genomic: TATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAGgtattttgtt ... tgtaaaatagCTTCAAGAATGAGGTTGGCTGCTACTGAGAAGGCCGAAGCTGAGAAGATAT
EST: gi|27580089|gb|CB002784.1|CB002784
EST:     GAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAG                         CTTCAAGAATGAGGTTGGCTGCTACTGAGAAGGCCGAAGCTGAGAAGATAT
genomic: GAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAGgtattttgtt ... tgtaaaatagCTTCAAGAATGAGGTTGGCTGCTACTGAGAAGGCCGAAGCTGAGAAGATAT
EST: gi|110382334|gb|EC939189.1|EC939189
EST:     TATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAG                         CTTCTAGAATGAGGTTGGCTGCTACTGAGAAGGCCGAAGCTGAGAAGATAT
genomic: TATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAGgtattttgtt ... tgtaaaatagCTTCAAGAATGAGGTTGGCTGCTACTGAGAAGGCCGAAGCTGAGAAGATAT
EST: gi|110687599|gb|EE065191.1|EE065191
EST:     TATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAG                         CTTCAAGAATGAGGTTGGCTGCTACTGAGAAGGCCGAAGCTGAGAA-ATAT
genomic: TATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAGgtattttgtt ... tgtaaaatagCTTCAAGAATGAGGTTGGCTGCTACTGAGAAGGCCGAAGCTGAGAAGATAT
EST: gi|110389091|gb|EC953904.1|EC953904
EST:     TATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAG                         CTTCTAGAATGAGGTTGGCTGCTACTGAGAAGGCCGAAGCTGAGAAGATAT
genomic: TATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAGgtattttgtt ... tgtaaaatagCTTCAAGAATGAGGTTGGCTGCTACTGAGAAGGCCGAAGCTGAGAAGATAT
EST: gi|161715489|gb|FC069052.1|FC069052
EST:     TATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAG                         CTTCTAGAATGAGGTTGGCTGCTACT
genomic: TATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAGgtattttgtt ... tgtaaaatagCTTCAAGAATGAGGTTGGCTGCTACT
EST: gi|110375966|gb|EC940998.1|EC940998
EST:     TATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAG                         CTTCTAGAATGAGGTTGGCTGCTACTGAGAAGGCCGAAGCTGAGAAGATAT
genomic: TATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAGgtattttgtt ... tgtaaaatagCTTCAAGAATGAGGTTGGCTGCTACTGAGAAGGCCGAAGCTGAGAAGATAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAGgtattttgttcttatggtcacagattaggaaaaaaagggctgaattatgtaatttgttctttgacttattccccccaaaagaagaattgacatggcttaa

- - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagaa