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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGAAGGATGCGCGTTGCCTTCACTTGCAATGTTTGCGGTCAGCGGACCACTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaattttttctccctgtcctctgtttggttgatgggaaaagataatagaaaaataaaataaaatcaatatcttgttttatgttatttgtttccaaataa...

Basic information

species Vitis vinifera
transcript Vv18s0001g00750.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g00750.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G152056_T02 (Zea mays), 5'ss of exon 2
TCGAAGGATGCGCGTTGCCTTCACTTGCAATGTTTGCGGTCAGCGGACCACTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaattttttctccctgtcctctgtttggttgatgggaaaagataatagaaaaataaaataaaatcaatatcttgttttatgttatttgtttccaaataa--
 ||  | ||||| || |||||||| ||||| || ||||| ||||| || ||  | ||||||||||||||||| ||||| |||||||| || || || |||||| |    | |     |  | | |    |   |    ||   | |    ||  | | |      |    | | ||| |  || |||   | |    |    
GCGGCGCATGCGGGTGGCCTTCACCTGCAACGTGTGCGGGCAGCGTACGACCAGGGCCATCAATCCTCATGCCTACACTGATGGAACTGTGTTTGTTCAGgta-tggactatgtgattagtgtatccaatgcgttaataagagtcaagttaagctgatacttgccctgcctttagttatgcgt-attgactgctgcttctgt

upper sequence: Vv18s0001g00750.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: EFJ21589 (Selaginella moellendorffii), 5'ss of exon 1
TCGAAGGATGCGCGTTGCCTTCACTTGCAATGTTTGCGGTCAGCGGACCACTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaattttttctccctgtcctctgtttggttgatgggaaaagataatagaaaaataaaataaaatcaatatcttgttttatgttatttgtttccaaataa
 ||||| ||| | || || || |||||||| ||||| ||   ||| || |   | || ||||||||||| |||||||| |||||||| || ||||||||||||     |  ||| | |  ||  | |      |  | ||| |    ||          |  |                                     
ACGAAGAATGAGAGTGGCGTTTACTTGCAACGTTTGTGGAGCGCGAACTATGAGAGCTATCAATCCTCACGCTTACACAGATGGAACAGTCTTCGTCCAGgtagaaactcttccatttattccatctttcctctccgcaaacacgcaagcttctcttcgtgcag------------------------------------
















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|32272198|gb|CD721357.1|CD721357
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
EST: gi|351030673|gb|FQ438511.1|FQ438511
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGAACA-TCGGAATCTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGA-CAATCTGAATCTTTT
EST: gi|30326615|gb|CD009877.1|CD009877
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
EST: gi|32248331|gb|CD714150.1|CD714150
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
EST: gi|110367582|gb|EC931522.1|EC931522
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
EST: gi|30325841|gb|CD009103.1|CD009103
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
EST: gi|110426950|gb|EC993379.1|EC993379
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
EST: gi|110397725|gb|EC963577.1|EC963577
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
EST: gi|30327911|gb|CD011173.1|CD011173
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
EST: gi|110411458|gb|EC977172.1|EC977172
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
EST: gi|32267575|gb|CD716538.1|CD716538
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
EST: gi|30325217|gb|CD008479.1|CD008479
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
EST: gi|110721872|gb|EE097605.1|EE097605
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
EST: gi|30322568|gb|CD005830.1|CD005830
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCNATGTGTTTCATANACTGGTGGACAATCTGAATCTTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
EST: gi|30127790|gb|CB913129.1|CB913129
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
EST: gi|32248255|gb|CD714074.1|CD714074
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
EST: gi|110383972|gb|EC948381.1|EC948381
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
EST: gi|32249309|gb|CD715128.1|CD715128
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
EST: gi|18459473|gb|BM437751.1|BM437751
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
EST: gi|351023996|gb|FQ423419.1|FQ423419
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
EST: gi|32272050|gb|CD721209.1|CD721209
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
EST: gi|37186187|gb|CF605540.1|CF605540
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAA
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAA
EST: gi|351041477|gb|FQ431503.1|FQ431503
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
EST: gi|110695208|gb|EE072961.1|EE072961
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
EST: gi|18458574|gb|BM436852.1|BM436852
EST:     CACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
genomic: CACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
EST: gi|30325131|gb|CD008393.1|CD008393
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
EST: gi|110381520|gb|EC934681.1|EC934681
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
EST: gi|27579911|gb|CB002606.1|CB002606
EST:     CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAG                         TGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT
genomic: CTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaatttttt ... tgatttgcagTGCTGTGGATGCAATGTGTTTCATAAACTGGTGGACAATCTGAATCTTTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGAAGGATGCGCGTTGCCTTCACTTGCAATGTTTGCGGTCAGCGGACCACTCGTGCCATCAATCCTCATGCTTACACCGATGGAACCGTTTTCGTCCAGgtaattttttctccctgtcctctgtttggttgatgggaaaagataatagaaaaataaaataaaatcaatatcttgttttatgttatttgtttccaaataa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa