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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatttcctactaaatgttgttgtggatccattgttctttagaattggaatcctagttttgattcacaatgccttcattcaatgaatgcagGGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTGCATTACCAAGCATTCACCTCAGTACAGAATTTTAATGGTGGGGCGTGTG

Basic information

species Vitis vinifera
transcript Vv16s0098g01290.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0098g01290.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 2
------------gtgagatttcctactaaatgttgttgtggatccattgttctttagaattggaatcctagttttgattcacaatgccttcattcaatgaatgcagGGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTGCATTACCAAGCATTCACCTCAGTACAGAATTTTAATGGTGGGGCGTGTG
             |  | |||| |  |  || ||||||   | |  | ||    |    ||      ||| |  || |||         | |  |  ||||  ||| || |||||||| |||||||||||||| ||||| || || ||  |||| ||||| ||||||||||| ||||| |||| | |  | ||| |||| ||  | 
gtgagacgtctttttcggtttcttgtttcatcttgttgcatacctgtcgtataatttttttcagtgtctaatggtgcttcttg-----cttaccctgtgaaatcagAGGCCGGAAGAGGGCTTGTGTGACTTACTGCATAACCTACATTTTGAGTTGCATCACCAAGCATTCTCCTCAATACAAAGTCCTGATGTTGGGCCGCATT

upper sequence: Vv16s0098g01290.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G13760.2 (Glycine max), 3'ss of exon 2
gtgagatttcctactaaatgttgttgtggatccattgttctt-tagaattggaatcctagttttgattcacaatgccttcattcaatgaatgcagGGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTGCATTACCAAGCATTCACCTCAGTACAGAATTTTAATGGTGGGGCGTGTG
||||||| || |  |   | || ||||   | |||   | |  |||||||    |   ||| |    |||  |||| ||| | |  ||||  ||| || |||||||| |||||||||||||| ||||| || || ||  |||| ||||| ||||||||||| ||||| |||| | |  | ||| |||| ||| | 
gtgagatgtcttttttggt-ttcttgt---ttcataactgtcatagaatt----tttcagtgtc---tcatgatgc-ttcttaccctgaaatcagAGGCCGGAAGAGGGCTTGTGTGACTTACTGCATAACCTACATTTTGAGTTGCATCACCAAGCATTCTCCTCATTACAAAGTCCTGATGTTGGGCCGTATT

upper sequence: Vv16s0098g01290.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgagatttcctactaaatgttgttgtggatccattgttctttagaattggaatcctagttttgattcacaatgccttcattcaatgaatgcagGGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTGCATTACCAAGCATTCACCTCAGTACAGAATTTTAATGGTGGGGCGTGTG
|||||  |||   |   ||| | ||  | |   || |   | |  | |     |  ||||  || | || ||||      |||  || || |||||| || ||||| || ||||| || ||||| ||||| |||||| |||||||||| ||||||||||| ||||| || |   |||| ||||| || ||||| 
gtgagcattctctc-gtatgcttttaagtaat-atggaaatcttaactc----ttttagtaatgttgcataatggt---gttc--tgtat-cagGGGTCGTAAGAGGGCATGTGTTACCTATTGTATTACCTATATATTGAGCTGCATCACCAAGCATTCTCCTCAATATAAGGTTTTGATGGTAGGCCGTGTC

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|110688923|gb|EE068027.1|EE068027
EST:     GGGTCCTCCATGTTGTTTGGCACAATTGTTGGATCTCTAGCTGACAAACA                         GGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG
genomic: GGGTCCTCCATGTTGTTTGGCACGATTGTTGGATCTCTAGCTGACAAACAgtgagatttc ... atgaatgcagGGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG
EST: gi|161705940|gb|FC054828.1|FC054828
EST:     GGGTCCTCCATGTTGTTTGGCACGATTGTTGGATCTCTAGCTGACAAACA                         GGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG
genomic: GGGTCCTCCATGTTGTTTGGCACGATTGTTGGATCTCTAGCTGACAAACAgtgagatttc ... atgaatgcagGGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG
EST: gi|46918112|gb|CN547441.1|CN547441
EST:     GGGTCCTCCATGTTGTTTGGCACAATTGTTGGATCTCTAGCTGACAAACA                         GGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG
genomic: GGGTCCTCCATGTTGTTTGGCACGATTGTTGGATCTCTAGCTGACAAACAgtgagatttc ... atgaatgcagGGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG
EST: gi|77586406|gb|DV222324.1|DV222324
EST:     GGGTCCTCCATGTTGTTTGGCACGATTGTTGGATCTCTAGCTGACAAACA                         GGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG
genomic: GGGTCCTCCATGTTGTTTGGCACGATTGTTGGATCTCTAGCTGACAAACAgtgagatttc ... atgaatgcagGGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG
EST: gi|161718412|gb|FC067288.1|FC067288
EST:     GGGTCCTCCATGTTGTTTGGCACGATTGTTGGATCTCTAGCTGACAAACA                         GGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG
genomic: GGGTCCTCCATGTTGTTTGGCACGATTGTTGGATCTCTAGCTGACAAACAgtgagatttc ... atgaatgcagGGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG
EST: gi|33402269|gb|CF207896.1|CF207896
EST:     TCTAGCTGACAAACA                         GGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG
genomic: TCTAGCTGACAAACAgtgagatttc ... atgaatgcagGGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG
EST: gi|71872970|gb|DT022025.1|DT022025
EST:     GGGTCCTCCATGTTGTTTGGCACGATTGTTGGATCTCTAGCTGACAAACA                         GGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG
genomic: GGGTCCTCCATGTTGTTTGGCACGATTGTTGGATCTCTAGCTGACAAACAgtgagatttc ... atgaatgcagGGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG
EST: gi|161715635|gb|FC066793.1|FC066793
EST:     GGGTCCTCCATGTTGTTTGGCACGATTGTTGGATCTCTAGCTGACAAACA                         GGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG
genomic: GGGTCCTCCATGTTGTTTGGCACGATTGTTGGATCTCTAGCTGACAAACAgtgagatttc ... atgaatgcagGGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG
EST: gi|161706950|gb|FC056819.1|FC056819
EST:     GGGTCCTCCATGTTGTTTGGCACGATTGTTGGATCTCTAGCTGACAAACA                         GGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG
genomic: GGGTCCTCCATGTTGTTTGGCACGATTGTTGGATCTCTAGCTGACAAACAgtgagatttc ... atgaatgcagGGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG
EST: gi|71872927|gb|DT021982.1|DT021982
EST:     GGGTCCTCCATGTTGTTTGGCACGATTGTTGGATCTCTAGCTGACAAACA                         GGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG
genomic: GGGTCCTCCATGTTGTTTGGCACGATTGTTGGATCTCTAGCTGACAAACAgtgagatttc ... atgaatgcagGGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG
EST: gi|161708566|gb|FC060425.1|FC060425
EST:     GGGTCCTCCATGTTGTTTGGCACGATTGTTGGATCTCTAGCTGACAAACA                         GGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG
genomic: GGGTCCTCCATGTTGTTTGGCACGATTGTTGGATCTCTAGCTGACAAACAgtgagatttc ... atgaatgcagGGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG
EST: gi|161721644|gb|FC069774.1|FC069774
EST:     GGGTCCTCCATGTTGTTTGGCACGATTGTTGGATCTCTAGCTGACAAACA                         GGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG
genomic: GGGTCCTCCATGTTGTTTGGCACGATTGTTGGATCTCTAGCTGACAAACAgtgagatttc ... atgaatgcagGGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG
EST: gi|110380688|gb|EC945972.1|EC945972
EST:     GGGTCCTCCATGTTGTTTGGCACGATTGTTGGATCTCTAGCTGACAAACA                         GGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG
genomic: GGGTCCTCCATGTTGTTTGGCACGATTGTTGGATCTCTAGCTGACAAACAgtgagatttc ... atgaatgcagGGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttagaattggaatcctagttttgattcacaatgccttcattcaatgaatgcagGGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTGCATTACCAAGCATTCACCTCAGTACAGAATTTTAATGGTGGGGCGTGTG
                    ttttgat  putative branch site (score: 4)
                    ttttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagatttcctactaaatgttgttgtggatccattgttctttagaattggaatcctagttttgattcacaatgccttcattcaatgaatgcagGGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTGCATTACCAAGCATTCACCTCAGTACAGAATTTTAATGGTGGGGCGTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG