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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatctctttttacacactatgacctttcattctttcggatttagaattttgttatttagattttgagtttttcgtaaaattaagagtatttattcacaatctcttatgatactggctactcactgagtttgaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAATTAAATAAAAGTTGGTGGAGTGGCAGTGTGGAGGATTTTGTGCAAAAAT

Basic information

species Vitis vinifera
transcript Vv00s0399g00020.t01
intron # 1
splice site 3'
intron type U2

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|110397896|gb|EC963871.1|EC963871
EST:     TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAA                         GGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAG
genomic: TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAAgtaatatctc ... gaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
EST: gi|254916648|gb|GR905474.1|GR905474
EST:     TGCAAGCTCAATATCAACATTCCTATCAGCCCCAATGTTGACTGCAACAA                         GGTTCAGTGAAACGTGGAAATTGTACTAGAGTGGCTATGATTTGAAGAAAA
genomic: TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAAgtaatatctc ... gaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
EST: gi|254917502|gb|GR903154.1|GR903154
EST:     TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAA                         GGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
genomic: TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAAgtaatatctc ... gaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
EST: gi|28969208|gb|CB348241.1|CB348241
EST:     TGCAAGCTCAATATCGACATTCCTATCAGCCCCAATGTTGACTGCAACAA                         GGTTCAGTGAAGCGTGGAAATTGTACTAGAGTGGCTATGATTTGAAGAAAA
genomic: TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAAgtaatatctc ... gaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
EST: gi|30297959|gb|CB974753.1|CB974753
EST:     TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAA                         GGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
genomic: TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAAgtaatatctc ... gaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
EST: gi|110694050|gb|EE070819.1|EE070819
EST:     TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAA                         GGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
genomic: TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAAgtaatatctc ... gaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
EST: gi|254917249|gb|GR906075.1|GR906075
EST:     TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAA                         GGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
genomic: TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAAgtaatatctc ... gaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
EST: gi|254917885|gb|GR903537.1|GR903537
EST:     TGCAAGCTCAATATCAACATTCCTATCAGCCCCAATGTTGACTGCAACAA                         GGTTCAGTGAAACGTAGAAATTGTACTAGAGTGGCTATGAT
genomic: TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAAgtaatatctc ... gaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGAT
EST: gi|27585760|gb|CB008455.1|CB008455
EST:     TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAA                         GGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
genomic: TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAAgtaatatctc ... gaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
EST: gi|110400699|gb|EC967274.1|EC967274
EST:     TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAA                         GGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
genomic: TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAAgtaatatctc ... gaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
EST: gi|30126489|gb|CB911828.1|CB911828
EST:     TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAA                         GGTTCAGTGAAACGTGGAAATTCTACTAGAGTGGCTATGATATGAAGAAAA
genomic: TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAAgtaatatctc ... gaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
EST: gi|110398926|gb|EC965407.1|EC965407
EST:     TGCAAGCTCAATATCAACATTCCTATCAGCCCCAATGTTGACTGCAACAA                         GGTTCAGTGAAACGTGGAAATTGTACTAGAGTGGCTATGATTTGAAGAAAA
genomic: TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAAgtaatatctc ... gaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
EST: gi|110402054|gb|EC968687.1|EC968687
EST:     TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAA                         GGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
genomic: TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAAgtaatatctc ... gaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
EST: gi|87585862|gb|DY474405.1|DY474405
EST:     TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAA                         GGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
genomic: TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAAgtaatatctc ... gaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
EST: gi|110397149|gb|EC962872.1|EC962872
EST:     TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAA                         GGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
genomic: TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAAgtaatatctc ... gaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
EST: gi|30298858|gb|CB975652.1|CB975652
EST:     TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGCCTGCAACAA                         GGTTCAGTGAAACGTGGAAATTTTACTAGAGTGACTATGATATGAAGAAAA
genomic: TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAAgtaatatctc ... gaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
EST: gi|30126116|gb|CB911455.1|CB911455
EST:     TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAA                         GGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
genomic: TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAAgtaatatctc ... gaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
EST: gi|30298022|gb|CB974816.1|CB974816
EST:     TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAA                         GGTTCAGTGAAACGTGGAAATTTTACTAGAGTGACTATGATATGAAGAAAA
genomic: TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAAgtaatatctc ... gaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
EST: gi|71868776|gb|DT017831.1|DT017831
EST:     TGCAAGCTCAATATCAACATTCCTATCAGCCCCAATGTTGACTGCAACAA                         GGTTCAGTGAAACGTGGAAATTGTACTAGAGTGGCTATGATTTCAAGAAAA
genomic: TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAAgtaatatctc ... gaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
EST: gi|110363481|gb|EC927073.1|EC927073
EST:     TGCAAGCTCAATATCAACATTCCTATCAGCCCCAATGTTGACTGCAACAA                         GGTTCAGTGAAACGTGGAAATTGTACTAGAGTGGCTATGATTTGAAGAAAA
genomic: TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAAgtaatatctc ... gaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
EST: gi|30124947|gb|CB910286.1|CB910286
EST:     TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAA                         GGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
genomic: TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAAgtaatatctc ... gaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
EST: gi|34548230|gb|CF516462.1|CF516462
EST:     TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAA                         GGTTCAGTGAAACGTGGAAATTTTACTAGAGTGACTATGATATGAAGAAAA
genomic: TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAAgtaatatctc ... gaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
EST: gi|110428818|gb|EC995299.1|EC995299
EST:     TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAA                         GGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
genomic: TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAAgtaatatctc ... gaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
EST: gi|110700328|gb|EE078244.1|EE078244
EST:     TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAA                         GGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTAGGATATGAAGAAAA
genomic: TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAAgtaatatctc ... gaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
EST: gi|34551022|gb|CF519222.1|CF519222
EST:     TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAA                         GGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA
genomic: TGCAAGCTCAATATCAACATTCCTGTCACCCCCAATGTTGACTGCAACAAgtaatatctc ... gaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatttattcacaatctcttatgatactggctactcactgagtttgaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAATTAAATAAAAGTTGGTGGAGTGGCAGTGTGGAGGATTTTGTGCAAAAAT
                               tactcac  putative branch site (score: 1)
                                          tttgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatctctttttacacactatgacctttcattctttcggatttagaattttgttatttagattttgagtttttcgtaaaattaagagtatttattcacaatctcttatgatactggctactcactgagtttgaatttgcagGGTTCAGTGAAACGTGGAAATTCTACTAGAGTGACTATGATATGAAGAAAATTAAATAAAAGTTGGTGGAGTGGCAGTGTGGAGGATTTTGTGCAAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT