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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattctcatttttcttgatttgataatgaatagcagtaaattttcctcagcaattgaattcatggtaattggagtatttgattttggttgactactgcagTTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAACGGCTAGTGGCTGCCATTGATGGCCTTCCAGATGCTGGTGGCCCATCAGT

Basic information

species Vitis vinifera
transcript Vv14s0128g00050.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0128g00050.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G37520.1 (Glycine max), 3'ss of exon 2
------gattctcatttttcttgatttgataatgaatagcagtaaattttcctcagcaattgaattcatggtaattggagtatttgattttggttgactactgcagTTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAACGGCTAGTGGCTGCCATTGATGGCCTTCCAGATGCTGGTGGCCCATCAGT
      |||  || |    ||| | |   ||| ||| |||  ||| |  |  | |    |||||     ||  |    | ||  |   | ||||| |    |||||| || || || || || ||||||||||||||  |||| |||| ||| ||||||||||  |||||||||||||| ||||||||| ||||||| ||| ||||
cttgttgatcttc-tgaagctttactcagtaaggaacagctataa-tcatttttactttttgaag----gggtacaaaactacctatgtctggtttatatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAACGGCTAGCTGCTGCCATTGATGGGCTTCCAGATCCTGGTGGGCCAACAGT

upper sequence: Vv14s0128g00050.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G29810.1 (Glycine max), 3'ss of exon 2
----gattctcatttttcttgatttgataatgaatagcagtaaattttcctcagcaattgaattcatggtaattggagtatttgattttggttgactactgcagTTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAACGGCTAGTGGCTGCCATTGATGGCCTTCCAGATGCTGGTGGCCCATCAGT
      || ||| | ||||  |  |  || | | ||      |  | |  |||   ||| | ||  ||  |   | | ||  |   | ||||| |    |||||| || || || || || ||||||||||||||  |||| |||| ||| |||||||||| ||||||||| ||||| ||||| ||| ||||||| ||| ||||
taaaacttgtcaatcttctgaagctt-tactcagtaaggaacagctataatcat--atttactttttga-aggggtactacctatgtctggtttatatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAACGGCTAGCGGCTGCCATAGATGGGCTTCCGGATCCTGGTGGGCCAACAGT
















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|351040205|gb|FQ425291.1|FQ425291
EST:     GGCTGTTGGTGATACCATTCTTGATGCTACAGTATCAGAGAACCTTCCGG                         TTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAAC
genomic: GGCTGTTGGTGATACCATTCTTGATGCTACAGTATCAGAGAACCTTCCGGgtataaaaac ... actactgcagTTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAAC
EST: gi|349808323|gb|FQ405467.1|FQ405467
EST:     GGCTGTTGGTGATACCATTCTTGATGCTACAGTATCAGAGAACCTTCCGG                         TTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCCGCAGTGCCCAAC
genomic: GGCTGTTGGTGATACCATTCTTGATGCTACAGTATCAGAGAACCTTCCGGgtataaaaac ... actactgcagTTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAAC
EST: gi|351019285|gb|FQ429445.1|FQ429445
EST:     GGCTGTTGGTGATACCATTCTTGATGCTACAGTATCAGAGAACCTTCCGG                         TTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAAC
genomic: GGCTGTTGGTGATACCATTCTTGATGCTACAGTATCAGAGAACCTTCCGGgtataaaaac ... actactgcagTTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAAC
EST: gi|33408060|gb|CF213687.1|CF213687
EST:     GGCTGTTGGTGATACCATTCTTGATGCTACAGTATCAGAGAACCTTCCGG                         TTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAAC
genomic: GGCTGTTGGTGATACCATTCTTGATGCTACAGTATCAGAGAACCTTCCGGgtataaaaac ... actactgcagTTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAAC
EST: gi|110384796|gb|EC949258.1|EC949258
EST:     GGCTGTTGGTGATACCATTCTTGATGCTACAGTATCAGAGAACCTTCCGG                         TTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAAC
genomic: GGCTGTTGGTGATACCATTCTTGATGCTACAGTATCAGAGAACCTTCCGGgtataaaaac ... actactgcagTTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAAC
EST: gi|110388378|gb|EC953120.1|EC953120
EST:     GGCTGTTGGTGATACCATTCTTGATGCTACAGTATCAGAGAACCTTCCGG                         TTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAAC
genomic: GGCTGTTGGTGATACCATTCTTGATGCTACAGTATCAGAGAACCTTCCGGgtataaaaac ... actactgcagTTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAAC
EST: gi|32268811|gb|CD717970.1|CD717970
EST:     GGCTGTTGGTGATACCATTCTTGATGCTACAGTATCAGAGAACCTTCCGG                         TTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAAC
genomic: GGCTGTTGGTGATACCATTCTTGATGCTACAGTATCAGAGAACCTTCCGGgtataaaaac ... actactgcagTTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAAC
EST: gi|110383081|gb|EC947430.1|EC947430
EST:     GGCTGTTGGTGATACCATTCTTGATGCTACAGTATCAGAGAACCTTCCGG                         TTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAAC
genomic: GGCTGTTGGTGATACCATTCTTGATGCTACAGTATCAGAGAACCTTCCGGgtataaaaac ... actactgcagTTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAAC
EST: gi|351040265|gb|FQ425351.1|FQ425351
EST:     GGCTGTTGGTGATACCATTCTTGATGCTACAGTATCAGAGAACCTTCCGG                         TTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAAC
genomic: GGCTGTTGGTGATACCATTCTTGATGCTACAGTATCAGAGAACCTTCCGGgtataaaaac ... actactgcagTTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAAC
EST: gi|110422621|gb|EC988948.1|EC988948
EST:     GGCTGTTGGTGATACCATTCTTGATGCTACAGTATCAGAGAACCTTCCGG                         TTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAAC
genomic: GGCTGTTGGTGATACCATTCTTGATGCTACAGTATCAGAGAACCTTCCGGgtataaaaac ... actactgcagTTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcagcaattgaattcatggtaattggagtatttgattttggttgactactgcagTTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAACGGCTAGTGGCTGCCATTGATGGCCTTCCAGATGCTGGTGGCCCATCAGT
                                        ggttgac  putative branch site (score: 4)
                             tatttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattctcatttttcttgatttgataatgaatagcagtaaattttcctcagcaattgaattcatggtaattggagtatttgattttggttgactactgcagTTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAACGGCTAGTGGCTGCCATTGATGGCCTTCCAGATGCTGGTGGCCCATCAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - aatgaata
- - - - - - - - - - - - - - - - - - - - - - - - - -aattgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcatgg