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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattttaatagcagtgacctgagatgcttagtactcagaatcatgaaatctggattccttttggcattaatacatctccttgtatcgtaaatcgttgcagTTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGTCAGGGGCAAACAGTTGGCTCATTCAATTGGAG

Basic information

species Vitis vinifera
transcript Vv14s0060g00230.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g00230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G22210.1 (Glycine max), 3'ss of exon 1
aattttaatagcagtgacctgagatgcttagtactcagaatca--tgaaatctggattccttttggcattaatacatct-ccttgtatcgtaaatcgttgcagTTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGTCAGGGGCAAACAGTTGGCTCATTCAATTGGAG
     ||| |   |       |||  |||| || |  |    |  | | | || |   || |||    |   || || |   |  | || |     ||  ||||||| || ||||||||||| || || |||||||||||||| |||||||| ||||| |||||||| ||| || || | || |||
---cctaaaaaatgcatatatagagccttattattaggtgatagttaagaacttgtagccctttaatttagctaaatatatttcttttcttttgctgtgacagTTTGCTTGGATGGAACATTGCCTGGTTATCATTTGCATCGGGGATATGGATCAGGAGCAAACAGCTGGGTCGTTAATTTAGAG

upper sequence: Vv14s0060g00230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G28230.1 (Glycine max), 3'ss of exon 1
aattttaatagcagtgacctgagatgcttagtactcagaatca--tgaaatctggattccttttggcattaatacatct-ccttgtatcgtaaatcgttgcagTTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGTCAGGGGCAAACAGTTGGCTCATTCAATTGGAG
     |||    ||       |||  |||| |  |  |    |  | | |  | |   || |||    |   || || |   |  | || |   | || |||||||| || ||||||||||| || |  |||||||||||||| |||||||| ||||| |||||||| ||| || || | || |||
---actaaagaaagcatatatagagccttatttttgggtgatagataagaatttgtagccctttaatttagctaaatatatttcttttctttcgttgtcgcagTTTGCTTGGATGGAACATTGCCTGCTTATCATTTGCATCGGGGATATGGATCAGGAGCAAACAGCTGGATCGTTAATTTAGAG

upper sequence: Vv14s0060g00230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G38650.1 (Glycine max), 3'ss of exon 1
aattttaatagcagtgacctgagatgcttagtactcagaatcatgaaatctggattccttttggcattaatacatctc-cttgtatcgtaaatcgttgcagTTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGTCAGGGGCAAACAGTTGGCTCATTCAATTGGAG
  ||||   |  | ||   |  | |      |  | |  || ||  | | |   || | |||  | |   || || |   |  | || |  |   | ||||| || || || ||||||||||| || |||||||||||||| |||||||| ||||| ||||| || ||||| ||| | || |||
-tttttcggaaaattggaatacggtcgcagtttttaaccataattgagtatactttgcctttaacttggctaaatataattcctttctttgactttggcagTCTGCTTGGACGGAACATTACCTGGTTATCATTTGCATCGGGGATATGGATCAGGAGCAAATAGCTGGCTTATTAATTTAGAG

upper sequence: Vv14s0060g00230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G41240.1 (Glycine max), 3'ss of exon 1
aattttaatagcagtgacctgagatgcttagtactcag-aatcatgaaatctggattccttttggcattaatacatctc-cttgtatcgtaaatcgttgcagTTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGTCAGGGGCAAACAGTTGGCTCATTCAATTGGAG
  ||   | |    ||   |  |  ||  |||  | |  ||| ||  | | |   || | |||    |   || || |   |  | || |      | ||||| || || ||||||||||| || || ||||||| |||||| |||||||| ||||| ||||| || ||||| ||| | || |||
ttttcggaaaattttggaataggtcgc--agtttttaacaataattgagtatactttgcctttaatttggctaaatataattcctttctttggctttggcagTCTGCTTGGATGGAACATTGCCTGGTTATCATTGGCATCGGGGATATGGATCAGGAGCAAATAGCTGGCTTATTAATTTAGAG

upper sequence: Vv14s0060g00230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G05910.2 (Arabidopsis thaliana), 3'ss of exon 1
-aattttaatagcagtgacctgagatgcttagtactcagaatcatgaaatctggattccttttggcattaatacatctccttgtatcgtaaatcgttgcagTTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGTCAGGGGCAAACAGTTGGCTCATTCAATTGGAG
    | |  |    ||     || |  |     |  || |||  |  ||| | |||   ||| ||| || | || | |   ||| | ||   |  |  |||||||||| ||||||||||| || || ||||| ||||| |||||| |||| || || || || || ||||||||||||||||||
tgtgtatgttctgtgtcggtagaaaaacaataaaaacaaaatatttgaatttagatatgtttgggcctttacacgtttgtgtgtgt-gtgtttgttcacagTTTGTTTGGATGGAACATTGCCTGGATATCACTTGCACCGTGGACATGGATCTGGAGCTAATAGCTGGCTCATTCAATTGGAG

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|32271244|gb|CD720403.1|CD720403
EST:     GCTTAACCCTTATTCACGCTGCTGCTGCGAAAGGGGCAG                         TTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGT
genomic: GCTTAACCCTTATTCACGCTGCTGCTGCGAAAGGGGCAGgtactttttt ... atcgttgcagTTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGT
EST: gi|161715681|gb|FC068376.1|FC068376
EST:     TATGATGGTAGGCTTAACCCTTATTCACGCTGCTGCTGCGAAAGGGGCAG                         TTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGT
genomic: TATGATGGTAGGCTTAACCCTTATTCACGCTGCTGCTGCGAAAGGGGCAGgtactttttt ... atcgttgcagTTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGT
EST: gi|30324545|gb|CD007807.1|CD007807
EST:     GCTTAACCCTTATTCACGCTGCTGCTGCGAAAGGGGCAG                         TTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGT
genomic: GCTTAACCCTTATTCACGCTGCTGCTGCGAAAGGGGCAGgtactttttt ... atcgttgcagTTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGT
EST: gi|71864790|gb|DT013845.1|DT013845
EST:     TATGATGGTAGGCTTAACCCTTATTCACGCTGCTGCTGCGAAAGGGGCAG                         TTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGT
genomic: TATGATGGTAGGCTTAACCCTTATTCACGCTGCTGCTGCGAAAGGGGCAGgtactttttt ... atcgttgcagTTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGT
EST: gi|110373337|gb|EC937563.1|EC937563
EST:     TATGATGGTAGGCTTAACCCTTATTCACGCTGCTGCTGCGAAAGGGGCAG                         TTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGT
genomic: TATGATGGTAGGCTTAACCCTTATTCACGCTGCTGCTGCGAAAGGGGCAGgtactttttt ... atcgttgcagTTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGT
EST: gi|352781141|gb|FQ466454.1|FQ466454
EST:     TATGATGGTAGGCTTAACCCTTATTCACGCTGCTGCTGCGAAAGGGGCAG                         TTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGCGGATATGGGT
genomic: TATGATGGTAGGCTTAACCCTTATTCACGCTGCTGCTGCGAAAGGGGCAGgtactttttt ... atcgttgcagTTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGT
EST: gi|30327012|gb|CD010274.1|CD010274
EST:     GCTTAACCCTTATTCACGCTGCTGCTGCGAAAGGGGCAG                         TTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGT
genomic: GCTTAACCCTTATTCACGCTGCTGCTGCGAAAGGGGCAGgtactttttt ... atcgttgcagTTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGT
EST: gi|30327090|gb|CD010352.1|CD010352
EST:     GCTTAACCCTTATTCACGCTGCTGCTGCGAAAGGGGCAG                         TTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGT
genomic: GCTTAACCCTTATTCACGCTGCTGCTGCGAAAGGGGCAGgtactttttt ... atcgttgcagTTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGT
EST: gi|32268077|gb|CD717236.1|CD717236
EST:     GCTTAACCCTTATTCACGCTGCTGCTGCGAAAGGGGCAG                         TTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGT
genomic: GCTTAACCCTTATTCACGCTGCTGCTGCGAAAGGGGCAGgtactttttt ... atcgttgcagTTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGT
EST: gi|161714504|gb|FC062954.1|FC062954
EST:     TATGATGGTAGGCTTAACCCTTATTCACGCTGCTGCTGCGAAAGGGGCAG                         TTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGT
genomic: TATGATGGTAGGCTTAACCCTTATTCACGCTGCTGCTGCGAAAGGGGCAGgtactttttt ... atcgttgcagTTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGT
EST: gi|30326319|gb|CD009581.1|CD009581
EST:     GCTTAACCCTTATTCACGCTGCTGCTGCGAAAGGGGCAG                         TTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGT
genomic: GCTTAACCCTTATTCACGCTGCTGCTGCGAAAGGGGCAGgtactttttt ... atcgttgcagTTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatctggattccttttggcattaatacatctccttgtatcgtaaatcgttgcagTTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGTCAGGGGCAAACAGTTGGCTCATTCAATTGGAG
                   cattaat  putative branch site (score: 3)
                    attaatacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattttaatagcagtgacctgagatgcttagtactcagaatcatgaaatctggattccttttggcattaatacatctccttgtatcgtaaatcgttgcagTTTGTTTAGATGGAACATTACCGGGGTATCATTTGCATCGTGGATATGGGTCAGGGGCAAACAGTTGGCTCATTCAATTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - tgcttag
- - - - - - - - - - - - - - - - - - - - -catgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catctcc