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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttcagggaatgaagtctgctggtagtaagcaggctggtttagctgaggagtgttaatcatttaaatacaacttgtggctcaatgttcattgtcttgtagGTTGTAGCAGCTGTTGGTTTTAAGGGCAAAAGGCTTGAGATCCCACGTGATTTAAATCCTCAAGTGGCTTCCATAATTGAAGCATGTTGGGCAAA

Basic information

species Vitis vinifera
transcript Vv08s0007g03910.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g03910.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os02g32610.2 (Oryza sativa), 3'ss of exon 14
gttcagggaatgaagtctgctggtagtaagcaggctggtttagctgaggagtgttaatcatttaaatacaacttg--tggctcaatgttca----ttgtcttgtagGTTGTAGCAGCTGTTGGTTTTAAGGGCAAAAGGCTTGAGATCCCACGTGATTTAAATCCTCAAGTGGCTTCCATAATTGAAGCATGTTGGGCAAA
                  | | ||| |   | |  |  || | |  | |  | ||   ||  |    || |  ||  | |  ||| ||  |    ||  |||| ||||||||||||||||||||||||| ||   ||||||||| || ||| ||    |  ||||  |||||||  | ||||| ||| | || ||| ||||
------------------gtttgta-tctcctgttttcttcatcacacggatattttccaacttcggacgaactgaattgaacaaagtctacctgttcacttgcagGTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAA

upper sequence: Vv08s0007g03910.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA19G37570.2 (Glycine max), 3'ss of exon 14
--gttcagggaatgaagtctgctggtagtaagcaggctggtttagctgaggagtgttaatcatttaaatacaacttgtggctcaatgttcattgtcttgtagGTTGTAGCAGCTGTTGGTTTTAAGGGCAAAAGGCTTGAGATCCCACGTGATTTAAATCCTCAAGTGGCTTCCATAATTGAAGCATGTTGGGCAAA
   |  |   | | |  | ||||| ||  ||  |  ||  | |    || |   |  | |   |   |   |   |       | | |  | ||| ||||||||||| ||||||||||| |||||||| ||||| |||||||| ||||||||||||||||||||| | || || ||||||||  | |||||||| ||
atatatatatatttatttttgctgataaaaaaaaaactaatgtgttagatgcagggcattttgtattacttagtcttca--caagtctgtaatgttttgtagGTTGTGGCAGCTGTTGGCTTTAAGGGAAAAAGACTTGAGATACCACGTGATTTAAATCCTCAATTAGCCTCTATAATTGAGTCTTGTTGGGCCAA

upper sequence: Vv08s0007g03910.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA03G34890.1 (Glycine max), 3'ss of exon 14
-gttcagggaatgaagtctgctggtagtaagcaggctggtttagctgaggagt--gttaatcatttaaatacaacttgtggctcaatgttcattgtcttgtagGTTGTAGCAGCTGTTGGTTTTAAGGGCAAAAGGCTTGAGATCCCACGTGATTTAAATCCTCAAGTGGCTTCCATAATTGAAGCATGTTGGGCAAA
  |||| ||    | ||   |      |||     |||   |  ||||    |   | |||  ||  | | ||   | |     | | |  | ||| ||||||||||| || |||||||| |||||||| ||||| |||||||| ||||||||||||||||||||| | || || |||||||| || |||||||| ||
gtttcatggtggcatgttatcgaaatataattttactg---tgactgaaattttcatcaatatttgtattgcatagtcttcacaagtctgtaatgttttgtagGTTGTGGCGGCTGTTGGCTTTAAGGGAAAAAGACTTGAGATACCACGTGATTTAAATCCTCAATTAGCCTCAATAATTGAGGCTTGTTGGGCCAA

upper sequence: Vv08s0007g03910.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA10G07610.1 (Glycine max), 3'ss of exon 15
gttcagggaatgaagtctgc----tggtagtaagcaggctggtttagctgaggagtgttaatcatttaaatacaacttgtggctcaatgttcattgtcttgtagGTTGTAGCAGCTGTTGGTTTTAAGGGCAAAAGGCTTGAGATCCCACGTGATTTAAATCCTCAAGTGGCTTCCATAATTGAAGCATGTTGGGCAAA
  | |||   |  | ||  |    |      |   |   | ||||        |   ||| | ||||   | |||  |||     || |   |||| | |||||||||| ||||||||||| |||||||| |||||||| |||||||||| |||| | ||||||||||| ||| |  ||||||| || || ||||| ||
--taaggagctagattccacattttctcttcacatactatagttttctactacatatttatttattttgcttcaa--tgttcacaaacgcatattggcatgtagGTTGTGGCAGCTGTTGGCTTTAAGGGGAAAAGGCTAGAGATCCCACATGATGTGAATCCTCAAGTAGCTGCACTAATTGATGCTTGCTGGGCGAA

upper sequence: Vv08s0007g03910.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA13G21480.1 (Glycine max), 3'ss of exon 13
gttcagggaatgaagtctgctggtagtaagcaggctggtttagctgaggagtgt-taatcatttaaatacaacttgtggctcaa-tgttcattgtcttgtagGTTGTAGCAGCTGTTGGTTTTAAGGGCAAAAGGCTTGAGATCCCACGTGATTTAAATCCTCAAGTGGCTTCCATAATTGAAGCATGTTGGGCAAA
 |  | |||   |  ||  |   |  |   ||      | ||| |    | |   || |||||||  |        || | ||| ||   || | | |||||||||| ||||||||||| |||||| | ||||||||||||||||||| |||| | ||||| ||||| ||| |  ||||||| || || |||||  |
ttgtaaggagctagatccaccttttctcttcacat--atatagttttctactacatattcatttattttgcttcaatgtcacaaatgcatatgggcgtgtagGTTGTGGCAGCTGTTGGCTTTAAGAGAAAAAGGCTTGAGATCCCACATGATGTGAATCCCCAAGTAGCTGCGCTAATTGAGGCTTGCTGGGCCTA

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|30321464|gb|CD004726.1|CD004726
EST:     GGGAACTTGCAACATTGCAACAACCTTGGAGTAATTTAAATCCAGCACAG                         GTTGTAGCAGCTGTTGGTTTTAAGGGCAAAAGGCTTGAGATCCCACGTGAT
genomic: GGGAACTTGCAACATTGCAACAACCTTGGAGTAATTTAAATCCAGCACAGgtttgtcttc ... tgtcttgtagGTTGTAGCAGCTGTTGGTTTTAAGGGCAAAAGGCTTGAGATCCCACGTGAT
EST: gi|27580407|gb|CB003102.1|CB003102
EST:     GGGAACTTGCAACATTGCAACAACCTTGGAGTAATTTAAATCCAGCACAG                         GTTGTAGCAGCTGTTGG
genomic: GGGAACTTGCAACATTGCAACAACCTTGGAGTAATTTAAATCCAGCACAGgtttgtcttc ... tgtcttgtagGTTGTAGCAGCTGTTGG
EST: gi|27579678|gb|CB002373.1|CB002373
EST:     GGGAACTTGCAACATTGCAACAACCTTGGAGTAATTTAAATCCAGCACAG                         GTTGTAGCAGCTGTTGGTTTTAAGGGCAAAAGGCTTGAGATCCCACGTGAT
genomic: GGGAACTTGCAACATTGCAACAACCTTGGAGTAATTTAAATCCAGCACAGgtttgtcttc ... tgtcttgtagGTTGTAGCAGCTGTTGGTTTTAAGGGCAAAAGGCTTGAGATCCCACGTGAT
EST: gi|32249917|gb|CD715736.1|CD715736
EST:     GGGAACTTGCAACATTGCAACAACCTTGGAGTAATTTAAATCCAGCACAG                         GTTGTAGCAGCTGTTGGTTTTAAGGGCAAAAGGCTTGAGATCCCACGTGAT
genomic: GGGAACTTGCAACATTGCAACAACCTTGGAGTAATTTAAATCCAGCACAGgtttgtcttc ... tgtcttgtagGTTGTAGCAGCTGTTGGTTTTAAGGGCAAAAGGCTTGAGATCCCACGTGAT
EST: gi|27580570|gb|CB003265.1|CB003265
EST:     GGGAACTTGCAACATTGCAACAACCTTGGAGTAATTTAAATCCAGCACAG                         GTTGTAGCAGCTGTTGGTTTTAAGGGCAAAAGGCTTGAGATCCCACGTGAT
genomic: GGGAACTTGCAACATTGCAACAACCTTGGAGTAATTTAAATCCAGCACAGgtttgtcttc ... tgtcttgtagGTTGTAGCAGCTGTTGGTTTTAAGGGCAAAAGGCTTGAGATCCCACGTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaggagtgttaatcatttaaatacaacttgtggctcaatgttcattgtcttgtagGTTGTAGCAGCTGTTGGTTTTAAGGGCAAAAGGCTTGAGATCCCACGTGATTTAAATCCTCAAGTGGCTTCCATAATTGAAGCATGTTGGGCAAA
      tgttaat  putative branch site (score: 3)
                                            ttgtctt  putative PPT
        ttaatcatttaaatac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcagggaatgaagtctgctggtagtaagcaggctggtttagctgaggagtgttaatcatttaaatacaacttgtggctcaatgttcattgtcttgtagGTTGTAGCAGCTGTTGGTTTTAAGGGCAAAAGGCTTGAGATCCCACGTGATTTAAATCCTCAAGTGGCTTCCATAATTGAAGCATGTTGGGCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - ggaatga
- - - - - - - -tctgctg
- - - - - - - - - - - - - - -gcaggct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcaatg