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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catggaaattatagctactaacaaaatagtttattttgttgttgtttagtaatttaatgttattatgtatgtgatttatgttaaattctccaaacttcagTCTGTGGTATGGAGAAGAACGTCCTCGCTGGCTTGGTCCAATCCCATATGACTATCCTGCATATCTCACTGGAGAACTTCCTGGGGATTATGGCTTTGAT

Basic information

species Vitis vinifera
transcript Vv18s0122g00430.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0122g00430.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G38220.2 (Glycine max), 3'ss of exon 2
---catggaaattatagctac-taacaaaatagtttattttgttgttgtttagtaatttaatgttattatgtatgtgatttatgttaaattctccaaacttcagTCTGTGGTATGGAGAAGAACGTCCTCGCTGGCTTGGTCCAATCCCATATGACTATCCTGCATATCTCACTGGAGAACTTCCTGGGGATTATGGCTTTGAT
     |  | ||| |   | | | |||  ||  ||  | |   ||||| ||     |  ||    ||| | |   |  ||  |   | |||| | ||  |||||  | |||||||||||||| || ||||| ||||||||||| ||  ||||||| || ||  ||||||| ||||| ||||| || |||||||| |||||||| 
agagcttcagattgtcatttcattacatgattattattctcactgttgcttgtgtgtccaa----attttatgcttatttcgttaaacattcactaattttcagCTTTTGGTATGGAGAAGATCGGCCTCGTTGGCTTGGTCCTATTTCATATGAATACCCATCATATCTTACTGGGGAACTGCCCGGGGATTACGGCTTTGAC

upper sequence: Vv18s0122g00430.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G76570.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------------------------------catggaaattatagctactaacaaaatagtttattttgttgttgtttagtaa--tttaatgttattatg--tatgtgatttat-----------gttaaattctccaaactt-cagTCTGTGGTATGGAGAAGAACGTCCTCGCTGGCTTGGTCCAATCCCATATGACTATCCTGCATATCTCACTGGAGAACTTCCTGGGGATTATGGCTTTGAT
                                                      |   |||||  || |     |   |  | ||||||  | | |   ||  ||  ||  |||||| | |   ||| ||  | |            |||   | ||  ||   | |||   |||||||||| |||||||||| || ||| ||||||||||||||||||| |||||| |||| || || ||||||||||| ||||||||||| || || 
gtaagattgagtttatcagtgtttttttgtgaaggcaatgtttgataaaatggtagataaatt-cagttttctgcggcaacgattatttgatagatacatacaaaagttctatgttactgtaactatatggatcaaacatttccttggtttgttcctgtaagtgtgcagCAAGTGGTATGGAAAAGAACGTCCCCGTTGGTTTGGTCCAATCCCATATGATTATCCTCCATACCTTACAGGAGAACTTCCAGGGGATTATGGTTTCGAC
















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|349823595|gb|FQ415005.1|FQ415005
EST:     AAGAATTCTTCAAAGTTCAGGGCCTTAGCTGAAAAGGCTAAAAACGAGAG                         TCTGTGGTATGGAGAAGAACGTCCTCGCTGGCTTGGTCCAATCCCATATGA
genomic: AAGAATTCTTCAAAGTTCAAGGCCTTAGCTGAAAAGGCTAAAAACGAGAGgtaatacgag ... caaacttcagTCTGTGGTATGGAGAAGAACGTCCTCGCTGGCTTGGTCCAATCCCATATGA
EST: gi|161718087|gb|FC067604.1|FC067604
EST:     AAGAATTCTTCAAAGTTCAAGGCCTTAGCTGAAAAGGCTAAAAACGAGAG                         TCTGTGGTATGGAGAAGAACGTCCTCGCTGGCTTGGTCCAATCCCATATGA
genomic: AAGAATTCTTCAAAGTTCAAGGCCTTAGCTGAAAAGGCTAAAAACGAGAGgtaatacgag ... caaacttcagTCTGTGGTATGGAGAAGAACGTCCTCGCTGGCTTGGTCCAATCCCATATGA
EST: gi|122690646|gb|EC955583.1|EC955583
EST:     GAAAAGGCTAAAAACGAGAG                         TCTGTGGTATGGAGAAGAGCGTCCTCGCTGGCTTGGTCCAATCCCATATGA
genomic: GAAAAGGCTAAAAACGAGAGgtaatacgag ... caaacttcagTCTGTGGTATGGAGAAGAACGTCCTCGCTGGCTTGGTCCAATCCCATATGA
EST: gi|161714259|gb|FC063523.1|FC063523
EST:     AAGAATTCTTCAAAGTTCAAGGCCTTAGCTGAAAAGGCTAAAAACGAGAG                         TCTGTGGTATGGAGAAGAACGTCCTCGCTGGCTTGGTCCAATCCCATATGA
genomic: AAGAATTCTTCAAAGTTCAAGGCCTTAGCTGAAAAGGCTAAAAACGAGAGgtaatacgag ... caaacttcagTCTGTGGTATGGAGAAGAACGTCCTCGCTGGCTTGGTCCAATCCCATATGA
EST: gi|349814847|gb|FQ410070.1|FQ410070
EST:     AAGAATTCTTCAAAGTTCAGGGCCTTAGCTGAAAAGGCTAAAAACGAGAG                         TCTGTGGTATGGAGAAGAACGTCCTCGCTGGCTTGGTCCAATCCCATATGA
genomic: AAGAATTCTTCAAAGTTCAAGGCCTTAGCTGAAAAGGCTAAAAACGAGAGgtaatacgag ... caaacttcagTCTGTGGTATGGAGAAGAACGTCCTCGCTGGCTTGGTCCAATCCCATATGA
EST: gi|122690609|gb|EC954944.1|EC954944
EST:     AAGAATTCTTCAAAGTTCAAGGCCTTAGCTGAAAAGGCTAAAAACGAGAG                         TCTGTGGTATGGAGAAGAGCGTCCTCGCTGGCTTGGTCCAATCCCATATGA
genomic: AAGAATTCTTCAAAGTTCAAGGCCTTAGCTGAAAAGGCTAAAAACGAGAGgtaatacgag ... caaacttcagTCTGTGGTATGGAGAAGAACGTCCTCGCTGGCTTGGTCCAATCCCATATGA
EST: gi|110421925|gb|EC988231.1|EC988231
EST:     AGCTGAAAAGGCTAAAAACGAGAG                         TCTGTGGTATGGAGAAGAGCGTCCTCGCTGGCTTGGTCCAATCCCATATGA
genomic: AGCTGAAAAGGCTAAAAACGAGAGgtaatacgag ... caaacttcagTCTGTGGTATGGAGAAGAACGTCCTCGCTGGCTTGGTCCAATCCCATATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagtaatttaatgttattatgtatgtgatttatgttaaattctccaaacttcagTCTGTGGTATGGAGAAGAACGTCCTCGCTGGCTTGGTCCAATCCCATATGACTATCCTGCATATCTCACTGGAGAACTTCCTGGGGATTATGGCTTTGAT
      atttaat  putative branch site (score: 4)
                                        ttctcc  putative PPT
     aatttaatgttattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catggaaattatagctactaacaaaatagtttattttgttgttgtttagtaatttaatgttattatgtatgtgatttatgttaaattctccaaacttcagTCTGTGGTATGGAGAAGAACGTCCTCGCTGGCTTGGTCCAATCCCATATGACTATCCTGCATATCTCACTGGAGAACTTCCTGGGGATTATGGCTTTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
catggaa
- - - - - - - - - -aacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtatgtg