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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggtgttcggaaataataccaaaaagagaacaaagatacccaaaatgaccagagcaggtacggtcgtaatttaattattatactgcttacatattttcagGCAGTACGCTACCTAATGAGGTTTCAAACTGAGTACACATGTGGCTTATTGAATGTTGAGCGCCATGCTGCATTTGGATGGGAAGCTGCTAAAATGGTTC

Basic information

species Vitis vinifera
transcript Vv14s0036g01060.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0036g01060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA19G43720.1 (Glycine max), 3'ss of exon 9
---------------------tggtgttcggaaataataccaaaaagaga--acaaagatacccaaaatgaccagagcaggtacg-gtcgtaatttaattattatac-tgcttac--atattttcagGCAGTACGCTACCTAATGAGGTTTCAAACTGAGTACACATGTGGCTTATTGAATGTTGAGCGCCATGCTGCATTTGGATGGGAAGCTGCTAAAATGGTTC
                     |  | || | || |     ||| || |     ||  | ||  |    |         | || |  |   |||| |  ||   |||  |   ||   |||||||||||| ||||||||| |||||||||| | |||||||||||||||    ||||||||||  |  || |||||||| ||||||     ||| ||  |||||||||
gtacactcgttgcttgtgtcctcattttagcaatttgcctcaacaacaaccttcactgttattcttgtttctttacttatgttcatgatttaatgttgttgccataaataaatattaatattttcagGCTGTACGCTACTTAATGAGGTTCCCAACTGAGTACACATGCAATTTATTGAATGAAGCCCGGCATGCTGCCTTTGGAAAAATAGCAGCGGAAATGGTTC

upper sequence: Vv14s0036g01060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA03G41070.1 (Glycine max), 3'ss of exon 8
----------------------tggtgttcggaaataataccaaaaagagaacaaagatacccaaaatgaccagagcaggtacggtcgtaatttaattattatactgcttaca-----------tattttcagGCAGTACGCTACCTAATGAGGTTTCAAACTGAGTACACATGTGGCTTATTGAATGTTGAGCGCCATGCTGCATTTGGATGGGAAGCTGCTAAAATGGTTC
                      |  | || | || |  | ||  ||  | ||     |     |   |        ||  |||  || | |||||||  |  | |     | |           ||||||||||| ||||| ||| |||||||||||| |||||||||||||||    ||||||||||  |  || |||||||| ||||||     ||||||  |||||||||
gtacactccgatacttttttcctcattttagcaatt--tgcctcaacaacaatcttcacttttattcttgtttcttcacttactttcattatttaatgttgttgccataaataaatattggtaatattttcagGCTGTACGTTACTTAATGAGGTTTCCAACTGAGTACACATGCAATTTATTGAATGAAGCCCGGCATGCTGCCTTTGGAAAAATAGCTGCGGAAATGGTTC

upper sequence: Vv14s0036g01060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G30840.1 (Glycine max), 3'ss of exon 6
---tggtgttcggaaataataccaaaaagagaacaaagatacccaaaatgaccagagcaggtacggtcg-taatttaattattatactgcttacat-attttcagGCAGTACGCTACCTAATGAGGTTTCAAACTGAGTACACATGTGGCTTATTGAATGTTGAGCGCCATGCTGCATTTGGATGGGAAGCTGCTAAAATGGTTC
     |   || |  | | |  || |||  ||   |  |||  | || |   ||    ||  |   |   | |||| ||     | |     | ||  ||||||||||||||||||| |||||||||| | |||||| ||||||||    ||| ||||||  |  |||||||||   ||||||     ||||||  ||||||| |
gtaccggactctgttagacttgcagaaaaggagttat-atatgctaagtcctcattttagtaatacttaatgatttcatctagttgccataaatattgttttcagGCAGTACGCTACTTAATGAGGTTCCCAACTGAATACACATGCAATTTAATGAATGAGGCCCGCCATGCTAGCTTTGGAAAATTAGCTGCAGAAATGGTCC

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|110374577|gb|EC939433.1|EC939433
EST:     GTTTGATTGCTTATCATCGCAAAATGGATCGGAGGTGGTGGCGAGCACAG                         GCAGTACGCTACCTAATGAGGTTTCAAACTGAGTACACATGTGGCTTATTG
genomic: GTTTGATTGCTTATCATCGCAAAATGGATCGGAGGTGGTGGCGAGCACAGgtgaaaccaa ... atattttcagGCAGTACGCTACCTAATGAGGTTTCAAACTGAGTACACATGTGGCTTATTG
EST: gi|110703597|gb|EE080580.1|EE080580
EST:     GTTTGATTGCTTATCATCGCAAAATGGATCGGAGGTGGTGGCGAGCACAG                         GCAGTACGCTACCTAATGAGGTTTCAAACTGAGTACACATGTGGCTTATTG
genomic: GTTTGATTGCTTATCATCGCAAAATGGATCGGAGGTGGTGGCGAGCACAGgtgaaaccaa ... atattttcagGCAGTACGCTACCTAATGAGGTTTCAAACTGAGTACACATGTGGCTTATTG
EST: gi|34543598|gb|CF511830.1|CF511830
EST:     GTTTGATTGCTTATCATCGCAAAATGGATCGGAGGTGGTGGCGAGCACAG                         GCAGTACGCTACCTAATGAGGTTTCAAACTGAGTACACATGTGGCTTATTG
genomic: GTTTGATTGCTTATCATCGCAAAATGGATCGGAGGTGGTGGCGAGCACAGgtgaaaccaa ... atattttcagGCAGTACGCTACCTAATGAGGTTTCAAACTGAGTACACATGTGGCTTATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaccagagcaggtacggtcgtaatttaattattatactgcttacatattttcagGCAGTACGCTACCTAATGAGGTTTCAAACTGAGTACACATGTGGCTTATTGAATGTTGAGCGCCATGCTGCATTTGGATGGGAAGCTGCTAAAATGGTTC
                                      tgcttac  putative branch site (score: 2)
                                              tattttc  CT-rich tract
                     taatttaattattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggtgttcggaaataataccaaaaagagaacaaagatacccaaaatgaccagagcaggtacggtcgtaatttaattattatactgcttacatattttcagGCAGTACGCTACCTAATGAGGTTTCAAACTGAGTACACATGTGGCTTATTGAATGTTGAGCGCCATGCTGCATTTGGATGGGAAGCTGCTAAAATGGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
tggtgtt
- - - - ggaaata
- - - - - - - - - - aaaaaga
- - - - - - - - - - - - - -gaacaaa
- - - - - - - - - - - - - - - - - - - cccaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -gcaggta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttac