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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggctttaggaagttattttggatctttttaagattaaactttccatattgttctcagttttataatgtatatgggcagGCCTTAATCCAATTCACCGACGCTGAGACTGCTTCTTCAGCAAGGAATGCATTGGATGGAAGAAGTATTCCCAG

Basic information

species Vitis vinifera
transcript Vv14s0108g01030.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0108g01030.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G49580.1 (Glycine max), 3'ss of exon 3
gtgaggctttaggaagttattttggatctttttaagattaaactttccatattgttctcagtttt-ataatgtata-tg----ggcagGCCTTAATCCAATTCACCGACGCTGAGACTGCTTCTTCAGCAAGGAATGCATTGGATGGAAGAAGTATTCCCAG-
        ||||  | ||||| |  ||     |      ||  | | | |     | | |||||| | ||||| || ||    |||||||  | || || ||||| || |||||||| ||||||||||| ||| ||||| |||||||||||||||| || || 
--------ttagtgaattattatcaattgcactgcctccaatgtgttcctgactctgtaagttttgacaatgtttaatgccatggcaggCTCTGATTCAGTTCACTGATGCTGAGACCGCTTCTTCAGCTAGGGATGCACTGGATGGAAGAAGTATACCAAGG

upper sequence: Vv14s0108g01030.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 3
----gtgaggctttaggaagttattttggatctttttaagattaaactttccatattgttctcagttttataatgtatatgggcagGCCTTAATCCAATTCACCGACGCTGAGACTGCTTCTTCAGCAAGGAATGCATTGGATGGAAGAAGTATTCCCAG----
    ||||    |||  || ||    ||  ||  ||         |||  |  ||   ||      | | |||||   |||| |||||  | || || ||||| || ||||||||||||||||||||  || ||||| |||||||||||||||| || ||    
gttagtgaattattatcaa-ttgcactgcctccattgtgttcctgactcactgtaagttttgacaatgtttaatgc-catgg-cagGCTCTGATTCAGTTCACTGATGCTGAGACTGCTTCTTCAGCTCGGGATGCACTGGATGGAAGAAGTATACCAAGGCAA
















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|351026199|gb|FQ428211.1|FQ428211
EST:     TTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCTGCAGGTTTCCAG                         GCCTTAATCCAATTCACCGACGCTGAGACTGCTTCTTCAGCAAGGAATGCA
genomic: TTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCTGCAGGTTTCCAGgtgaggcttt ... atatgggcagGCCTTAATCCAATTCACCGACGCTGAGACTGCTTCTTCAGCAAGGAATGCA
EST: gi|351019653|gb|FQ439470.1|FQ439470
EST:     TTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCTGCAGGTTTCCAG                         GCCTTAATCCAATTCACCGACGCTGAGACTGCTTCTTCAGCAAGGAATGCA
genomic: TTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCTGCAGGTTTCCAGgtgaggcttt ... atatgggcagGCCTTAATCCAATTCACCGACGCTGAGACTGCTTCTTCAGCAAGGAATGCA
EST: gi|351017354|gb|FQ435706.1|FQ435706
EST:     TTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCTGCAGGTTTCCAG                         GCCTTAATCCAATTCACCGACGCTGAGACTGCTTCTTCAGCAAGGAATGCA
genomic: TTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCTGCAGGTTTCCAGgtgaggcttt ... atatgggcagGCCTTAATCCAATTCACCGACGCTGAGACTGCTTCTTCAGCAAGGAATGCA
EST: gi|351023752|gb|FQ448303.1|FQ448303
EST:     TTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCTGCAGGTTTCCAG                         GCCTTAATCCAATTCACCGACGCTGAGACTGCTTCTTCAGCAAGGAATGCA
genomic: TTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCTGCAGGTTTCCAGgtgaggcttt ... atatgggcagGCCTTAATCCAATTCACCGACGCTGAGACTGCTTCTTCAGCAAGGAATGCA
EST: gi|351016914|gb|FQ424341.1|FQ424341
EST:     TTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCTGCAGGTTTCCAG                         GCCTTAATCCAATTCACCGACGCTGAGACTGCTTCTTCAGCAAGGAATGCA
genomic: TTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCTGCAGGTTTCCAGgtgaggcttt ... atatgggcagGCCTTAATCCAATTCACCGACGCTGAGACTGCTTCTTCAGCAAGGAATGCA
EST: gi|349818542|gb|FQ403177.1|FQ403177
EST:     TTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCTGCAGGTTTCCAG                         GCCTTAATCCAATTCACCGACGCTGAGACTGCTTCTTCGGCAAGGAATGCA
genomic: TTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCTGCAGGTTTCCAGgtgaggcttt ... atatgggcagGCCTTAATCCAATTCACCGACGCTGAGACTGCTTCTTCAGCAAGGAATGCA
EST: gi|161716509|gb|FC066200.1|FC066200
EST:     TTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCTGCAGGTTTCCAG                         GCCTTAATCCAATTCACCGACGCTGAGACTGCTTCTTCAGCAAGGAATGCA
genomic: TTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCTGCAGGTTTCCAGgtgaggcttt ... atatgggcagGCCTTAATCCAATTCACCGACGCTGAGACTGCTTCTTCAGCAAGGAATGCA
EST: gi|351024488|gb|FQ426297.1|FQ426297
EST:     TTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCTGCAGGTTTCCAG                         GCCTTAATCCAATTCACCGACGCTGAGACTGCTTCTTCAGCAAGGAATGCA
genomic: TTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCTGCAGGTTTCCAGgtgaggcttt ... atatgggcagGCCTTAATCCAATTCACCGACGCTGAGACTGCTTCTTCAGCAAGGAATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttttaagattaaactttccatattgttctcagttttataatgtatatgggcagGCCTTAATCCAATTCACCGACGCTGAGACTGCTTCTTCAGCAAGGAATGCATTGGATGGAAGAAGTATTCCCAG
                                agttttataatgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggctttaggaagttattttggatctttttaagattaaactttccatattgttctcagttttataatgtatatgggcagGCCTTAATCCAATTCACCGACGCTGAGACTGCTTCTTCAGCAAGGAATGCATTGGATGGAAGAAGTATTCCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT