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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTAGATGGACTAATTATCTCCGCCCGGGTATCAAACGCGGTAACTTTACTGATCAGGAGGAGAAGACGATAATCCACCTCCAGGCTCTTTTGGGCAATAGgtaaaaccaccactctctcttagagctgatgcggttagggttaagcataggctttcaaaactgggttggatctatgatcatggattcccagattccagta...

Basic information

species Vitis vinifera
transcript Vv17s0000g06190.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g06190.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA05G01080.1 (Glycine max), 5'ss of exon 2
TTAGATGGACTAATTATCTCCGCCCGGGTATCAAACGCGGTAACTTTACTGATCAGGAGGAGAAGACGATAATCCACCTCCAGGCTCTTTTGGGCAATAGgtaaaaccaccactctctcttagagctgatgcg-gttagggttaagcataggctttcaaa--actgggttggatctatgatcatggattcccagattccagta
||||||||||||| ||||| || || ||||||||||| ||||| || || || || || ||||||| ||||||||||||||| || |||||||| || ||||| || |   |  | ||| |    ||  | |  |||    || | ||     | | ||    ||   ||  |||    | |  | ||| | || || |   |
TTAGATGGACTAACTATCTTCGACCAGGTATCAAACGAGGTAATTTCACGGAACATGAAGAGAAGATGATAATCCACCTCCAAGCCCTTTTGGGGAACAGgtacaatctagaaaccctcatcttcctactacttgtttcctttcatcaattaatgttaattttctctctttaatc---aagcgagaattacgaggtttccaaa

upper sequence: Vv17s0000g06190.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA06G20800.1 (Glycine max), 5'ss of exon 2
TTAGATGGACTAATTATCTCCGCCCGGGTATCAAACGCGGTAACTTTACTGATCAGGAGGAGAAGACGATAATCCACCTCCAGGCTCTTTTGGGCAATAGgtaaaaccaccactctctcttagagctgatgcggttagggttaagcataggct-ttcaaaactgggttggatctatgatcatggattcccagattccagta-----
| |||||||| || |||||||| || ||||||||||| || || || || ||||| || ||||| | ||||||||||||||| ||||||||||| || |||||   |||||     |   || |  | ||  | |||   | |||| ||   | ||||    |  | ||  | |    |     | |   ||  |  |  |     
TCAGATGGACCAACTATCTCCGACCTGGTATCAAACGAGGCAATTTCACCGATCATGAAGAGAAAATGATAATCCACCTCCAAGCTCTTTTGGGTAACAGgta---ccaccttgtccaaatatatttaatttg-ttatcttaaagcctaaattattcaggggtacgatg--tttgctctagaaaaatttaagggtatacaagtcag

upper sequence: Vv17s0000g06190.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA17G10820.1 (Glycine max), 5'ss of exon 2
TTAGATGGACTAATTATCTCCGCCCGGGTATCAAACGCGGTAACTTTACTGATCAGGAGGAGAAGACGATAATCCACCTCCAGGCTCTTTTGGGCAATAGgtaaaacc----accactctctcttagagctgatgcggttagggttaagcataggctttcaaaactgggttggatctatgatcatggattcccagattccagta
||||||||||||| ||||| || || ||||||||||| ||||| || || || || || ||||||| ||||||||||||||| || || ||||| || ||||| ||||    | | ||| | |||    |  |     || |  ||         ||||||  | |   |    ||| |  | |   |  |    ||| |    
TTAGATGGACTAACTATCTTCGACCTGGTATCAAACGAGGTAATTTCACGGAACATGAAGAGAAGATGATAATCCACCTCCAAGCCCTATTGGGGAACAGgtacaacctagaaaccctcacccttcctacctactttttttgctttgctttc---ctttcatcaattaatgttctctctctttaatcaagctagaattacgag-

upper sequence: Vv17s0000g06190.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA04G33720.1 (Glycine max), 5'ss of exon 2
TTAGATGGACTAATTATCTCCGCCCGGGTATCAAACGCGGTAACTTTACTGATCAGGAGGAGAAGACGATAATCCACCTCCAGGCTCTTTTGGGCAATAGgtaaaaccaccactctctcttagagctgatgcggttagggttaagcataggctttcaaaact---gggttggatctatgatcatggat--tcccagattccagta-
| |||||||| || |||||||| || || |||||||| || || || || ||||| || ||||| | ||||||||||||||| ||||||||||| || |||||  ||    | ||   |  | |  | ||  |  |    || |  | | ||    | || |   ||||  ||| | || ||  | |   |   ||  |  |  | 
TCAGATGGACCAACTATCTCCGACCTGGCATCAAACGAGGGAATTTCACCGATCATGAAGAGAAAATGATAATCCACCTCCAAGCTCTTTTGGGTAACAGgtactacgttgagtc---caaatatttaatttgtatc---ttgattaaaagccaaaataatttaggggtaagatttttgctctagaaaaatttaagggtttacaag

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|71859434|gb|DT008489.1|DT008489
EST:     GATCAGGAGGAGAAGACGATAATCCACCTCCAGGCTCTTTTGGGCAATAG                         ATGGGCTGCCATAGCTTCTTATCTTCCTCAGAGAACGGACAATGATATAAA
genomic: GATCAGGAGGAGAAGACGATAATCCACCTCCAGGCTCTTTTGGGCAATAGgtaaaaccac ... ttggatgcagATGGGCTGCCATAGCTTCTTATCTTCCTCAAAGAACGGACAATGATATAAA
EST: gi|110686690|gb|EE064618.1|EE064618
EST:     GATCAGGAGGAGAAGACGATAATCCACCTCCAGGCTCTTTTGGGCAATAG                         ATGGGCTGCCATAGCTTCTTATCTTCCTCAGAGAACGGACAATGATATAAA
genomic: GATCAGGAGGAGAAGACGATAATCCACCTCCAGGCTCTTTTGGGCAATAGgtaaaaccac ... ttggatgcagATGGGCTGCCATAGCTTCTTATCTTCCTCAAAGAACGGACAATGATATAAA
EST: gi|32271694|gb|CD720853.1|CD720853
EST:     GATCAGGAGGAGAAGACGATAATCCACCTCCAGGCTCTTTTGGGCAATAG                         ATGGGCTGCCATAGCTTCTTATCTTCCTCAGAGAACGGACAATGATATAAA
genomic: GATCAGGAGGAGAAGACGATAATCCACCTCCAGGCTCTTTTGGGCAATAGgtaaaaccac ... ttggatgcagATGGGCTGCCATAGCTTCTTATCTTCCTCAAAGAACGGACAATGATATAAA
EST: gi|294965744|gb|GW839199.1|GW839199
EST:     GATCAGGAGGAGAAGACGATAATCCACCTCCAGGCTCTTTTGGGCAATAG                         ATGGGGCTGC-ATAGCTTCTT
genomic: GATCAGGAGGAGAAGACGATAATCCACCTCCAGGCTCTTTTGGGCAATAGgtaaaaccac ... ttggatgcagATGGG-CTGCCATAGCTTCTT
EST: gi|33408386|gb|CF214013.1|CF214013
EST:     GATCAGGAGGAGAAGACGATAATCCACCTCCAGGCTCTTTTGGGCAATAG                         ATGGGCTGCCATAGCTTCTTATCTTCCTCAAAGAACGGACAATGATATAAA
genomic: GATCAGGAGGAGAAGACGATAATCCACCTCCAGGCTCTTTTGGGCAATAGgtaaaaccac ... ttggatgcagATGGGCTGCCATAGCTTCTTATCTTCCTCAAAGAACGGACAATGATATAAA
EST: gi|32272593|gb|CD721752.1|CD721752
EST:     GATCAGGAGGAGAAGACGATAATCCACCTCCAGGCTCTTTTGGGCAATAG                         ATGGGCTGCCATAGCTTCTTATCTTCCTCAGAGAACGGACAATGATATAAA
genomic: GATCAGGAGGAGAAGACGATAATCCACCTCCAGGCTCTTTTGGGCAATAGgtaaaaccac ... ttggatgcagATGGGCTGCCATAGCTTCTTATCTTCCTCAAAGAACGGACAATGATATAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTAGATGGACTAATTATCTCCGCCCGGGTATCAAACGCGGTAACTTTACTGATCAGGAGGAGAAGACGATAATCCACCTCCAGGCTCTTTTGGGCAATAGgtaaaaccaccactctctcttagagctgatgcggttagggttaagcataggctttcaaaactgggttggatctatgatcatggattcccagattccagta

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctctc