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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGACTAAAGATGGTGAAACAATGACAGCATATGCTCCTTTAACCATTGTATGTGATGGTTGTTTCTCAAACTTGCGCCGCTCCCTTTGTACCCCTAAGgtgaggatgacctcagtcttctccaaaataaataaaataaaataaaactcacctaaatacacttccattgttcctgaattatgtttttcaccttgccatt...

Basic information

species Vitis vinifera
transcript Vv18s0001g08550.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g08550.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA0041S00260.2 (Glycine max), 5'ss of exon 4
CAAGACTAAAGATGGTGAAACAATGACAGCATATGCTCCTTTAACCATTGTATGTGATGGTTGTTTCTCAAACTTGCGCCGCTCCCTTTGTACCCCTAAGgtgaggatgacctcagtcttctccaaaataaataaaataaaataaaactcacctaaatacacttccattgttcctgaattatgtttttcaccttgccatt---
 ||||  ||||||||  |     ||||| ||||||||||| | |||||||| ||||||||||| ||||||||||| ||||| || |||||||  ||||||||||| |   | |    |||         | |      |  || ||| |||   || | |  ||||  |   |     | |    |  ||||     |     
TAAGAACAAAGATGGCCAGGAGTTGACAACATATGCTCCTCTTACCATTGTTTGTGATGGTTGCTTCTCAAACTTACGCCGTTCTCTTTGTAATCCTAAGgtgagaactcctttcagcttaattctgtgagagtttccatgatcaaa-tcagtcaacttc--ttcctataaactaatctcagcactcgcacccaaaaagcttt

upper sequence: Vv18s0001g08550.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA04G05110.1 (Glycine max), 5'ss of exon 4
CAAGACTAAAGATGGTGAAACAATGACAGCATATGCTCCTTTAACCATTGTATGTGATGGTTGTTTCTCAAACTTGCGCCGCTCCCTTTGTACCCCTAAGgtgaggatgacctcagtcttctccaaaataaataaaataaaataaaactc-acctaaatacacttccattgttcctgaattatgtttttcaccttgccatt-
||| || || ||| || ||  | |  |||| | ||| ||  | |||||||| |||||||| |||||||||||||||||||| || |||||||  ||||||||||  |     |||| ||  |  |   |||||| |  |   |    |   |   ||||| | ||   || |  ||  || | ||     ||      |   
CAAAACGAAGGATAGTCAAGAATTATCAGCTTGTGCACCCCTTACCATTGTTTGTGATGGCTGTTTCTCAAACTTGCGCCGTTCTCTTTGTAATCCTAAGgtgattaacttttcag-ctcattaagcttaaatacatgattctgtttccagagtcaaataaaatttggtt-tctctctatgaagtaacagactcctatacag

upper sequence: Vv18s0001g08550.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA06G05200.1 (Glycine max), 5'ss of exon 4
CAAGACTAAAGATGGTGAAACAATGACAGCATATGCTCCTTTAACCATTGTATGTGATGGTTGTTTCTCAAACTTGCGCCGCTCCCTTTGTACCCCTAAGgtgaggatgacctcagtcttctccaaaataaataaaataaaataaaactc--acctaaatacacttccattgttcctgaattatgtttttcaccttgccatt
||| || || ||| || ||  | |  |||| | ||| ||  | ||| |||| |||||||| |||||||||||||||||||| || |||||||  ||||||||||  |     |||| ||| |  |   |||||| |   |  ||     |  |   ||||| | ||   || |  ||  || | ||     ||      |  
CAAAACGAAGGATAGTCAAGAATTATCAGCTTGTGCACCCCTTACCGTTGTTTGTGATGGCTGTTTCTCAAACTTGCGCCGATCTCTTTGTAATCCTAAGgtgattaacttttcag-cttattaagcttaaataca-cgatttagtttccggagtcaaataaaattggtttctctctatatgaagtaacagacacccttaca

upper sequence: Vv18s0001g08550.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA14G10290.2 (Glycine max), 5'ss of exon 4
CAAGACTAAAGATGGTGAAACAATGACAGCATATGCTCCTTTAACCATTGTATGTGATGGTTGTTTCTCAAACTTGCGCCGCTCCCTTTGTACCCCTAAGgtgaggatgacct-cagtcttctccaaaataaataaaataaaataaaactcacctaaatacacttccattgttcctgaattatgtttttcaccttgccatt-
 ||||| ||||||||| |   | || || ||||||| ||| | |||||||| |||||||| || ||||||||||| ||||| || |||||||  ||||||||||| ||  | | |||  |  | |    | |   |  |   |  || | |    ||||       | || | |   ||           | |   | |   
TAAGACCAAAGATGGTCAGGAATTGGCAACATATGCACCTCTTACCATTGTTTGTGATGGCTGCTTCTCAAACTTACGCCGTTCTCTTTGTAATCCTAAGgtgagaattcctttcagcttaattctg--tgatagagtttccacgaatcacgatcaaatcagtcaactttttcctataaactaaccagcaatcacactagaa

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|161707918|gb|FC057765.1|FC057765
EST:     TATGTGATGGTTGTTTCTCAAACTTGCGCCGCTCCCTTTGTACCCCTAAG                         GTAGATGTGCCCTCATGTTTTGTCGGTTAGTTGCTGGAAGACTGTGAGCTC
genomic: TATGTGATGGTTGTTTCTCAAACTTGCGCCGCTCCCTTTGTACCCCTAAGgtgaggatga ... acttctgcagGTAGATGTGCCCTCATGTTTTGTCGGTTTGTTGCTGGAAGACTGTGAGCTC
EST: gi|71859760|gb|DT008815.1|DT008815
EST:     TATGTGATGGTTGTTTCTCAAACTTGCGCCGCTCCCTTTGTACCCCTAAG                         GTAGATGTGCCCTCATGTTTTGTCGGTTTGTTGCTGGAAGACTGTGAGCTC
genomic: TATGTGATGGTTGTTTCTCAAACTTGCGCCGCTCCCTTTGTACCCCTAAGgtgaggatga ... acttctgcagGTAGATGTGCCCTCATGTTTTGTCGGTTTGTTGCTGGAAGACTGTGAGCTC
EST: gi|71858042|gb|DT007097.1|DT007097
EST:     TATGTGATGGTTGTTTCTCAAACTTGCGCCGCTCCCTTTGTACCCCTAAG                         GTAGATGTGCCCTCATGTTTTGTCGGTTTGTTGCTGGAAGACTGTGAGCTC
genomic: TATGTGATGGTTGTTTCTCAAACTTGCGCCGCTCCCTTTGTACCCCTAAGgtgaggatga ... acttctgcagGTAGATGTGCCCTCATGTTTTGTCGGTTTGTTGCTGGAAGACTGTGAGCTC
EST: gi|33405835|gb|CF211462.1|CF211462
EST:     TATGTGATGGTTGTTTCTCAAACTTGCGCCGCTCCCTTTGTACCCCTAAG                         GTAGATGTGCCCTCATGTTTTGTCGGTTTGTTGCTGGAAGACTGTGAGCTC
genomic: TATGTGATGGTTGTTTCTCAAACTTGCGCCGCTCCCTTTGTACCCCTAAGgtgaggatga ... acttctgcagGTAGATGTGCCCTCATGTTTTGTCGGTTTGTTGCTGGAAGACTGTGAGCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGACTAAAGATGGTGAAACAATGACAGCATATGCTCCTTTAACCATTGTATGTGATGGTTGTTTCTCAAACTTGCGCCGCTCCCTTTGTACCCCTAAGgtgaggatgacctcagtcttctccaaaataaataaaataaaataaaactcacctaaatacacttccattgttcctgaattatgtttttcaccttgccatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataca