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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGATGAGGGATCTGTGGCTCGCCATTTACATTGTTGATGCTGTACTCGTATTCTTTGTTATTCCCTTCGCCATGTTCTACTACGAAGGCGACCAGGACAAgtcggtactttagggtttctattaatattgctgagatttcgtatttctccttttgttagagttgattggttgctgcgagactgaaggaaaataaaataaa...

Basic information

species Vitis vinifera
transcript Vv08s0007g02270.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g02270.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os06g03760.2 (Oryza sativa), 5'ss of exon 1
CGATGAGGGATCTGTGGCTCGCCATTTACATTGTTGATGCTGTACTCGTATTCTTTGTTATTCCCTTCGCCATGTTCTACTACGAAGGCGACCAGGACAAgtcggtactttagggtttc--tattaatattgctgagatttcgtatttctccttttgttagagt-tgattggttgctgcgagactgaaggaaaataaaataaa---------
| |||| |   || ||||||||| | ||||| |  || || || ||||| ||| | || || ||||||||||||||||||||||| ||||||||||||||||  ||| | ||    | |  |   | | || |    ||  | |    |  ||  || || | | | | ||  || ||   || || |      |    |            
CCATGAAGACCCTCTGGCTCGCCGTCTACATCGCCGACGCCGTCCTCGTCTTCCTCGTCATCCCCTTCGCCATGTTCTACTACGAGGGCGACCAGGACAAgtaagtagtatacatatacatttccactctttcctctatcccattgcgcatctgctgctaaactctcactgaatgttgtt-gattggatccgtgtgttgttgcttcctgcag

upper sequence: Vv08s0007g02270.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM5G871262_T02 (Zea mays), 5'ss of exon 1
CGATGAGGGATCTGTGGCTCGCCATTTACATTGTTGATGCTGTACTCGTATTCTTTGTTATTCCCTTCGCCATGTTCTACTACGAAGGCGACCAGGACAAgtcggtactttagggtttctattaatattgctgagatttcgtatttctccttttgttaga-gttgattggttgctgcgagactgaaggaaaataaaataaa
| ||||||   || ||||||| | ||||||| ||||| || || ||||| ||| | || || |||||||| |||||||||||||| ||||||||||||||||    || | |      |  |   | || |      ||| | ||  ||| |  ||  |  | ||||| |   | ||    |     |             
CCATGAGGACGCTCTGGCTCGTCGTTTACATCGTTGACGCCGTCCTCGTCTTCCTCGTCATCCCCTTCGCAATGTTCTACTACGAGGGCGACCAGGACAAgta---acctca---cccccctcgctgtttccctaccttc-tcttcttccatccgtccgctgatgatttggacccgccttccctgcag-------------

upper sequence: Vv08s0007g02270.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA01G30400.1 (Glycine max), 5'ss of exon 1
CGATGAGGGATCTGTGGCTCGCCATTTACATTGTTGATGCTGTACTCGTATTCTTTGTTATTCCCTTCGCCATGTTCTACTACGAAGGCGACCAGGACAAgtcggtac-tttagggtttctattaatattgctgagatttcgtatttctccttttgttagagttgattggttgctgcgagactgaaggaaaataaaataaa----
| |||| ||| || |||||||| ||||||||  | || || || ||||| ||||| ||||| ||||| ||||||||||||||||||||||||||||||||||  ||   | | | | | || ||||| ||| ||   |||  | ||| |  ||||  |     | ||    | |||  | | |||| |||    |  |       
CCATGAAGGACCTCTGGCTCGCAATTTACATCCTCGACGCCGTCCTCGTCTTCTTCGTTATCCCCTTTGCCATGTTCTACTACGAAGGCGACCAGGACAAgtaagtgtatgtcgtggtgcttttaat-ttgatgt--ttttttttttttgtttttaatttttgtaatcatatactg--aaattgaacgaaccagacgttggtccg

upper sequence: Vv08s0007g02270.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA03G07890.1 (Glycine max), 5'ss of exon 1
CGATGAGGGATCTGTGGCTCGCCATTTACATTGTTGATGCTGTACTCGTATTCTTTGTTATTCCCTTCGCCATGTTCTACTACGAAGGCGACCAGGACAAgtcggtactttagggtttctattaatattgctgagatttcgtatttctccttttgttagagttgattggttgctgcgagactgaaggaaaataaaataaa--------------------------------------------
| |||| ||| || |||||||| ||||||||  | || || || ||||| ||||| || || ||||||||||||||||||||||||||||||||||||||||  ||  | |  |||   | ||||| ||    | ||||    ||| |  || |   | | |  | | | | ||  | |     || |   ||| | |||                                            
CCATGAAGGACCTCTGGCTCGCAATTTACATCCTCGACGCCGTCCTCGTCTTCTTCGTCATCCCCTTCGCCATGTTCTACTACGAAGGCGACCAGGACAAgtaagtg-tatgtggtgctttttaatttttaaaaaatttaagttttgtgattattagatactgaaattgatactttgtgctaatagcatggtaacaaaaaaaatactgaaattgaaaatgtgttgtgattttgggaatgtgcag

upper sequence: Vv08s0007g02270.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA07G18160.1 (Glycine max), 5'ss of exon 1
CGATGAGGGATCTGTGGCTCGCCATTTACATTGTTGATGCTGTACTCGTATTCTTTGTTATTCCCTTCGCCATGTTCTACTACGAAGGCGACCAGGACAAgtcggtactttagggtttctattaatattgctga--gatttcgtatttctccttttgttagagttgattggttgctgcgagactgaaggaaaataaaataaa
| |||| ||| || ||||||||| | |||||  | || ||||| ||||| || || ||||| |||||||||||||||| |||||| ||||||||||||||||  |   |||    |||   ||  | | | ||   | ||    || || || ||||   ||  || |   ||| |  | | ||   |     |  |     
CCATGAAGGACCTCTGGCTCGCCGTCTACATCCTCGACGCTGTCCTCGTCTTTTTCGTTATCCCCTTCGCCATGTTCTTCTACGAGGGCGACCAGGACAAgtacgagtttt----ttttcttttctttcgttggttgcttcaaaatatcaccatttgaatgaaatgttgtattggtttgtggcttt-gttgtgtgcag----

upper sequence: Vv08s0007g02270.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA18G43020.1 (Glycine max), 5'ss of exon 1
CGATGAGGGATCTGTGGCTCGCCATTTACATTGTTGATGCTGTACTCGTATTCTTTGTTATTCCCTTCGCCATGTTCTACTACGAAGGCGACCAGGACAAgtcggtactttagggtttctattaatattgctgagatttcgt--atttctccttttgttagagttgattggttgctgcgagactgaaggaaaataaaataaa
| |||| ||| || ||||||||  | |||||  | || || || ||||| ||||| || || |||||||||||||||| |||||| ||||||||||||||||  |   |||  | | |   || | |||  |||   |||||  | |  | | |  ||| || |  | || |||    ||   ||   | |           
CCATGAAGGACCTCTGGCTCGCAGTCTACATCCTCGACGCCGTCCTCGTCTTCTTCGTCATCCCCTTCGCCATGTTCTTCTACGAGGGCGACCAGGACAAgtacgaggtttttgttattgtttgaaatt--tgaatcttcgtcaagtgtttcgtgggtttgaatgaaatgtttgt---gactttgtgtgcag----------

upper sequence: Vv08s0007g02270.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT5G01460.1 (Arabidopsis thaliana), 5'ss of exon 1
CGATGAGGGATCTGTGGCTCGCCATTTACATTGTTGATGCTGTACTCGTATTCTTTGTTATTCCCTTCGCCATGTTCTACTACGAAGGCGACCAGGACAAgtc-ggtactttagggtttctattaatattgctgagatttcgtatttctccttttgttagagttgattggttgctgcgagactgaaggaaaataaaataaa
| |||| |||||| ||||| ||| ||||||||||||| ||||| || || |||||  | || |||||||| ||||| | ||| |||||||||||||||||||  | | ||  | | ||| | ||  | ||  |  || ||  ||||  |   |    || ||||| |  | || || | |  ||  |     ||    |  
CTATGAAGGATCTTTGGCTTGCCGTTTACATTGTTGACGCTGTGCTTGTCTTCTTCATCATCCCCTTCGCTATGTTTTTCTATGAAGGCGACCAGGACAAgtttgtttctccacgatttttttttttttttttttgagttattattagttggtaatgtaaagttgtt--gatgttgtgggcttgt-gttttttactgcag-

upper sequence: Vv08s0007g02270.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT3G08930.1 (Arabidopsis thaliana), 5'ss of exon 1
CGATGAGGGATCTGTGGCTCGCCATTTACATTGTTGATGCTGTACTCGTATTCTTTGTTATTCCCTTCGCCATGTTCTACTACGAAGGCGACCAGGACAAgtcggtacttta--gggtttctattaatat--tgctgagatttcgtatttctccttttgttagagttgattggttg-ctgcgagactgaaggaaaataaaataaa
| |||| |||||| ||||| || ||||| || || || ||| | ||||| |||||||| || |||||||| ||||| | ||| |||||||||||||||||||  |||  ||   |   || || ||      || ||  | ||   | ||   |   |  |   |   ||| || | ||      ||   |     | | |    
CCATGAAGGATCTTTGGCTTGCTATTTATATCGTGGACGCTATTCTCGTGTTCTTTGTCATCCCCTTCGCAATGTTTTTCTATGAAGGCGACCAGGACAAgttcgtagcttgatgaaattttagtatctctatgttgtaagttttgagttaatcgaatactgatgacaatttgtgggctttttttctttcgttttttcacag---

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|110730881|gb|EE108469.1|EE108469
EST:     TTCTTTGTTATTCCCTTCGCCATGTTCTACTACGAAGGCGACCAGGACAA                         GAGCGTTGGCAAGCGGATAAAAAGTGCCTTATTATGGGTCATCACTACAGC
genomic: TTCTTTGTTATTCCCTTCGCCATGTTCTACTACGAAGGCGACCAGGACAAgtcggtactt ... ttgtttgcagGAGCGTTGGCAAGCGGATAAAAAGTGCCTTATTATGGGTCATCACTACAGC
EST: gi|161708327|gb|FC057028.1|FC057028
EST:     TTCTTTGTTATTCCCTTCGCCATGTTCTACTACGAAGGCGACCAGGACAA                         GAGCGTAGGCAAGCGGATAAAAAGTGCCTTATTATGGGTCATCACTACAGC
genomic: TTCTTTGTTATTCCCTTCGCCATGTTCTACTACGAAGGCGACCAGGACAAgtcggtactt ... ttgtttgcagGAGCGTTGGCAAGCGGATAAAAAGTGCCTTATTATGGGTCATCACTACAGC
EST: gi|110730406|gb|EE107450.1|EE107450
EST:     TTCTTTGTTATTCCCTTCGCCATGTTCTACTACGAAGGCGACCAGGACAA                         GAGCGTTGGCAAGCGGATAAAAAGTGCCTTATTATGGGTCATCACTACAGC
genomic: TTCTTTGTTATTCCCTTCGCCATGTTCTACTACGAAGGCGACCAGGACAAgtcggtactt ... ttgtttgcagGAGCGTTGGCAAGCGGATAAAAAGTGCCTTATTATGGGTCATCACTACAGC
EST: gi|161716762|gb|FC065585.1|FC065585
EST:     TTCTTTGTTATTCCCTTCGCCATGTTCTACTACGAAGGCGACCAGGACAA                         GAGCGTTGGCAAGCGGATAAAAAGTGCCTTATTATGGGTCATCACTACAGC
genomic: TTCTTTGTTATTCCCTTCGCCATGTTCTACTACGAAGGCGACCAGGACAAgtcggtactt ... ttgtttgcagGAGCGTTGGCAAGCGGATAAAAAGTGCCTTATTATGGGTCATCACTACAGC
EST: gi|110372187|gb|EC936337.1|EC936337
EST:     TTCTTTGTTATTCCCTTCGCCATGTTCTACTACGAAGGCGACCAGGACAA                         GAGCGTTGGCAAGCGGATAAAAAGTGCCTTATTATGGGTCATCACTACAGC
genomic: TTCTTTGTTATTCCCTTCGCCATGTTCTACTACGAAGGCGACCAGGACAAgtcggtactt ... ttgtttgcagGAGCGTTGGCAAGCGGATAAAAAGTGCCTTATTATGGGTCATCACTACAGC
EST: gi|110708808|gb|EE086769.1|EE086769
EST:     TTCTTTGTTATTCCCTTCGCCATGTTCTACTACGAAGGCGACCAGGACAA                         GAGCGTTGGCAAGCGGATAAAAAGTGCCTTATTATGGGTCATCACTACAGC
genomic: TTCTTTGTTATTCCCTTCGCCATGTTCTACTACGAAGGCGACCAGGACAAgtcggtactt ... ttgtttgcagGAGCGTTGGCAAGCGGATAAAAAGTGCCTTATTATGGGTCATCACTACAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGATGAGGGATCTGTGGCTCGCCATTTACATTGTTGATGCTGTACTCGTATTCTTTGTTATTCCCTTCGCCATGTTCTACTACGAAGGCGACCAGGACAAgtcggtactttagggtttctattaatattgctgagatttcgtatttctccttttgttagagttgattggttgctgcgagactgaaggaaaataaaataaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa