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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTTTTATTATGAGGGAAAGGCTATTATGTCAAATGAGGAATTTGACAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTATGCTAAgtacatatttagattatcttaatcaatatctttatgatataatagtttgtaatactttttaaatctctaaaatgtaaaattggcttatgtgtaatgcag

Basic information

species Vitis vinifera
transcript Vv02s0025g04710.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g04710.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os03g64020.1 (Oryza sativa), 5'ss of exon 1
---TCTTTTTATTATGAGGGAAAGGCTATTATGTCAAATGAGGAATTTGACAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTATGCTAAgtacatatttagattatcttaatcaatatctttatgatataatagtttgtaatactttttaaatctctaaaatgtaaaattggcttatgtgtaatgcag
    | || || || ||    ||||| || ||||| || ||||| || |||||||||||||| || |||||||||||||| ||||||||||| ||||||||||  || |   | |   |  |||  |         |  ||   ||| |||   ||| ||    | ||||     |  | |  ||| |  |        
CAGGCCTTCTACTACGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtact---actccttccatctcttctgcggatacctatctgttagtat--cttctttgcccactaattaacactaatatcttttcag--------

upper sequence: Vv02s0025g04710.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os08g41460.6 (Oryza sativa), 5'ss of exon 1
---TCTTTTTATTATGAGGGAAAGGCTATTATGTCAAATGAGGAATTTGACAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTATGCTAAgtacatatt-tagattatcttaatcaatatctttatgatataatagtttgtaatactttttaaatctctaaaatgtaaaattggcttatgtgtaatgcag----
    | |||||||| ||    |||||  | ||||| |||||||| || || ||||||||||| || || ||||||||||||||||||||||| ||||||||||  |  | || | |||     |       | ||   | ||  || |       |||  |  |      || |||  |    ||| |   | ||   |     
TAGGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAAgtaagtggtataaaatattcctttt----cttctagcttgtacgagatcccggcccttactgtacactataagtgtgcatgccgctgaaaagaaaaagattatt

upper sequence: Vv02s0025g04710.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os08g41460.2 (Oryza sativa), 5'ss of exon 2
TCTTTTTATTATGAGGGAAAGGCTATTATGTCAAATGAGGAATTTGACAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTATGCTAAgtacata-tttagattatcttaatcaatatctttatgatataatagtttgtaatactttttaaatctctaaaatgtaaaattggcttatgtgtaatgcag----
 | |||||||| ||    |||||  | ||||| |||||||| || || ||||||||||| || || ||||||||||||||||||||||| ||||||||||  |  | || | |||     |       | ||   | ||  || |       |||  |  |      || |||  |    ||| |   | ||   |     
GCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAAgtaagtggtataaaatattcctttt----cttctagcttgtacgagatcccggcccttactgtacactataagtgtgcatgccgctgaaaagaaaaagattatt

upper sequence: Vv02s0025g04710.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os08g21900.1 (Oryza sativa), 5'ss of exon 2
TCTTTTTATTATGAGGGAAAGGCTATTATGTCAAATGAGGAATTTGACAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTATGCTAAgtacata-tttagattat--cttaatcaatatctttatgatataatagtttgtaatactttttaaatctctaaaatgtaaaattggcttatgtgtaatgcag
 | |||||||| ||    ||||| || || || || ||||  || || ||||||||||| || || ||||||||||||||||||||||| ||||||||||  |  | || | |||  |||      || || ||   |||||  ||        ||    | |       | |||   |     | |    |||| |  
GCCTTTTATTACGACAAGAAGGCCATAATATCGAACGAGGTGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAAgtaagtggtataaaatattccttttcttctagctgtacactataactgtgcacgccgctgaaaagaaaagattattgttgga--aattcagagataatccta

upper sequence: Vv02s0025g04710.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM5G885392_T01 (Zea mays), 5'ss of exon 2
TCTTTTTATTATGAGGGAAAGGCTATTATGTCAAATGAGGAATTTGACAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTATGCTAAgtacatatttagattatcttaatcaatatctttatgatataatagtttgtaat-actttttaaatctctaaaatgtaaaattggcttatgtgtaatgcag---
 | || || || || || ||||| || ||||| || ||||| || |||||||||||||| || |||||||||||||| |||||||| || |||||||||   |   |   | |   |||| ||   |    |  |   |   ||| | || ||| | |  ||  |  | |    |||     ||   |  |   |     
GCCTTCTACTACGAAGGCAAGGCGATCATGTCGAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAAGGGAGCAGCGTCGTGATGCTAAgtgagtgcgtttttcac--taattaa-gcccccctcctgcgactttttattattactgtgtcgatgacgtatactagaaacgtatttccttagacgacgacaa

upper sequence: Vv02s0025g04710.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM5G896082_T03 (Zea mays), 5'ss of exon 3
TCTTTTTATTATGAGGGAAAGGCTATTATGTCAAATGAGGAATTTGACAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTATGCTAAgta--catatttagattatcttaatcaatatctttatgatat-aatagtttgtaatactttttaa-----atctctaaaatgtaaaattggcttatg-tgtaatgcag--------------
 | || || |||||    ||||| || ||||| || ||||| || |||||||||||||| || ||||||||||| || |||||||| || ||||||||||  ||| ||||| | || |    || || ||   || | | ||    ||| || |    ||||     | | | ||  |||    | |    |   |    | | |              
GCCTTCTACTATGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATGCTAAgtaagcatttttagttaatttgctccactaactgcctgctctcaagtccttgaaaaaaaaattaatgctaacccccaaggtgtggcgtcgatacaaactacgttcctgtgtgttgtttccag

upper sequence: Vv02s0025g04710.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AC203966.5_FGT002 (Zea mays), 5'ss of exon 3
TCTTTTTATTATGAGGGAAAGGCTATTATGTCAAATGAGGAATTTGACAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTAT-GCTAAgtacatatttagattatcttaatcaatatctttatgatataatagtttgtaatactttttaaatctctaaaatgtaa-aattggcttatgtgtaatgcag----
 | || || |||||    ||||| || ||||| || ||||| ||||||||||||||||| || ||||||||||| || |||||||| || || ||||||||   ||||   |||  ||| |   |  |   |  |  |    |||   ||  | ||  |||    ||||   |    |    |  | ||||   |  |    
GCCTTCTACTATGACCAGAAGGCCATCATGTCCAACGAGGAGTTTGACAACCTCAAGGAGGAGCTCATGTGGGAGGGGAGCAGCGTCGTCATTGCTAAgtaagcattt---ttagtttatttgct-ccaccactaactgcctgttctcaagtccttgaaaaaaaataaataatgctgaccccccaaggtgtggcgttgatac

upper sequence: Vv02s0025g04710.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA17G14240.1 (Glycine max), 5'ss of exon 3
TCTTTTTATTATGAGGGAAAGGCTATTATGTCAAATGAGGAATTTGACAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTATGCTAAgtacatatttagattatcttaatcaatatcttta--tgatataatagtttgtaatactttttaaatctctaaaatgtaaaattggcttatgtgtaatgcag
 | || |||||||||||||||||||| ||||||||||| |||||||| || |||||||||||||||||||||||||||||||||||||| ||||||||||        |   |  |   || |||  |  |  || | | |||  ||   ||  |||| || ||| ||          |||| | || ||||  |   
GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAATTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatg-----gggcaacttcgctctatagttgcagctgttgtcataacttc--atctttttaaagtcttta----------ttggttgat-tgtacag---

upper sequence: Vv02s0025g04710.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA05G03730.1 (Glycine max), 5'ss of exon 3
TCTTTTTATTATGAGGGAAAGGCTATTATGTCAAATGAGGAATTTGACAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTATGCTAAgtacatatttagatta-tcttaatcaatatctttat-gatataat--agtttgtaatactttttaaatctctaaaatgtaaaa---ttggcttatgtgtaatgcag
 | || |||||||||||||||||||| ||||||||||| || ||||| || |||||||||||||||||||||||||||||||||||||| ||||||||||       |  | | ||| | |   |     | | | | | ||  | |||||  ||         | | ||   | |  ||   || | |  |   |  | |||
GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatgaggcaacttcactctcagtagctgcagctgttgttgtcattgaatttgtgttaacgcgggtgtatttatcttttttaagtctttgttggttgattgtacag

upper sequence: Vv02s0025g04710.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA01G42360.2 (Glycine max), 5'ss of exon 3
TCTTTTTATTATGAGGGAAAGGCTATTATGTCAAATGAGGAATTTGACAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTATGCTAAgtacatatttagattatct-taatcaatatctttatgatataatagtttgtaatactttttaaatctctaaaa---tgtaaaattggcttatgtgtaatgcag---------------------
 | || ||||||||||| ||||||||||||||||||||||||||||| || || ||||||||||||||||||||||| |||| |||||| |||||||||| ||  |||   ||| | |    |  |  || ||    | | ||||  ||  |    | || ||     ||   |||||| |    |||| | | |  ||                      
GCATTCTATTATGAGGGGAAGGCTATTATGTCAAATGAGGAATTTGATAATCTTAAGGAAGAACTCATGTGGGAAGGGAGCACCGTTGTGATGCTAAgtatattattattatatatgtggctagcaatttcattcactgacagttgctagcatgcatgaattcctgctaactttgtaaattgattttatttttgagtcattataattggttcgctgtgtag

upper sequence: Vv02s0025g04710.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT4G11960.1 (Arabidopsis thaliana), 5'ss of exon 3
TCTTTTTATTATGAGGGAAAGGCTATTATGTCAAATGAGGAATTTGACAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTATGCTAAgtacatatttagattatcttaatcaatatctttatgatataatagtttgtaatactttttaaatctctaaaatgtaaaattggcttatgtgtaatgcag
|| |||||||| || || || || |||||||| ||||| || ||||| ||||| || |||||  | ||||||||||||||||| ||||| ||||||||||      |  |   |  | ||  |||  ||| | |   |    || |      || || | |||     || |||  ||  ||    |||| || ||
TCGTTTTATTACGAAGGCAAAGCGATTATGTCTAATGAAGAGTTTGATAACCTTAAAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAAgtaa-----tgaacacttatgatttatagttttgtcaataatccattcgcctaggttcttgattctt---gatctaattttatct---atgtattgtag

upper sequence: Vv02s0025g04710.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT4G22890.1 (Arabidopsis thaliana), 5'ss of exon 3
TCTTTTTATTATGAGGGAAAGGCTATTATGTCAAATGAGGAATTTGACAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTATGCTAAgtacatatttagattatcttaatcaatatctttatgatataatagtttgtaatactttttaaatctctaaaatgtaaaattggcttatgtgtaatgcag
||||| |||||||| || || || || ||||| ||||| || ||||| ||||| || |||||  | ||||||||||||||||| ||||| ||||||||||   ||    | |||   | | ||| || ||    | |  | |||| |     |  |  ||  ||  |||| |   ||||| | || || ||  |||
TCTTTCTATTATGATGGCAAAGCGATCATGTCTAATGAAGAGTTTGATAACCTTAAAGAAGAGTTAATGTGGGAAGGAAGCAGTGTTGTGATGCTAAgtaatcatc--aactatgggactaaatttcatttctttgttttggtttct----ttggtgcaaagtcctaaatcttttattgg-taatatgaaacacag

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|32247639|gb|CD713458.1|CD713458
EST:     CATGTGGGAAGGAAGCAGCGTTGTTATGCTAA                         GTTCTGATGAACAGAAGTTTCTTGAAGCCTCCATGGCCTATGTTGCAGGGA
genomic: CATGTGGGAAGGAAGCAGCGTTGTTATGCTAAgtacatattt ... tgtaatgcagGTTCTGATGAACAGAAGTTTCTTGAAGCCTCCATGGCCTATGTTGCAGGGA
EST: gi|34549756|gb|CF517988.1|CF517988
EST:     CAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTATGCTAA                         GTTCTGATGAACAGAAGTTTCTTGAAGCCTCCATGGCCTATGTTGCAGGGA
genomic: CAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTATGCTAAgtacatattt ... tgtaatgcagGTTCTGATGAACAGAAGTTTCTTGAAGCCTCCATGGCCTATGTTGCAGGGA
EST: gi|110375639|gb|EC940647.1|EC940647
EST:     CAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTATGCTAA                         GTTCTGATGAACAGAAGTTTCTTGAAGCCTCCATGGCCTATGTTGCAGGGA
genomic: CAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTATGCTAAgtacatattt ... tgtaatgcagGTTCTGATGAACAGAAGTTTCTTGAAGCCTCCATGGCCTATGTTGCAGGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTTTTATTATGAGGGAAAGGCTATTATGTCAAATGAGGAATTTGACAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTATGCTAAgtacatatttagattatcttaatcaatatctttatgatataatagtttgtaatactttttaaatctctaaaatgtaaaattggcttatgtgtaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA