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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGTCCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAGgttggtttctgtttcttttcttcattttttgccattatctggaattgtatttcctaaatactgactgttactattgatttttctctttag

Basic information

species Vitis vinifera
transcript Vv17s0000g00620.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g00620.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA04G37630.1 (Glycine max), 5'ss of exon 5
TCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGTCCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAGgttggtttctgtttcttttcttcattttttgccatta--tctggaattgtatttcctaa-atactgactgttactattgatttttctctttag-----
||||||| || || || ||||||||||| || |||||||||||||||| |||||||| ||||||| | |||||||   || | |||||||||| |  |||   |   |||  |||| |||| ||| |||    || |  |||||| |  | || | |    | | |  | | | |  || ||||  | |  |      
TCTTTACCACAGAGCCTTATGCTTGTGAACCATCAAGTTTGCCAAAGTATCCTCCCAGCAAAGAATTGGATGTAA---AACTGAGAGATGAAGAAGCAAGAAGgtcctcttcttctcttct-catgtttgagaataacttctggactgattttgctttttgtccagtttctcattgatggttttcatttcaacctcag

upper sequence: Vv17s0000g00620.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA06G17460.1 (Glycine max), 5'ss of exon 5
TCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGTCCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAGgttggtttctgtttcttttcttcattttttgccatta--tctgga---attgtatttccta----aatactgactgttactattgatttttctctttag
||||||| || || || ||||||||||| || |||||||||||||||| |||||||| ||||||| | |||||||   || | |||||||| | |  |||   |   |||  |||| |||| | | |||  | || |  ||||||   ||| |  ||  |       | || | || | || || ||||   || | ||
TCTTTACCACAGAGCCCTATGCTTGTGAACCATCAAGTTTGCCAAAGTATCCTCCCAGCAAAGAATTGGATGTAA---AACTGAGAGATGAGGAAGCAAGAAGgtcctctagttctcttct-cgtgtttgacaataacttctggactgattttgctttttgtccggtttctcattgatgcttttcatttca-tcctcag

upper sequence: Vv17s0000g00620.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA05G38410.1 (Glycine max), 5'ss of exon 5
TCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGTCCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAGgttggtttctgtttcttttcttcattttttgccattatctggaattgtatttcctaaatactgactgttactattgatttttctctttag---------
||||||| ||||| || ||||||||||| || || | ||| ||||||| |||||||||||||||| | |||   |||||| | |||||||||| |  |||    | |||  ||  |    |       ||| ||   ||| || |  | |||  | | |  || |  |||  | |  ||||| | ||||          
TCTTTACCACTGAGCCCTATGCTTGTGAACCATCTAATTTACCAAAGTATCCTCCCACCAAAGAATTGGAT---ATAAAACTGAGAGATGAAGAAGCAAGA--AGgttcaattattcagttattgcccttgacaagttctagactgattttttgtca-tggtgcccattaaaactt-tttttttttttaccattctcag

upper sequence: Vv17s0000g00620.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA08G01250.1 (Glycine max), 5'ss of exon 5
TCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGTCCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGA---AGCAAGAAGgttggtttctgtttcttttcttcattttttgccat-tatctggaattgtatttcctaaatactgactgttactattgatttttctctttag
||||||| ||||  || ||||||||||| || || | ||| ||||||| |||||||||||||||| | |||   |||||| | ||||||||   ||||||||||||   ||   ||   ||  | | |||  |   || || |||   ||||  ||  |    | | |   ||  | ||  ||    || | ||
TCTTTACCACTGTGCCCTATGCTTGTGAACCATCTAATTTACCAAAGTATCCTCCCACCAAAGAATTGGAT---ATAAAACTGAGAGATGAAAAAGCAAGAAGgttcaatt--attcagttattgcctttgataagatctaactgattttgt-cttggtgcccattaaacctttttttttgttgccatcatcag

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|352795543|gb|FQ480131.1|FQ480131
EST:     CCTCTCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAG                         GCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
genomic: CCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAGgttggtttct ... ttctctttagGCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
EST: gi|351046377|gb|FQ452993.1|FQ452993
EST:     ACTCTCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAG                         GCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
genomic: CCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAGgttggtttct ... ttctctttagGCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
EST: gi|351055934|gb|FQ453395.1|FQ453395
EST:     CCTCTCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAG                         GCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
genomic: CCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAGgttggtttct ... ttctctttagGCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
EST: gi|352786901|gb|FQ481276.1|FQ481276
EST:     CCTCTCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAG                         GCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
genomic: CCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAGgttggtttct ... ttctctttagGCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
EST: gi|351043417|gb|FQ451469.1|FQ451469
EST:     CCTCTCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAG                         GCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
genomic: CCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAGgttggtttct ... ttctctttagGCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
EST: gi|351043887|gb|FQ452681.1|FQ452681
EST:     CCTCTCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAG                         GCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
genomic: CCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAGgttggtttct ... ttctctttagGCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
EST: gi|351038967|gb|FQ457642.1|FQ457642
EST:     ACTCTCACCAAAGAAATTGATGTAATAAAATTAAGAGATGGAGCAAGAAG                         GCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
genomic: CCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAGgttggtttct ... ttctctttagGCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
EST: gi|351055161|gb|FQ440500.1|FQ440500
EST:     ACTCTCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAG                         GCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
genomic: CCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAGgttggtttct ... ttctctttagGCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
EST: gi|110382073|gb|EC938409.1|EC938409
EST:     AAAATTAAGAGATGAAGCAAGAAG                         GCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
genomic: AAAATTAAGAGATGAAGCAAGAAGgttggtttct ... ttctctttagGCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
EST: gi|351032086|gb|FQ460343.1|FQ460343
EST:     CCTCTCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAG                         GCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
genomic: CCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAGgttggtttct ... ttctctttagGCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
EST: gi|351043841|gb|FQ452635.1|FQ452635
EST:     CCTCTCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAG                         GCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
genomic: CCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAGgttggtttct ... ttctctttagGCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
EST: gi|349824254|gb|FQ417641.1|FQ417641
EST:     CCTCTCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAG                         GCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
genomic: CCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAGgttggtttct ... ttctctttagGCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
EST: gi|351013309|gb|FQ425014.1|FQ425014
EST:     CCTCTCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAG                         GCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
genomic: CCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAGgttggtttct ... ttctctttagGCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
EST: gi|352795551|gb|FQ480139.1|FQ480139
EST:     ACTCTCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAG                         GCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
genomic: CCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAGgttggtttct ... ttctctttagGCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
EST: gi|351034440|gb|FQ463253.1|FQ463253
EST:     CCTCTCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAG                         GCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
genomic: CCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAGgttggtttct ... ttctctttagGCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
EST: gi|352790536|gb|FQ478176.1|FQ478176
EST:     CCTCTCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAG                         GCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
genomic: CCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAGgttggtttct ... ttctctttagGCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
EST: gi|352791008|gb|FQ480001.1|FQ480001
EST:     CCTCTCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAG                         GCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
genomic: CCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAGgttggtttct ... ttctctttagGCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
EST: gi|33408038|gb|CF213665.1|CF213665
EST:     AAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAG                         GCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT
genomic: AAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAGgttggtttct ... ttctctttagGCAAAGAGGGGTGAGCGGGAAAGCCAATGTTGTTGATGGTAACAGAAGAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGTCCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAAGgttggtttctgtttcttttcttcattttttgccattatctggaattgtatttcctaaatactgactgttactattgatttttctctttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG