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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgattcactagctggtgaagaaagtgttcaagctgaggtgaagcctgagctttccatgtaaaattgttctaatttttttcttttcatattgtttcaacagTCTTGCAACAGCTGGATATGGTACTGCTCTCGGTGTAATCCGTTCCGTTCATGCTGAAGGAATTTTACTGAGGGCCTATTGCACAGAGACACGTCCATTC

Basic information

species Vitis vinifera
transcript Vv11s0016g00830.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g00830.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA09G08190.1 (Glycine max), 3'ss of exon 5
--tgattcactagctggtgaagaaagtgttcaagctgaggtgaagcctgagctttccatgtaaaattgttctaatttttttcttttcatattgtttcaa----cagTCTTGCAACAGCTGGATATGGTACTGCTCTCGGTGTAATCCGTTCCGTTCATGCTGAAGGAATTTTACTGAGGGCCTATTGCACAGAGACACGTCCATTC
  |  | |   |  |    || ||   |||    ||    |||    |||        ||   |  ||||   | |   || |  |  ||||   | ||    |||||| || ||||||||||||||||||||||| ||||| |||||| |  |||||  ||  ||| || ||   ||||| ||||||||||| ||||| ||||| 
tttagtccttcaaatttgaaaaaataagttattacttgtttgacaaatgaa------gtgatgaggtgtttggactcacttgtacttgtatttgattaatactcagTCTAGCCACAGCTGGATATGGTACTGCTCTGGGTGTCATCCGTGCACTTCATAGTGCCGGAGTTCTAAAAAGGGCTTATTGCACAGAAACACGCCCATTT

upper sequence: Vv11s0016g00830.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA15G19690.1 (Glycine max), 3'ss of exon 1
-tgattcactagctggtgaagaaagtgttcaagctgaggtgaagcctgagctttccatgtaaaattgttctaatttttttctt-ttcatattgtttcaacagTCTTGCAACAGCTGGATATGGTACTGCTCTCGGTGTAATCCGTTCCGTTCATGCTGAAGGAATTTTACTGAGGGCCTATTGCACAGAGACACGTCCATTC
 |  | |   |  |  | || |    |||    ||    |||    |||  |    | ||    |||  || | || |  ||| ||  |  |   |   |||||| || ||||||||||||||||||||||| ||||| |||||| |  ||||   ||  ||| || ||   ||||  ||||||||||| ||||| ||||||
ttagtccctcaaattttaaaaagtacgtttttacttgtttgacaaatgaagtgaagaggtgt--ttggactcacttgtaacttgtttttgattaatgctcagTCTAGCCACAGCTGGATATGGTACTGCTCTGGGTGTGATCCGTGCACTTCACAGTGCTGGAGTTCTAGAAAGGGTTTATTGCACAGAAACACGCCCATTC
















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|110719863|gb|EE095357.1|EE095357
EST:     ATAAAAGACTCTAAGAATCTGTCTATTTTGACACATTGCAACACTGGAAG                         TCTTGCAACAGCTGGATATGGTACTGCTCTCGGTGTAATCCCGTTC-GTTC
genomic: ATAAAAGACTCTAAGAATCTGTCTATTTTGACACATTGCAACACTGGAAGgtactgtcct ... gtttcaacagTCTTGCAACAGCTGGATATGGTACTGCTCTCGGTGTAATCC-GTTCCGTTC
EST: gi|30252087|gb|CB968726.1|CB968726
EST:     ATAAAAAACTCTAAGAATCTGTCTATTTTGACACATTGCAACACTGGAAG                         TCTTGCAACAGCTGGATATGGTACTGCTCTCGGTGTAATCCGTTCCGTTCA
genomic: ATAAAAGACTCTAAGAATCTGTCTATTTTGACACATTGCAACACTGGAAGgtactgtcct ... gtttcaacagTCTTGCAACAGCTGGATATGGTACTGCTCTCGGTGTAATCCGTTCCGTTCA
EST: gi|30133085|gb|CB918424.1|CB918424
EST:     ATAAAAGACTCTAAGAATCTGTCTATTTTGACACATTGCAACACTGGAAG                         TCTTGCAACAGCTGGATATGGTACTGCTCTCGGTGTAATCCGTTCCGTTCA
genomic: ATAAAAGACTCTAAGAATCTGTCTATTTTGACACATTGCAACACTGGAAGgtactgtcct ... gtttcaacagTCTTGCAACAGCTGGATATGGTACTGCTCTCGGTGTAATCCGTTCCGTTCA
EST: gi|110363814|gb|EC927433.1|EC927433
EST:     TTTTGACACATTGCAACACTGGAAG                         TCTTGCAACAGCTGGATATGGTACTGCTCTCGGTGTAATCCGTTCCGTTCA
genomic: TTTTGACACATTGCAACACTGGAAGgtactgtcct ... gtttcaacagTCTTGCAACAGCTGGATATGGTACTGCTCTCGGTGTAATCCGTTCCGTTCA
EST: gi|110420049|gb|EC986310.1|EC986310
EST:     ATTTTGACACATTGCAACACTGGAAG                         TCTTGCAACAGCTGGATATGGTACTGCTCTCGGTGTAATCCGTTCCGTTCA
genomic: ATTTTGACACATTGCAACACTGGAAGgtactgtcct ... gtttcaacagTCTTGCAACAGCTGGATATGGTACTGCTCTCGGTGTAATCCGTTCCGTTCA
EST: gi|161721519|gb|FC070079.1|FC070079
EST:     ATAAAAAACTCTAAGAATCTGTCTATTTTGACACATTGCAACACTGGAAG                         TCTTGCAACAGCTGGATATGGTACTGCTCTCGGTGTAATCCG
genomic: ATAAAAGACTCTAAGAATCTGTCTATTTTGACACATTGCAACACTGGAAGgtactgtcct ... gtttcaacagTCTTGCAACAGCTGGATATGGTACTGCTCTCGGTGTAATCCG
EST: gi|110707370|gb|EE083712.1|EE083712
EST:     ATAAAAGACTCTAAGAATCTGTCTATTTTGACACATTGCAACACTGGAAG                         TCTTGGCA-CAGCTGGATATGGTACTGCTCTCGGTGTAATCCGTTCCGTTC
genomic: ATAAAAGACTCTAAGAATCTGTCTATTTTGACACATTGCAACACTGGAAGgtactgtcct ... gtttcaacagTCTTG-CAACAGCTGGATATGGTACTGCTCTCGGTGTAATCCGTTCCGTTC
EST: gi|110366059|gb|EC929706.1|EC929706
EST:     ATAAAAAACTCTAAGAATCTGTCTATTTTGACACATTGCAACACTGGAAG                         TCTTGCAACAGCTGGATATGGTACTGCTCTCGGTGTAATCCGTTCCGTTCA
genomic: ATAAAAGACTCTAAGAATCTGTCTATTTTGACACATTGCAACACTGGAAGgtactgtcct ... gtttcaacagTCTTGCAACAGCTGGATATGGTACTGCTCTCGGTGTAATCCGTTCCGTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagctttccatgtaaaattgttctaatttttttcttttcatattgtttcaacagTCTTGCAACAGCTGGATATGGTACTGCTCTCGGTGTAATCCGTTCCGTTCATGCTGAAGGAATTTTACTGAGGGCCTATTGCACAGAGACACGTCCATTC
                     ttctaat  putative branch site (score: 2)
                           tttttttcttttcata  CT-rich tract
             taaaattgttctaatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgattcactagctggtgaagaaagtgttcaagctgaggtgaagcctgagctttccatgtaaaattgttctaatttttttcttttcatattgtttcaacagTCTTGCAACAGCTGGATATGGTACTGCTCTCGGTGTAATCCGTTCCGTTCATGCTGAAGGAATTTTACTGAGGGCCTATTGCACAGAGACACGTCCATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - -ctagctg
- - - - - - - - gaagaaa
- - - - - - - - - - - - - -tcaagct
- - - - - - - - - - - - - - - - - - - - -agcctga
- - - - - - - - - - - - - - - - - - - - - - - - - - -ccatgta