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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctcaaatgatgacatccctaagtgcacgtcgcttcataaatgctttttcttctttatgtaattacagtaatttagatcccacttaattgttattcatagGTTGAAGCAACAATTGAACATATTTGTCGCCATGAAGGGGAAGGAGCAATTCTTGTATTCCTCACTGGCTGGGATGACATTTCTAATCTACTTGACAAAG

Basic information

species Vitis vinifera
transcript Vv08s0032g01230.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0032g01230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G399212_T01 (Zea mays), 3'ss of exon 11
tctcaaatgatgacatccctaagtgcacgtcg--cttcataaatgctttttcttctttatgtaattacagtaatttagatcccacttaattgttattcatagGTTGAAGCAACAATTGAACATATTTGTCGCCATGAAGGGGAAGGAGCAATTCTTGTATTCCTCACTGGCTGGGATGACATTTCTAATCTACTTGACAAAG
| ||| ||     || ||  || |     | |  ||| ||| |    |   | |    | | ||      |  |    |  || ||   |||  |||  ||||| |||   ||||||||| ||||||||||| ||||||  ||||| ||||| ||||| ||||| |||||||||||||| ||||| || || || |||||  
tgtcacatttgtgca-ccagaactattatttgaacttaatacactgctaaccatacccaggaaaaatagttgctgctaacacctctatgttgacattt-tagGTGGAAAATACAATTGAATATATTTGTCGCTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTACTGGCTGGGATGAAATTTCGAAGCTTCTGGACAAGA

upper sequence: Vv08s0032g01230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G119671_T01 (Zea mays), 3'ss of exon 2
tctcaaatgatgacatccctaagtgcacgtcg--cttcataaatgctttttcttctttatgtaattacagtaatt-tagatcccacttaattgttattcatagGTTGAAGCAACAATTGAACATATTTGTCGCCATGAAGGGGAAGGAGCAATTCTTGTATTCCTCACTGGCTGGGATGACATTTCTAATCTACTTGACAAAG
| ||| ||     || |   || |     | |  ||| ||| |    |   | |    | | ||  | |||  ||    |  || ||   |||  |||  ||||| |||   ||||||||  ||||||||||| ||||||  ||||| ||||| ||||| ||||| |||||||||||||| ||||| || || || |||||  
tgtcacatttgtgca-ctagaactattatttgaacttaatacactgctaaccatacccaggaaaa-atagttgttgctaacacctctatgttgacattt-tagGTGGAAAGTACAATTGAGTATATTTGTCGCTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTACTGGCTGGGATGAAATTTCGAAGCTTCTGGACAAGA

upper sequence: Vv08s0032g01230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G052798_T01 (Zea mays), 3'ss of exon 3
tctcaaatgatgacatccctaagtgcacgtcg--cttcataaatgctttttcttctttatgtaattacagtaatttagatcccacttaattgttattcatagGTTGAAGCAACAATTGAACATATTTGTCGCCATGAAGGGGAAGGAGCAATTCTTGTATTCCTCACTGGCTGGGATGACATTTCTAATCTACTTGACAAAG
| ||| ||     || ||  || |     | |  ||| ||| |    |   | |    | | ||    | |  |    |  || ||   |||  |||  ||||| |||   ||||||||  ||||||||||| ||||||  ||||| ||||| ||||| ||||| |||||||||| ||| ||||| || || || || ||  
tgtcacatttgtgca-ccagaactattatttgaacttaatacactactaaccatacccaggaaaaataattgctgctaacacctctatgttgacattt-tagGTGGAAAGTACAATTGAGTATATTTGTCGCTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTACTGGCTGGGTTGAAATTTCGAAGCTTCTAGATAAGA

upper sequence: Vv08s0032g01230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM5G863698_T01 (Zea mays), 3'ss of exon 4
tctcaaatgatgacatccctaagtgcacgtcg--cttcataaatgctttttcttctttatgtaattacagtaatttagatcccacttaattgttattcatagGTTGAAGCAACAATTGAACATATTTGTCGCCATGAAGGGGAAGGAGCAATTCTTGTATTCCTCACTGGCTGGGATGACATTTCTAATCTACTTGACAAAG
| ||| ||     || ||  || |     | |  ||| ||| |    |   | |    | | ||      |  |    |  || ||   |||  |||  ||||| |||   ||||||||  ||||||||| | ||||||  ||||| ||||| ||||| ||||| | |||||||||||| ||||| || || || |||||  
tgtcacatttgtgca-ccagaactattatttgaacttaatacactgctaaccatacccaggaaaaatagttgctgctaacacctctatgttgacattt-tagGTGGAAAGTACAATTGAGTATATTTGTCACTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTATTGGCTGGGATGAAATTTCGAAGCTTCTGGACAAGA

upper sequence: Vv08s0032g01230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G395467_T01 (Zea mays), 3'ss of exon 3
tctcaaatgatgacatccctaagtgcacgtcg--cttcataaatgctttttcttctttatgtaattacagtaatttagatcccacttaattgttattcatagGTTGAAGCAACAATTGAACATATTTGTCGCCATGAAGGGGAAGGAGCAATTCTTGTATTCCTCACTGGCTGGGATGACATTTCTAATCTACTTGACAAAG
|  || ||     || ||  || |     | |  ||| ||| |    |   | |    | | ||      |  |    |  || ||   |||  |||  ||||| |||   ||||||||  ||||||||| | ||||||  ||||| ||||| ||||| ||||| | |||||||||||| ||||| || || || |||||  
tgccacatttgtgca-ccagaactattatttgaacttaatacactgctaaccatacccaggaaaaatagttgctgctaacacctctatgttgacattt-tagGTGGAAAGTACAATTGAGTATATTTGTCACTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTATTGGCTGGGATGAAATTTCGAAGCTTCTGGACAAGA

upper sequence: Vv08s0032g01230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA02G35240.1 (Glycine max), 3'ss of exon 12
---tctcaaatgatgacatccctaagtgcacgtcgcttcataaatgctttttcttctttatgtaattacagtaatttagatcccacttaattgttattcatagGTTGAAGCAACAATTGAACATATTTGTCGCCATGAAGGGGAAGGAGCAATTCTTGTATTCCTCACTGGCTGGGATGACATTTCTAATCTACTTGACAAAG
   ||    |     | |||     |    | |  | |||||| || ||    | |||| || || |       |||   |   | |    || | ||   |||| || |||||||||||  |||| |||||| ||||||  |  ||||||||||||||||| ||||||||||||||||| |||||||| || ||||||||| 
taatcagtgagctcaatatcttcctgattccttttcctcataa-tgattcaaatactttttg-aagtgtgcctgtttcattttaattactatgatgttt-cagGTAGAGGCAACAATTGAGTATATATGTCGCAATGAAGCTGGTGGAGCAATTCTTGTATTTCTCACTGGCTGGGATGAAATTTCTAAACTGCTTGACAAAC

upper sequence: Vv08s0032g01230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA10G10180.1 (Glycine max), 3'ss of exon 10
----tctcaaatgatgacatccctaagtgcacgtcgcttcataaatgctttttcttctttatgtaattacagtaatttagatcccacttaat-tgttattcatagGTTGAAGCAACAATTGAACATATTTGTCGCCATGAAGGGGAAGGAGCAATTCTTGTATTCCTCACTGGCTGGGATGACATTTCTAATCTACTTGACAAAG
      | |  | |  |  | ||| | | |  ||  | |||| | || ||    | |||| || || |       |||  ||   | ||| | || | ||   |||| || |||||||||||  |||| |||||  ||||||  |  ||||||||||||||||| ||||||||||||||||| |||||||| || ||||||||| 
agtcagttagctcaatattttcctgattac-tgtt-cctcatga-tgattcaaatcctttttg-aagtgtgcctgtttc-attttagttactatgatgttttcagGTAGAGGCAACAATTGAGTATATATGTCGGAATGAAGCTGGTGGAGCAATTCTTGTATTTCTCACTGGCTGGGATGAAATTTCTAAGCTGCTTGACAAAC

upper sequence: Vv08s0032g01230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 9
-------tctcaaatgatgacatccctaagtgcacgtcgcttca-taaatgctttttcttctttatgtaattacagtaatttagatcccacttaattgttattcatagGTTGAAGCAACAATTGAACATATTTGTCGCCATGAAGGGGAAGGAGCAATTCTTGTATTCCTCACTGGCTGGGATGACATTTCTAATCTACTTGACAAAG
       | |||  | ||    |   ||| | ||  |   | ||    ||    | | ||  | | | |||  ||  |  | |  |     || |   |   || ||||| || ||||||||||||||||||||||| | |||||| |  || || |||||||| ||||| |||||||||||||| ||||| || || ||||| ||| 
gtatgaatttcactttattctcttggtaa-tccagctaattccagcccatatcatcttttactgaag-aatctcatca--tgaactgatctttgaaactctgtcgtagGTGGAGGCAACAATTGAACATATTTGTCGTCTTGAAGGTGGTGGGGCGATTCTTGTCTTCCTTACTGGCTGGGATGAGATTTCAAAACTGCTTGAAAAAA

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|352778146|gb|FQ468808.1|FQ468808
EST:     CAAGACGTTCTCTTGAAGCTTGGTCTGGTTCACAGCTTGATTTGGGTCTT                         GTTGAAGCAACATTTGAACATATTTGTCGCCCTGAAGGGGAA
genomic: CAAGACGTTCTCTTGAAGCTTGGTCTGGTTCACAGCTTGATTTGGGTCTTgtatgtacct ... ttattcatagGTTGAAGCAACAATTGAACATATTTGTCGCCATGAAGGGGAA
EST: gi|352764590|gb|FQ472947.1|FQ472947
EST:     CAAGACGTTCTCTTGAAGCTTGGTCTGGTTCACAGCTTGATTTGGGTCTT                         GTTGAAGCAACAATTGAACATATTTGTC
genomic: CAAGACGTTCTCTTGAAGCTTGGTCTGGTTCACAGCTTGATTTGGGTCTTgtatgtacct ... ttattcatagGTTGAAGCAACAATTGAACATATTTGTC
EST: gi|352773574|gb|FQ472356.1|FQ472356
EST:     CAAGACGTTCTCTTGAAGCTTGGTCTGGTTCACAGCTTGATTTGGGTCTT                         GTTGAAGCAACAATTGAACATATTTGTCGCCATGAAGGGGAAGGAGCA-TT
genomic: CAAGACGTTCTCTTGAAGCTTGGTCTGGTTCACAGCTTGATTTGGGTCTTgtatgtacct ... ttattcatagGTTGAAGCAACAATTGAACATATTTGTCGCCATGAAGGGGAAGGAGCAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcttctttatgtaattacagtaatttagatcccacttaattgttattcatagGTTGAAGCAACAATTGAACATATTTGTCGCCATGAAGGGGAAGGAGCAATTCTTGTATTCCTCACTGGCTGGGATGACATTTCTAATCTACTTGACAAAG
                                    acttaat  putative branch site (score: 4)
        tttatgtaattacagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctcaaatgatgacatccctaagtgcacgtcgcttcataaatgctttttcttctttatgtaattacagtaatttagatcccacttaattgttattcatagGTTGAAGCAACAATTGAACATATTTGTCGCCATGAAGGGGAAGGAGCAATTCTTGTATTCCTCACTGGCTGGGATGACATTTCTAATCTACTTGACAAAG

- - - - - - -catccct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcccact