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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagtgtgttgcattacagagatttttccgcttcttcacacatagtacaatgggaaagttctatctgctgatgaccttgtgttattctaattctaatgcagATTGAAGGAGCATTTGTGCAAGGTCTGGGTTGGGTTGCCTTAGAAGAGCTAAAATGGGGAGATGCAGCTCACAAATGGATTCCACCTGGTTGCCTGTACA

Basic information

species Vitis vinifera
transcript Vv06s0004g02030.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g02030.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G050984_T01 (Zea mays), 3'ss of exon 8
cagtgtgttgcattacagag--atttttccgcttcttcacacatagtacaatgggaaagttctatctgctgatgaccttgtgttattctaattctaatgcagATTGAAGGAGCATTTGTGCAAGGTCTGGGTTGGGTTGCCTTAGAAGAGCTAAAATGGGGAGATGCAGCTCACAAATGGATTCCACCTGGTTGCCTGTACA
  || ||| ||  | | |||  | | ||  |||  ||  |    |  || |  |  | ||||  ||| |  ||  |||   |||   |  | | || | |||||||||||||| ||| | |||||  |||| ||||  ||| ||||||||||||||||||| ||||     || || ||||||| ||||||   ||| | ||
--gtatgt-gctctgcggaggaaatgttttgctaatttgctt-caacacgaaagagaggttccttctacatatttcctgtagtttaacgtactgtatttcagATTGAAGGAGCTTTTATCCAAGGATTGGGCTGGGCAGCCATAGAAGAGCTAAAATGGGGGGATGATAACCATAAGTGGATTCGACCTGGACACCTCTTCA

upper sequence: Vv06s0004g02030.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA13G41520.1 (Glycine max), 3'ss of exon 13
cagtgtgttgcattacagagatttttccgcttcttcacacatagtacaat--gggaaagttctatctgctga--tgaccttgtgttattctaattc--taatgcagATTGAAGGAGCATTTGTGCAAGGTCTGGGTTGGGTTGCCTTAGAAGAGCTAAAATGGGGAGATGCAGCTCACAAATGGATTCCACCTGGTTGCCTGTACA
       || || |      |||||||| |    |     | | ||   |  |    | || |   || | |  | |  || |||| ||   |||   |    ||||| || ||||| ||| | |||||| |||||||||| || |||||||| || ||||||||||||| ||| || |||||||| ||  |||| ||||| ||||
------attccaatttcctaatttttcctccctattcttgaaaataagttttgctgtatttttgcatgataaattcatattttgttcttgctatttattttcacagATCGAGGGAGCTTTTATCCAAGGTTTGGGTTGGGTAGCTTTAGAAGAACTTAAATGGGGAGATGAAGCACATAAATGGATCCCGTCTGGGTGCCTTTACA

upper sequence: Vv06s0004g02030.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT4G34890.1 (Arabidopsis thaliana), 3'ss of exon 12
cagtgtgttgcattacagagatttttccgcttcttcacacatagtacaatgggaaagttctatctgctgatgaccttgtgttattctaattctaatgcagATTGAAGGAGCATTTGTGCAAGGTCTGGGTTGGGTTGCCTTAGAAGAGCTAAAATGGGGAGATGCAGCTCACAAATGGATTCCACCTGGTTGCCTGTACA
  ||| || |   | |    |   | |      |||  |  |  || ||    |  ||| ||||||   |||||       ||||          | ||||| |||||||| ||||| ||||| ||||||||||| || |||||||| || |||||||||||||||||||| |||||||||  ||| ||  |  |   ||
--gtgcgt-gttcttcccttaccctcctatactttcttatcttttagaagaatagtgttgtatctga-aatgac-------tatt----------tacagATAGAAGGAGCGTTTGTACAAGGACTGGGTTGGGTAGCTTTAGAAGAACTCAAATGGGGAGATGCAGCTCATAAATGGATTAAACCAGGAAGTTTACTCA

upper sequence: Vv06s0004g02030.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT4G34900.1 (Arabidopsis thaliana), 3'ss of exon 12
----------------cagtgtgttgca-ttacagagatttttccgcttcttcacacatagtacaat--gggaaagttctatctgctgatgaccttgtgttattctaattctaatgcagATTGAAGGAGCATTTGTGCAAGGTCTGGGTTGGGTTGCCTTAGAAGAGCTAAAATGGGGAGATGCAGCTCACAAATGGATTCCACCTGGTTGCCTGTACA
                ||   |  | |  ||  ||   ||  |  || | ||   |  |  || |||    |||| |  ||        ||   ||     | |  |    |  ||||||| |||||||| ||||| ||||| || |||||||| ||  ||||||| || || ||||||||||||||||| |||||||||  ||| ||  |  |   ||
gtgcgcaatcttctctcaacatcctacgcttttagctgttcgttggccttttgcaatgtt-taaaatccaagaaaatcatagagaaaagtgttatttctgaaattcaccatt--tgcagATAGAAGGAGCGTTTGTACAAGGACTAGGTTGGGTAGCTCTAGAAGAACTCAAGTGGGGAGATGCAGCTCATAAATGGATTAAACCAGGAAGTTTACTCA

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|22014660|gb|BQ799694.1|BQ799694
EST:     TTTTCTTGGATCTTGGACATTCGATAAATCCAGCCATTGATGTTGGACAG                         ATTGAAGGAGCATTTGTGCAAGGTCTGGGTTGGGTTGCCTTAGAAGAGCTA
genomic: TTTTCTTGGATCTTGGACATTCGATAAATCCAGCCATTGATGTTGGACAGgtgctttttc ... tctaatgcagATTGAAGGAGCATTTGTGCAAGGTCTGGGTTGGGTTGCCTTAGAAGAGCTA
EST: gi|22014527|gb|BQ799561.1|BQ799561
EST:     TTTTCTTGGATCTTGGACATTCGATAAATCCAGCCATTGATGTTGGACAG                         ATTGAAGGAGCATTTGTGCAAGGTCTGGGTTGGGTTGCCTTAGAAGAGCTA
genomic: TTTTCTTGGATCTTGGACATTCGATAAATCCAGCCATTGATGTTGGACAGgtgctttttc ... tctaatgcagATTGAAGGAGCATTTGTGCAAGGTCTGGGTTGGGTTGCCTTAGAAGAGCTA
EST: gi|110428986|gb|EC995472.1|EC995472
EST:     CTTGGATCTTGGACATTCCATAAATCCAGCCATTGATGTTGGACAG                         ATTGAAGGAGCATTTGTGCAAGGTCTGGGTTGGGTTGCCTTAGAAGAGCTA
genomic: CTTGGATCTTGGACATTCGATAAATCCAGCCATTGATGTTGGACAGgtgctttttc ... tctaatgcagATTGAAGGAGCATTTGTGCAAGGTCTGGGTTGGGTTGCCTTAGAAGAGCTA
EST: gi|161719982|gb|FC067724.1|FC067724
EST:     TTTTCTTGGATCTTGGACATTCCATAAATCCAGCCATTGATGTTGGACAG                         ATTGAAGGAGCATTT
genomic: TTTTCTTGGATCTTGGACATTCGATAAATCCAGCCATTGATGTTGGACAGgtgctttttc ... tctaatgcagATTGAAGGAGCATTT
EST: gi|22014556|gb|BQ799590.1|BQ799590
EST:     TTTTCTTGGATCTTGGACATTCGATAAATCCAGCCATTGATGTTGGACAG                         ATTGAAGGAGCATTTGTGCAAGGTCTGGGTTGGGTTGCCTTAGAAGAGCTA
genomic: TTTTCTTGGATCTTGGACATTCGATAAATCCAGCCATTGATGTTGGACAGgtgctttttc ... tctaatgcagATTGAAGGAGCATTTGTGCAAGGTCTGGGTTGGGTTGCCTTAGAAGAGCTA
EST: gi|110368506|gb|EC932487.1|EC932487
EST:     TTTTCTTGGATCTTGGACATTCCATAAATCCAGCCATTGATGTTGGACAG                         ATTGAAGGAGCATTTGTGCAAGGTCTGGGTTGGGTTGCCTTAGAAGAGCTA
genomic: TTTTCTTGGATCTTGGACATTCGATAAATCCAGCCATTGATGTTGGACAGgtgctttttc ... tctaatgcagATTGAAGGAGCATTTGTGCAAGGTCTGGGTTGGGTTGCCTTAGAAGAGCTA
EST: gi|161706729|gb|FC055894.1|FC055894
EST:     TTTTCTTGGATCTTGGACATTCCATAAATCCAGCCATTGATGTTGGACAG                         ATTGAAGGAGCATTTGTGCAAGGTCT
genomic: TTTTCTTGGATCTTGGACATTCGATAAATCCAGCCATTGATGTTGGACAGgtgctttttc ... tctaatgcagATTGAAGGAGCATTTGTGCAAGGTCT
EST: gi|110422800|gb|EC989131.1|EC989131
EST:     TTTTCTTGGATCTTGGACATTCCATAAATCCAGCCATTGATGTTGGACAG                         ATTGAAGGAGCATTTGTGCAAGGTCTGGGTTGGGTTGCCTTAGAAGAGCTA
genomic: TTTTCTTGGATCTTGGACATTCGATAAATCCAGCCATTGATGTTGGACAGgtgctttttc ... tctaatgcagATTGAAGGAGCATTTGTGCAAGGTCTGGGTTGGGTTGCCTTAGAAGAGCTA
EST: gi|110699874|gb|EE077267.1|EE077267
EST:     TTTTCTTGGATCTTGGACATTCGATAAATCCAGCCATTGATGTTGGACAG                         ATTGAAGGAGCATTTGTGCAAGGTCTGGGTTGGGTTGCCTTAGAAGAGCTA
genomic: TTTTCTTGGATCTTGGACATTCGATAAATCCAGCCATTGATGTTGGACAGgtgctttttc ... tctaatgcagATTGAAGGAGCATTTGTGCAAGGTCTGGGTTGGGTTGCCTTAGAAGAGCTA
EST: gi|22014924|gb|BQ799958.1|BQ799958
EST:     -TTTCTTGGATCTTGGACATTCGATAAATCCAGCCATTGATG-TGGACAG                         ATTGAAGGAGCATTTGTGCAAGGTCTGGGTTGGGTTGCCTTAGAAGAGCTA
genomic: TTTTCTTGGATCTTGGACATTCGATAAATCCAGCCATTGATGTTGGACAGgtgctttttc ... tctaatgcagATTGAAGGAGCATTTGTGCAAGGTCTGGGTTGGGTTGCCTTAGAAGAGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaatgggaaagttctatctgctgatgaccttgtgttattctaattctaatgcagATTGAAGGAGCATTTGTGCAAGGTCTGGGTTGGGTTGCCTTAGAAGAGCTAAAATGGGGAGATGCAGCTCACAAATGGATTCCACCTGGTTGCCTGTACA
                                            ttctaat  putative branch site (score: 2)
                                   ttattctaattctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagtgtgttgcattacagagatttttccgcttcttcacacatagtacaatgggaaagttctatctgctgatgaccttgtgttattctaattctaatgcagATTGAAGGAGCATTTGTGCAAGGTCTGGGTTGGGTTGCCTTAGAAGAGCTAAAATGGGGAGATGCAGCTCACAAATGGATTCCACCTGGTTGCCTGTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - -tgttgca
- - - - - - - acagaga
- - - - - - - - - - - - - ccgcttc
- - - - - - - - - - - - - - - - - tcacaca
- - - - - - - - - - - - - - - - - - - - - - - caatggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttgtg