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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAGTACAGAATTTTAATGGTGGGGCGTGTGTTGGGAGGTATCGCCACTTCTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAGgtgagatgttgtcgctttgtccttaatcttaaaatatattagtgctaacaaatttatcttgcatttgttaaattgattaactgtttaattgggcggatca...

Basic information

species Vitis vinifera
transcript Vv16s0098g01290.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0098g01290.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA04G41090.1 (Glycine max), 5'ss of exon 3
TCAGTACAGAATTTTAATGGTGGGGCGTGTGTTGGGAGGTATCGCCACTTCTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAGgtgagatgttgtcgctttgtccttaatcttaaaatatattagtgctaacaaatttatcttgcatttgttaaattgattaactgtttaattgggcggatca-
||| |||| | |  | ||| |||| ||  | ||||||||||| |||||||| || ||||||||||||||||| |||||||||||||||||||||  |||||||||   |  |   ||  |  | ||  |||     | ||  |  | | | ||||    || || |||| | |  |  |  ||    |     |  || | 
TCAATACAAAGTCCTGATGTTGGGCCGCATTTTGGGAGGTATTGCCACTTCACTTCTGTTTTCAGCATTTGAATCATGGCTTGTTGCCGAGCACTTCAAGgtgaggaatatttttttgcttttaaaagttatctgctgtttattatga-atattttctctggatatgttgattataagacatgcaggaagttcctcataat

upper sequence: Vv16s0098g01290.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA06G13760.2 (Glycine max), 5'ss of exon 3
TCAGTACAGAATTTTAATGGTGGGGCGTGTGTTGGGAGGTATCGCCACTTCTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAGgtgagatgttgtcgctttgtccttaatcttaaaatatattagtgctaacaaatttatcttgcatttgttaaattgattaactgtttaattgggcggatca-
||| |||| | |  | ||| |||| ||| | ||||||||||| |||||||| || ||||||||||||||||| || ||||||||||||||||||  |||||||||      |   ||  |  | ||  |||   | | ||  |  | | | || |    || || |||| | || |  |  ||    |     |  || | 
TCATTACAAAGTCCTGATGTTGGGCCGTATTTTGGGAGGTATTGCCACTTCACTTCTGTTTTCAGCATTTGAATCGTGGCTTGTTGCCGAGCACTTCAAGgtgaggaacaattttttgcttttaaaagttatcttctgtttattatga-atatcttctctggatatgttgattttaagacatgcaggaagttcctcataat

upper sequence: Vv16s0098g01290.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: PP1S8_271V6.1 (Physcomitrella patens), 5'ss of exon 3
TCAGTACAGAATTTTAATGGTGGGGCGTGTGTTGGGAGGTATCGCCACTTCTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAGgtg----agatgttgtcgctttgtccttaatcttaaaatatattag---tgctaacaaatttatcttgcatttgttaaattgatta-actgtt--taattgggcggatca-------------------------------------------
    |||||| | || ||| |||| ||||||||||||||||||||||| || || || || ||| |||||||||||||||| || || |||||    |||||     |  |     | ||||    |||   ||   || ||| |    |  | |  || | |  |   |||||     |   ||| |||| |   | |  | || |||                                            
AGCATACAGAGTGTTGATGTTGGGACGTGTGTTGGGAGGTATCGCCACGTCACTGCTTTTCTCATCATTTGAGTCATGGCTCGTGGCTGAGCATTTTAAGgtagctaaactacctacacttttaggttatgtttgcgatgtatcaagtatagtcatgaagtgagttcatatttgggggttattttacactgctgtcattaagacgaatctttaggatacactaacggcgtccttttgcacgtcatggatgtag

upper sequence: Vv16s0098g01290.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: PP1S18_8V6.2 (Physcomitrella patens), 5'ss of exon 3
TCAGTACAGAATTTTAATGGTGGGGCGTGTGTTGGGAGGTATCGCCACTTCTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAGgtgagatgttgtcgctttgtccttaatcttaaaatatattagtgctaacaaatttatcttgcatttgttaaattgattaactgtttaattgggcggatca-------------------------------------------------------------------------------------------------------
  |||||||  | || ||| |||| ||||| |||||||| |||||||| || || || || ||  |||||||||| ||||||||||| |||||    ||||| |     ||   || |  |    || |||   | | || |||    |  ||   |||  |      || ||  |  || |  || |||    || | |                                                                                                       
AGAGTACAGGGTGTTGATGTTGGGACGTGTATTGGGAGGCATCGCCACATCACTGCTTTTCTCTTCATTTGAGTCCTGGCTTGTTGCTGAGCATTTTAAGgttac---ctgagtctctaact---attttaggttttctttgtgacg-cggatcattctctctgcaagtacatacaacaagtaattgattttatggctgaagataaaatggtgttttactgaatcattgtgcgtatgtgtatgtgtatttgtatgtcgaatttaaaactcattgacggtgatttctacttgtcgtcaatacag

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|110688923|gb|EE068027.1|EE068027
EST:     CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAG                         AGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATTTTCAAAGGCGATATTT
genomic: CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAGgtgagatgtt ... atctgtgcagAGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATTTTCAAAGGCAATATTT
EST: gi|161705940|gb|FC054828.1|FC054828
EST:     CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAG                         AGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATTTTCAAAGGCAATATTT
genomic: CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAGgtgagatgtt ... atctgtgcagAGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATTTTCAAAGGCAATATTT
EST: gi|46918112|gb|CN547441.1|CN547441
EST:     CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAG                         AGGGGCTTTGAGCAACAATGGTTGTCTGTGACATTTTCAAAGGCGATATTT
genomic: CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAGgtgagatgtt ... atctgtgcagAGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATTTTCAAAGGCAATATTT
EST: gi|77586406|gb|DV222324.1|DV222324
EST:     CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCATAACAAG                         AGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATTTTCAAAGGCAATATTT
genomic: CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAGgtgagatgtt ... atctgtgcagAGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATTTTCAAAGGCAATATTT
EST: gi|161718412|gb|FC067288.1|FC067288
EST:     CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAG                         AGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATTTTCAAAGGCAATATTT
genomic: CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAGgtgagatgtt ... atctgtgcagAGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATTTTCAAAGGCAATATTT
EST: gi|33402269|gb|CF207896.1|CF207896
EST:     CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAG                         AGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATTTTCAAAGGCAATATTT
genomic: CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAGgtgagatgtt ... atctgtgcagAGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATTTTCAAAGGCAATATTT
EST: gi|33408764|gb|CF214391.1|CF214391
EST:     CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAG                         AGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATTTTCAAAGGCAATATTT
genomic: CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAGgtgagatgtt ... atctgtgcagAGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATTTTCAAAGGCAATATTT
EST: gi|71872970|gb|DT022025.1|DT022025
EST:     CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCATAACAAG                         AGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATTTTCAAAGGCAATATTT
genomic: CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAGgtgagatgtt ... atctgtgcagAGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATTTTCAAAGGCAATATTT
EST: gi|161715635|gb|FC066793.1|FC066793
EST:     CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAG                         AGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATTTTCAAAGGCAATATTT
genomic: CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAGgtgagatgtt ... atctgtgcagAGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATTTTCAAAGGCAATATTT
EST: gi|161706950|gb|FC056819.1|FC056819
EST:     CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAG                         AGGGGCTTTGAGCAACAGTGGTAGTAC-GTGACATTTTCAAAGGCAATATT
genomic: CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAGgtgagatgtt ... atctgtgcagAGGGGCTTTGAGCAACAGTGGTTGT-CTGTGACATTTTCAAAGGCAATATT
EST: gi|71872927|gb|DT021982.1|DT021982
EST:     CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAG                         AGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATT
genomic: CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAGgtgagatgtt ... atctgtgcagAGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATT
EST: gi|161721644|gb|FC069774.1|FC069774
EST:     CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAG                         AGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATTTTCAAAGGCAATATTT
genomic: CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAGgtgagatgtt ... atctgtgcagAGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATTTTCAAAGGCAATATTT
EST: gi|110380688|gb|EC945972.1|EC945972
EST:     CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAG                         AGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATTTTCAAAGGCAATATTT
genomic: CTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAGgtgagatgtt ... atctgtgcagAGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATTTTCAAAGGCAATATTT
EST: gi|161706612|gb|FC057230.1|FC057230
EST:     GCCGAGCACAACAAG                         AGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATTTTCAAAGGCAATATTT
genomic: GCCGAGCACAACAAGgtgagatgtt ... atctgtgcagAGGGGCTTTGAGCAACAGTGGTTGTCTGTGACATTTTCAAAGGCAATATTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAGTACAGAATTTTAATGGTGGGGCGTGTGTTGGGAGGTATCGCCACTTCTCTCCTGTTTTCAGCATTTGAGTCATGGCTTGTTGCCGAGCACAACAAGgtgagatgttgtcgctttgtccttaatcttaaaatatattagtgctaacaaatttatcttgcatttgttaaattgattaactgtttaattgggcggatca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaatata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaattga