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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGATGATACAAGCATTCGTACAGATGTCAAAGTGCCTATTCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatcatgaactcttttcaccgtatttgtttctcttttgcaaccatatttcttatttgtggtttctttggttccacaaactggagaatactgtttt...

Basic information

species Vitis vinifera
transcript Vv03s0038g00450.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g00450.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA11G11960.3 (Glycine max), 5'ss of exon 3
AGGATGATACAAGCATTCGTACAGATGTCAAAGTGCCTATTCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatcatgaactcttttcaccgtatttgtttctcttttgcaaccatatttcttatttgtggtttc-tttggttccacaaac-----tggagaatactgtttt
|||||||||| |||||    ||||||||||| ||||| || |||||||| ||||| |||||||| ||||| ||||| ||||| ||| ||||||||     |||    || |    |  ||| ||| | |     ||   | || |  |  |  | ||   |    ||  |  |||     |  |   |  ||||||
AGGATGATACTAGCATAGAAACAGATGTCAAGGTGCCAATACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCATgtgag-----tgagtcattctttttgcttttctttttttaaaataatt-tcttgccaagataagattcaatacaatttgaacaaccttcttccaatctgttgtttt

upper sequence: Vv03s0038g00450.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA12G04220.3 (Glycine max), 5'ss of exon 3
AGGATGATACAAGCATTCGTACAGATGTCAAAGTGCCTATTCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatcatgaactcttttcaccgtatttgttt--ctcttttgcaaccatatttcttatttgtggtttctttggttccacaaactggagaatactgtttt
|||||||||| |||||    ||||||||||| ||||| || |||||||| ||||| |||||||| ||||| ||||| ||||| ||| ||||||||  |      || ||||     | ||| |||   |  |||    |||   |  | |  |    |    || |    |    ||  |   |  ||||  
AGGATGATACTAGCATAGAAACAGATGTCAAGGTGCCAATACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCATgtgagtgtgtcattcttttttgcttttctttttttaaataatttcttgccaagataataagattcaatacaatttgaataaacttcttcaatctgttgtt--

upper sequence: Vv03s0038g00450.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT4G34650.1 (Arabidopsis thaliana), 5'ss of exon 3
AGGATGATACAAGCATTCGTACAGATGTCAAAGTGCCTATTCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatcatgaac--tcttttcaccgtatttgtttctcttttgcaaccatatttcttatttgtggtttctttggttccacaaactggagaatactgtttt
||||||| |||||| | |     ||  ||||||| || |||||||||||||| || ||||||||||| ||  |||||||||||||| ||||| || |  | |||    ||||||||  | ||    | ||   || ||   | ||  ||     |  || || |   | || |   | |             
AGGATGACACAAGCGTACCAGTGGAGATCAAAGTTCCAATTCTGATAGCTTTCCACCGTCATATATACGATGGTGACTGGCATTTTTCATgtaagtaataagaagagacttttcac-atcttaacctttcagatgaaattcttttcttttaacttaattactcttcattca-attttag-------------

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|33405611|gb|CF211238.1|CF211238
EST:     TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCAT                         GTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
genomic: TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatca ... ttctgttaagGTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
EST: gi|37185001|gb|CF604354.1|CF604354
EST:     TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCAT                         GTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCAT
genomic: TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatca ... ttctgttaagGTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCAT
EST: gi|110723345|gb|EE100551.1|EE100551
EST:     TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCAT                         GTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
genomic: TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatca ... ttctgttaagGTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
EST: gi|110687328|gb|EE064642.1|EE064642
EST:     TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCAT                         GTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
genomic: TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatca ... ttctgttaagGTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
EST: gi|161707107|gb|FC057297.1|FC057297
EST:     TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCAT                         GTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
genomic: TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatca ... ttctgttaagGTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
EST: gi|37185181|gb|CF604534.1|CF604534
EST:     TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCAT                         GTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATG
genomic: TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatca ... ttctgttaagGTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATG
EST: gi|110687067|gb|EE064151.1|EE064151
EST:     TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCAT                         GTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
genomic: TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatca ... ttctgttaagGTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
EST: gi|110699270|gb|EE076122.1|EE076122
EST:     TCTGATAGCTTTTCATCGTCATATATATGACCGTCACTGGCATTTTGCAT                         GTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
genomic: TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatca ... ttctgttaagGTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
EST: gi|110710584|gb|EE087069.1|EE087069
EST:     TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCAT                         GTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
genomic: TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatca ... ttctgttaagGTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
EST: gi|161717774|gb|FC068163.1|FC068163
EST:     TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCAT                         GTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
genomic: TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatca ... ttctgttaagGTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
EST: gi|161713197|gb|FC063653.1|FC063653
EST:     TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCAT                         GTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
genomic: TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatca ... ttctgttaagGTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
EST: gi|110700987|gb|EE078120.1|EE078120
EST:     TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCAT                         GTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
genomic: TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatca ... ttctgttaagGTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
EST: gi|37186520|gb|CF605873.1|CF605873
EST:     TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCAT                         GTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
genomic: TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatca ... ttctgttaagGTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
EST: gi|110693784|gb|EE070316.1|EE070316
EST:     TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCAT                         GTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
genomic: TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatca ... ttctgttaagGTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
EST: gi|34546786|gb|CF515018.1|CF515018
EST:     TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCAT                         GTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
genomic: TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatca ... ttctgttaagGTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
EST: gi|22007996|gb|BQ793030.1|BQ793030
EST:     TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCAT                         GTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
genomic: TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatca ... ttctgttaagGTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
EST: gi|33405294|gb|CF210921.1|CF210921
EST:     TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCAT                         GTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
genomic: TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatca ... ttctgttaagGTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
EST: gi|71856514|gb|DT005569.1|DT005569
EST:     TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCAT                         GTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
genomic: TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatca ... ttctgttaagGTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
EST: gi|32269974|gb|CD719133.1|CD719133
EST:     TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCAT                         GTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
genomic: TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatca ... ttctgttaagGTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
EST: gi|110725866|gb|EE102817.1|EE102817
EST:     TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCAT                         GTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
genomic: TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatca ... ttctgttaagGTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
EST: gi|110369584|gb|EC933748.1|EC933748
EST:     TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCAT                         GTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
genomic: TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatca ... ttctgttaagGTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
EST: gi|110708357|gb|EE085806.1|EE085806
EST:     TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCAT                         GTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA
genomic: TCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatca ... ttctgttaagGTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGATGATACAAGCATTCGTACAGATGTCAAAGTGCCTATTCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCATgtgaggatcatgaactcttttcaccgtatttgtttctcttttgcaaccatatttcttatttgtggtttctttggttccacaaactggagaatactgtttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagaata