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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaaaaattataaattggtttagtcattactctatgagctttataaactctcttatcattaaaggaggttgaactgaaattgagtttttatttttgaagATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCAAGGATGGAGGCTTGTCACTTGCATCTGGTTACATGCTGGTATCATTCAT

Basic information

species Vitis vinifera
transcript Vv16s0100g00640.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0100g00640.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G38290.1 (Glycine max), 3'ss of exon 1
----aaaaaaaattataaattggtttagtcattactctatgagctttataaactctcttatcattaaaggaggttgaactgaaattgagtttttatttttgaagATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCAAGGATGGAGGCTTGTCACTTGCATCTGGTTACATGCTGGTATCATTCAT
       |  | | ||  |   |||||    |||   |||    ||  ||   |||      |  |||     ||||  ||||||    | || | ||||||||||||   ||| |||||||||||   ||| | || ||||| | ||  ||||| |||||||| |||||||||||||| ||||||||||||||  | ||||||
tgtatgcactattcatgtaacagtttaaatgttagcttattttgttcttatgttctag----aggaaaaattattgatttgaaatgttttattcacttttgaagATTGACCAAGATGGGAGCTCTTCGATGGGATAATGTTGTGAATAGACATCAGGGATGGAGACTTGTCACTTGCATTTGGTTACATGCTGGGGTTATTCAT

upper sequence: Vv16s0100g00640.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G07250.1 (Arabidopsis thaliana), 3'ss of exon 1
aaaaaaaattataaattggtttagtcattactctatgagctttataaactctcttatca---ttaaaggaggttgaactgaaattgagtttttatttttgaagATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCAAGGATGGAGGCTTGTCACTTGCATCTGGTTACATGCTGGTATCATTCAT
  |    ||  | |  || |  | | || |   |||| | || | |   |    ||  |   ||  |   | |||   |    ||||   | |||  |||||||||||| ||||| ||||| ||||||||||  ||||||||    ||| |  |||| ||| | ||  | || || || |||||||| || ||| | ||||||
ttactggatcttgagatgttgaaatgatgaagttatgtgattgagagtttgagatacaagattttgatatgattgtgttttggttga---tatatacttgaagATTGGAGAAGTTAGGAGCACTTGAGTGGAGCAAAGTTGTGGAGAAGAAGGAAGGTTGGCGTCTCTTGACATGTATATGGTTACACGCGGGTGTTATTCAT
















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|351035890|gb|FQ463735.1|FQ463735
EST:     TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGAC                         ATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCA
genomic: TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGACgtgaggagta ... atttttgaagATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCA
EST: gi|351055680|gb|FQ452145.1|FQ452145
EST:     TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGAC                         ATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCA
genomic: TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGACgtgaggagta ... atttttgaagATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCA
EST: gi|351034814|gb|FQ458171.1|FQ458171
EST:     TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGAC                         ATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCA
genomic: TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGACgtgaggagta ... atttttgaagATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCA
EST: gi|351047313|gb|FQ451825.1|FQ451825
EST:     TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGAC                         ATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCA
genomic: TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGACgtgaggagta ... atttttgaagATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCA
EST: gi|349814964|gb|FQ410187.1|FQ410187
EST:     TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGAC                         ATTGGAAAAATTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCA
genomic: TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGACgtgaggagta ... atttttgaagATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCA
EST: gi|161718477|gb|FC065046.1|FC065046
EST:     TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGAC                         ATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCA
genomic: TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGACgtgaggagta ... atttttgaagATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCA
EST: gi|349821089|gb|FQ404342.1|FQ404342
EST:     TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGAC                         ATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCA
genomic: TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGACgtgaggagta ... atttttgaagATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCA
EST: gi|351016253|gb|FQ446113.1|FQ446113
EST:     TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGAC                         ATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCA
genomic: TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGACgtgaggagta ... atttttgaagATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCA
EST: gi|351041883|gb|FQ456093.1|FQ456093
EST:     TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGAC                         ATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAA-GTTGTCAGTAAGCATCA
genomic: TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGACgtgaggagta ... atttttgaagATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCA
EST: gi|352789912|gb|FQ478727.1|FQ478727
EST:     TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGAC                         ATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCA
genomic: TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGACgtgaggagta ... atttttgaagATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCA
EST: gi|351048431|gb|FQ448705.1|FQ448705
EST:     TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGAC                         ATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAA-GTTGTCAGTAAGCATCA
genomic: TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGACgtgaggagta ... atttttgaagATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCA
EST: gi|351035144|gb|FQ458501.1|FQ458501
EST:     TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGAC                         ATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCA
genomic: TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGACgtgaggagta ... atttttgaagATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCA
EST: gi|351055425|gb|FQ442023.1|FQ442023
EST:     TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGAC                         ATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCA
genomic: TCGTTTCAGCCTCTGAAGGAGAATCCTCTGTTTGGCCCTTCTTCCAAGACgtgaggagta ... atttttgaagATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaactctcttatcattaaaggaggttgaactgaaattgagtttttatttttgaagATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCAAGGATGGAGGCTTGTCACTTGCATCTGGTTACATGCTGGTATCATTCAT
                                        tttttattttt  CT-rich tract
                                aaattgagtttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaaaaattataaattggtttagtcattactctatgagctttataaactctcttatcattaaaggaggttgaactgaaattgagtttttatttttgaagATTGGAAAAGTTGGGAGCTCTTGAGTGGAAAAAAGTTGTCAGTAAGCATCAAGGATGGAGGCTTGTCACTTGCATCTGGTTACATGCTGGTATCATTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
aaaaaaa
- - - - - - - - - - - - - - - ctctatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaagga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaattga