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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttacctttttagttgaaaaaaaataggtttggtcatggttctctggaaattgaaggttcttaaactacatgctaactaaaattgttgtgtgctttattagATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGACCGCTCCACCTCCACGTCTAGCTGATTTTGGCTATTCAAAAGACATATT

Basic information

species Vitis vinifera
transcript Vv05s0049g01180.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 5
-----------ttac-ctttttagttgaaaaaaaataggtttggtcatggttctc-------tg-gaaattgaaggttcttaaacta-catgctaactaaa--attgttgtgtgctt-tattagATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGACCGCTCCACCTCCACGTCTAGCTGATTTTGGCTATTCAAAAGACATATT
           |||  || | |  ||   |  ||    |||| |||||     ||       || || |||| |  |     ||| |  ||||| ||||||  ||| ||    | || ||||||||||||| ||| ||| ||| |||| ||||||||| ||||||||| |    ||| |||| ||||| || |||||||| ||||||||||| |  ||||| ||
gtgagttttcattattctatcttcttttcactaacagagtttcgtcattaacttcacaagcttgtgatattgcatatctgagaacaaatatgctcactaaattatttttcaacgtttctattagATGACCACAAAACCAAGGGAAGTGGATTGGCTCCATGGCCAGCTCGATTAACCTCTCCTCCTCCTCGGCTAGCTGACTTTGGCTATTCCACTGACATTTT

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G04430.1 (Arabidopsis thaliana), 3'ss of exon 5
-----------------ttacctttttagttgaaaaaaaataggtttggtcatggttctctggaaattgaaggttcttaaactacatgctaactaaaattgttgtgtgcttta---ttagATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGACCGCTCCACCTCCACGTCTAGCTGATTTTGGCTATTCAAAAGACATATT
                 ||  || ||  ||||   |     || ||||   |       |  ||  ||   | ||  ||  | | |||  |     |    |||| |  ||||     ||||||||||||| ||| ||| ||||  || ||||||||||||||||||  |||  || | ||||| ||||| || ||||| || |||||||  ||||| ||
gtaagtatttgcttcttttttctgttccgttggttattttgagttttgaggaattaggaccagatctttt-gttttgtatgccatatgtcacagtcatgctttgttttttttaaatacagATGACCATAAAACCAAGGGAAGTGGGTTAGCTCCTTGGCCAGCTAGGTTGACTTCTTCTCCTCCCCGTCTTGCGGATTTCGGTTATTCAACCGACATGTT
















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|110712757|gb|EE088080.1|EE088080
EST:     TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATC                         ATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
genomic: TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATCgtgagtgtct ... gctttattagATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
EST: gi|110699783|gb|EE077083.1|EE077083
EST:     TGTAGCATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATC                         ATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
genomic: TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATCgtgagtgtct ... gctttattagATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
EST: gi|56409526|gb|CX017778.1|CX017778
EST:     TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATC                         ATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
genomic: TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATCgtgagtgtct ... gctttattagATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
EST: gi|351017019|gb|FQ424446.1|FQ424446
EST:     TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATC                         ATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
genomic: TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATCgtgagtgtct ... gctttattagATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
EST: gi|34545484|gb|CF513716.1|CF513716
EST:     TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATC                         ATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
genomic: TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATCgtgagtgtct ... gctttattagATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
EST: gi|56409685|gb|CX017937.1|CX017937
EST:     TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATC                         ATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
genomic: TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATCgtgagtgtct ... gctttattagATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
EST: gi|71858970|gb|DT008025.1|DT008025
EST:     TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATC                         ATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
genomic: TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATCgtgagtgtct ... gctttattagATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
EST: gi|56409742|gb|CX017994.1|CX017994
EST:     TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATC                         ATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
genomic: TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATCgtgagtgtct ... gctttattagATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
EST: gi|349826528|gb|FQ418619.1|FQ418619
EST:     TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATC                         ATGACCATAAATCCACGGGTAGTGCATTGGCTCCATGGCCAGCTAGGGCGA
genomic: TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATCgtgagtgtct ... gctttattagATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
EST: gi|351025738|gb|FQ426752.1|FQ426752
EST:     TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATC                         ATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
genomic: TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATCgtgagtgtct ... gctttattagATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
EST: gi|349830601|gb|FQ416899.1|FQ416899
EST:     TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATC                         ATGACCATAAATCCAGGGGTAGTAAATTGGCTCCTTGGCCAGCTAGGGCGA
genomic: TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATCgtgagtgtct ... gctttattagATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
EST: gi|351027519|gb|FQ446682.1|FQ446682
EST:     TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATC                         ATGACCATAAATCCAGGGGTAGTAAATTGGCTCCTTGGCCAGCTAGGGCGA
genomic: TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATCgtgagtgtct ... gctttattagATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
EST: gi|110716290|gb|EE091140.1|EE091140
EST:     TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATC                         ATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
genomic: TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATCgtgagtgtct ... gctttattagATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
EST: gi|110689293|gb|EE065391.1|EE065391
EST:     TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATC                         ATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
genomic: TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATCgtgagtgtct ... gctttattagATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
EST: gi|110715719|gb|EE094088.1|EE094088
EST:     TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATC                         ATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
genomic: TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATCgtgagtgtct ... gctttattagATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
EST: gi|351024446|gb|FQ426255.1|FQ426255
EST:     TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATC                         ATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
genomic: TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATCgtgagtgtct ... gctttattagATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
EST: gi|349830626|gb|FQ416924.1|FQ416924
EST:     TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATC                         ATGACCATAAATCCAGGGGTAGTAAATTGGCTCCTTGGCCAGCTAGGGCGA
genomic: TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATCgtgagtgtct ... gctttattagATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
EST: gi|110694546|gb|EE071749.1|EE071749
EST:     TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATC                         ATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
genomic: TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATCgtgagtgtct ... gctttattagATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGA
EST: gi|351015441|gb|FQ447270.1|FQ447270
EST:     TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATC                         ATGACCATAAATCCAGGGGTAGTGAAATTGGCT
genomic: TGCAGTATGGGGTGTGCCGATGGAAGCCTGTATCACTCCTTACAGTGATCgtgagtgtct ... gctttattagATGACCATAAATCCAGGGGTAGTGAA-TTGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaattgaaggttcttaaactacatgctaactaaaattgttgtgtgctttattagATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGACCGCTCCACCTCCACGTCTAGCTGATTTTGGCTATTCAAAAGACATATT
                                              ctttatt  CT-rich tract
                           taactaaaattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttacctttttagttgaaaaaaaataggtttggtcatggttctctggaaattgaaggttcttaaactacatgctaactaaaattgttgtgtgctttattagATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGACCGCTCCACCTCCACGTCTAGCTGATTTTGGCTATTCAAAAGACATATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - ggtcatg
- - - - - - - - - - - - - - - - - - - - - - - aaattga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtg