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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttattatatgtgatctatgttggactgttatggtttgcctctatgttttttgccttctgtgtttgatttagcatcctgactgggaataactttttcagCACATCCATGGGTTAGAGAAGGAGGAGATGCCTCTGAGATTCCGATTGATATTTCTGTTCTGTCCAACATGCGTGAATTTGTCAAGTACAGTCACTTGAA

Basic information

species Vitis vinifera
transcript Vv04s0023g03420.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os02g03410.2 (Oryza sativa), 3'ss of exon 7
---ggttattatatgtgatctatgttggactgttatggtttgcctctatgttttttgccttctgtgtttgatttagcatcctgactgggaat-aactttttcagCACATCCATGGGTTAGAGAAGGAGGAGATGCCTCTGAGATTCCGATTGATATTTCTGTTCTGTCCAACATGCGTGAATTTGTCAAGTACAGTCACTTGAA
    |||  || || | ||||| | | | || | ||    |     |   | ||  | |  ||||   |   |||   |||||  |  |  |  |  | || ||| ||||||||||| |||||||||||||| || |||||||| ||  ||||||| |||||  |||||||||||||| | |||||||||||||| |  || ||
gtaagttcctacatctaatctaagatagtct-taatacaatagtagtgaatcttc-gtcagctgtcaatc-cttactgtcctgtttatgctttgatatgtttagCGCATCCATGGGTAAGAGAAGGAGGAGAAGCATCTGAGATCCCTGTTGATATATCTGTATTGTCCAACATGCGTCAGTTTGTCAAGTACAGCCGTTTTAA

upper sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 9
-ggttattatatgtgatctatgttggactgttat--ggtttgcctctatgttttttgccttctgtgtttgatttagcatcctgactgggaataactttttcagCACATCCATGGGTTAGAGAAGGAGGAGATGCCTCTGAGATTCCGATTGATATTTCTGTTCTGTCCAACATGCGTGAATTTGTCAAGTACAGTCACTTGAA
  ||||  |  | |  |||   ||    ||| |       ||| | ||||| |  |   |  ||  ||   || ||  |  ||| |     ||| | |||||||||||||||||||||||||||||||||| || |  |||||||| |||||||| ||||| |||  |||||||||  | ||||| || || ||||  || ||
aagttac-acttattgtcttcttttatatgtaactaaaagtgcttttatgtgtaat-tgtgttgcattatgttgagtgttttgattaaacctaa-tatttcagCACATCCATGGGTTAGAGAAGGAGGAGAAGCATTGGAGATTCCTATTGATATATCTGTCCTGAGCAACATGCGGCAGTTTGTGAAATATAGTCGATTCAA

upper sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA01G37100.1 (Glycine max), 3'ss of exon 8
ggttattatatgtgatctatgttggactgttatggtttgcctctatgtttttt-------gccttctgtgtttgatttagcatcctgactgggaataactttttcagCACATCCATGGGTTAGAGAAGGAGGAGATGCCTCTGAGATTCCGATTGATATTTCTGTTCTGTCCAACATGCGTGAATTTGTCAAGTACAGTCACTTGAA
       |  |||  ||||  |   | |  | |  |||  ||  | ||  ||        ||  |     | || | |    | |||||      | |  ||| ||||||||||||||||||||||||||||||| || |  |||||||| |||||||| ||||| |||  |||||||||  | ||||| || || ||||  |||||
-------aactgtattctaactataatttgtttcctttatctaaacgtagttaaaacaaagctatacccttatgttgtgttgtactgacgaattctgatatttccagCACATCCATGGGTTAGAGAAGGAGGAGAGGCATTAGAGATTCCTATTGATATATCTGTCCTGAACAACATGCGACAGTTTGTGAAATATAGTCGGTTGAA

upper sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G08180.1 (Glycine max), 3'ss of exon 8
ggttattatatgtgatctatgttggactgttatggtttgcctctatgtttttt-------gccttctgtgtttgatttagcatcctgactgggaataactttttcagCACATCCATGGGTTAGAGAAGGAGGAGATGCCTCTGAGATTCCGATTGATATTTCTGTTCTGTCCAACATGCGTGAATTTGTCAAGTACAGTCACTTGAA
      ||  |||  ||||   |||| | || |   ||  ||  |  | |||        ||  |       || | |    | ||||       | |  |||  |||||||||||||||||||||||||||||| || |  |||||||| |||||||| ||||| |||  |||||||||  | ||||| || || ||||  |||||
------taactgtattcta-actggagtttttttccttatctaaacatatttaaaacaaagctataccctaatgttgtgttgtactgatgaattctgatatttctagCACATCCATGGGTTAGAGAAGGAGGAGAGGCATTAGAGATTCCTATTGATATATCTGTCCTGAACAACATGCGACAGTTTGTGAAATATAGTCGGTTGAA

upper sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA02G05440.1 (Glycine max), 3'ss of exon 7
ggttattatatgtgatctatgttggac-tgttatggtttgcctctatgt-tttttgccttctgtgtttgatttagcatcctgactgggaataactttttcagCACATCCATGGGTTAGAGAAGGAGGAGATGCCTCTGAGATTCCGATTGATATTTCTGTTCTGTCCAACATGCGTGAATTTGTCAAGTACAGTCACTTGAA
  ||||| | |    | | | ||  |  |  |      ||| | ||||| |  |||  ||   | | || |  |   |  ||| |     ||| | ||||||||||||||||||||||||||||||| || || |  |||||||| |||||||| ||||| ||   |||||||||  | ||||| || || ||||   ||||
acttattgtcttctttttttcttatatgtaatcaaaagtgcttttatgtgtaattgtgttgcat-tatgttgaactgttttgattaaacctaa-tatttcagCACATCCATGGGTTAGAGAAGGAGGTGAAGCATTGGAGATTCCTATTGATATATCTGTCCTCAGCAACATGCGGCAGTTTGTGAAATATAGTCGAATGAA

upper sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT2G17890.1 (Arabidopsis thaliana), 3'ss of exon 7
ggttattatatgtgatctatgttggactgttatggtttgcctctatgttttttgccttctgtgtttgatttagcatcctgactgggaataactttttcagCACATCCATGGGTTAGAGAAGGAGGAGATGCCTCTGAGATTCCGATTGATATTTCTGTTCTGTCCAACATGCGTGAATTTGTCAAGTACAGTCACTTGAA
 || |   | |     | || ||  |   ||     |||    ||| |||| ||   | | |||  |  ||       |   |||         || |||||||||||||||||||||||||||||||||| ||||||||||| || || || |||||||||  |||||||||| | ||||| || |  || | | | ||
-gtaagcgttttgacaccattttaaatcatt-----ttgttcttatcttttctgatctttctgtaaggattgtggattttcttgg---------ttgcagCACATCCATGGGTTAGAGAAGGAGGAGATGCATCTGAGATTCCCATAGACATATCTGTTCTGAACAACATGCGTCAGTTTGTGAAATTTAGCCGCCTTAA

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|349814163|gb|FQ414782.1|FQ414782
EST:     GTTACTAGTGAAAGACCCTCGGGCAAGACTTACTGCTGCTCAGGCCCTAT                         CACATCCATGGGTTAGAGAAGGAGGAGATGCCTCTGAGATTCCGATCGATA
genomic: GTTACTAGTGAAAGACCCTCGGGCAAGACTTACTGCTGCTCAGGCCCTATgtgagtatcc ... actttttcagCACATCCATGGGTTAGAGAAGGAGGAGATGCCTCTGAGATTCCGATTGATA
EST: gi|161714014|gb|FC064089.1|FC064089
EST:     GTTACTAGTGAAAGACCCTCGGGCAAGACTTACTGCTGCTCAGGCCCTAT                         CACATCCATGGGTTAGAGAAGGAGGAGATGCCTCTGAGATTCCGATCGATA
genomic: GTTACTAGTGAAAGACCCTCGGGCAAGACTTACTGCTGCTCAGGCCCTATgtgagtatcc ... actttttcagCACATCCATGGGTTAGAGAAGGAGGAGATGCCTCTGAGATTCCGATTGATA
EST: gi|30255725|gb|CB971857.1|CB971857
EST:     GTTACTAGTGAAAGACCCTCGGGCAAGACTTACTGCTGCTTAGGCCCTAT                         CACATCCATGGGTTAGAGAAGGAGGAGATGCCTCTGAGATTCCGATCGATA
genomic: GTTACTAGTGAAAGACCCTCGGGCAAGACTTACTGCTGCTCAGGCCCTATgtgagtatcc ... actttttcagCACATCCATGGGTTAGAGAAGGAGGAGATGCCTCTGAGATTCCGATTGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttttgccttctgtgtttgatttagcatcctgactgggaataactttttcagCACATCCATGGGTTAGAGAAGGAGGAGATGCCTCTGAGATTCCGATTGATATTTCTGTTCTGTCCAACATGCGTGAATTTGTCAAGTACAGTCACTTGAA
                                        gaataac  putative branch site (score: 2)
                                              ctttttc  CT-rich tract
                                         aataacttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttattatatgtgatctatgttggactgttatggtttgcctctatgttttttgccttctgtgtttgatttagcatcctgactgggaataactttttcagCACATCCATGGGTTAGAGAAGGAGGAGATGCCTCTGAGATTCCGATTGATATTTCTGTTCTGTCCAACATGCGTGAATTTGTCAAGTACAGTCACTTGAA

- - - - - - - - - -tgttgga
- - - - - - - - - - - - - - - - - - -tgcctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatcct