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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATAATTGGCATTCGACAAGGTGAAACAAAGTCCTTTCCACTAGTATTTCCTGAATCATGGAGACAAGAAAATCTCCGTGGTGTTCATGCTCAGTTTACTgtgagttccttttggctatattttgtctatatttctatgtacaactaggcattttagtttgtgaaattgcggcaaagtattttcttgcatcgagctgtta...

Basic information

species Vitis vinifera
transcript Vv19s0090g01210.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0090g01210.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA14G02220.1 (Glycine max), 5'ss of exon 7
AATAATTGGCATTCGACAAGGTGAAACAAAGTCCTTTCCACTAGTATTTCCTGAATCATGGAGACAAGAAAATCTCCGTGGTGTTCATGCTCAGTTTACTgtgagttccttttg----gctatattttgtctatatttctatgtaca--actaggcattttagtttgtgaaattgcggcaaagtattttcttgcatcgagctgtta-
 |||||||| |||| |||||||||| ||||||| ||||| || |||||||||||| ||||||  ||||||||||| || ||||||||||||||||||||||| |||| ||  ||       | |     |  ||  || || | |||  |   | |||  |||||| |    ||  | |        ||     | | |  | ||  
TATAATTGGAATTCAACAAGGTGAATCAAAGTCTTTTCCTCTTGTATTTCCTGAAACATGGAACCAAGAAAATCTTCGAGGTGTTCATGCTCAGTTTACTgtaagtttctaatgctgaatcaaagaagtttaattgttttagggacatgaactgacatgatagtttttttcttttggtc-------ctttggataccaaattcttca

upper sequence: Vv19s0090g01210.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA02G46430.1 (Glycine max), 5'ss of exon 7
AATAATTGGCATTCGACAAGGTGAAACAAAGTCCTTTCCACTAGTATTTCCTGAATCATGGAGACAAGAAAATCTCCGTGGTGTTCATGCTCAGTTTACTgtgagttccttttggctatattttgtctatatttctatgtacaactaggcattttagtttgtgaaattgcggcaaagtattttcttgc-atcgagctgtta-
 |||||||| |||| || ||||||| ||||||| ||||| || |||||||||||| ||||||  ||||||||||| | |||||||||||||||||||||||| |||| ||  || ||  ||        | |  | || |  |   |       | |  ||  |  ||    |      |  | | |  | | |  | ||  
TATAATTGGAATTCAACGAGGTGAATCAAAGTCTTTTCCTCTTGTATTTCCTGAAACATGGAAGCAAGAAAATCTTCATGGTGTTCATGCTCAGTTTACTgtaagtttctaatg-ctgaatcaaagaagtttaaccat-tgtagggacatgacctggcatgatagtttttttcttttggtcctttcgttaccaaattcttca

upper sequence: Vv19s0090g01210.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA14G02390.1 (Glycine max), 5'ss of exon 9
-------------------------------------------------------AATAATTGGCATTCGACAAGGTGAAACAAAGTCCTTTCCA-CTAGTATTTCCTGAATCATGGAGACAAGAAAATCTCCGTGGTGTTCATGCTCAGTTTACTgtgagttccttttggctatattttgtctatatttctatgtacaactaggcattttagtttgtgaaattgcggcaaagtattttcttgcatcgagctgtta
                                                        |||||||| |||| |||||||||| ||||||| ||| || || |||||||||||| ||||||  ||||||||||| || ||||||||||||||||||||||| |||| ||  || ||  |                                                                                
GCTTTAATTTTGATACAGAATATGGTGAAAAAGTATTACCGGGTTTCCTTGATTGTATAATTGGAATTCAACAAGgtgaatcaaagtctttttcatcttgtatttcctgaaacatggaagcaagaaaatcttcgaggtgttcatgctcagtttactgtaagtttctaatg-ctgaa--------------------------------------------------------------------------------

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|351048256|gb|FQ442226.1|FQ442226
EST:     CTGAATCATGGAGACAAGAAAATCTCCGTGGTGTTCATGCTCAGTTTACT                         GTTGAATGCAAGGAATTATTTTATAGAGAGTTACCTGAATTAAACGACTCC
genomic: CTGAATCATGGAGACAAGAAAATCTCCGTGGTGTTCATGCTCAGTTTACTgtgagttcct ... ctttttttagGTTGAATGCAAGGAATTATTTTATAGAGAGTTACCTGAATTAAACGACTCC
EST: gi|254915760|gb|GR905191.1|GR905191
EST:     GAATCATGGAGACAAGAAAATCTCCGTGGTGTTCATGCTCAGTTTACT                         GTTGAATGCAAGGAATTATTTTATAGAGAGTTACCTGAATTAAACGACTCC
genomic: GAATCATGGAGACAAGAAAATCTCCGTGGTGTTCATGCTCAGTTTACTgtgagttcct ... ctttttttagGTTGAATGCAAGGAATTATTTTATAGAGAGTTACCTGAATTAAACGACTCC
EST: gi|71868474|gb|DT017529.1|DT017529
EST:     CTGAATCATGGAGACAAGAAAATCTCCGTGGTGTTCATGCTCAGTTTACT                         GTTGAATGCAAGGAATTATTTTATAGAGAGTTACCTGAATTAAACGACTCC
genomic: CTGAATCATGGAGACAAGAAAATCTCCGTGGTGTTCATGCTCAGTTTACTgtgagttcct ... ctttttttagGTTGAATGCAAGGAATTATTTTATAGAGAGTTACCTGAATTAAACGACTCC
EST: gi|351056173|gb|FQ453635.1|FQ453635
EST:     CTGAATCATGGAGACAAGAAAATCTCCGTGGTGTTCATGCTCAGTTTACT                         GTTGAATGCAAGGAATTATTTTATAGAGAGTTACCTGAATTAAACGACTCC
genomic: CTGAATCATGGAGACAAGAAAATCTCCGTGGTGTTCATGCTCAGTTTACTgtgagttcct ... ctttttttagGTTGAATGCAAGGAATTATTTTATAGAGAGTTACCTGAATTAAACGACTCC
EST: gi|351040007|gb|FQ425093.1|FQ425093
EST:     CTGAATCATGGAGACAAGAAAATCTCCGTGGTGTTCATGCTCAGCTTACT                         GTTGAATGCAAGGAATTATTTTATAGAGAGTTACCTGAATTAAACGACTCC
genomic: CTGAATCATGGAGACAAGAAAATCTCCGTGGTGTTCATGCTCAGTTTACTgtgagttcct ... ctttttttagGTTGAATGCAAGGAATTATTTTATAGAGAGTTACCTGAATTAAACGACTCC
EST: gi|254915870|gb|GR905301.1|GR905301
EST:     GAATCATGGAGACAAGAAAATCTCCGTGGTGTTCATGCTCAGTTTACT                         GTTGAATGCAAGGAATTATTTTATAGAGAGTTACCTGAATTAAACGACTCC
genomic: GAATCATGGAGACAAGAAAATCTCCGTGGTGTTCATGCTCAGTTTACTgtgagttcct ... ctttttttagGTTGAATGCAAGGAATTATTTTATAGAGAGTTACCTGAATTAAACGACTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATAATTGGCATTCGACAAGGTGAAACAAAGTCCTTTCCACTAGTATTTCCTGAATCATGGAGACAAGAAAATCTCCGTGGTGTTCATGCTCAGTTTACTgtgagttccttttggctatattttgtctatatttctatgtacaactaggcattttagtttgtgaaattgcggcaaagtattttcttgcatcgagctgtta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcaaag