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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCTTGATGATTTTGTGGATGTGACTAAAGATGAGAAGCAACTAATGCATCTATGGAACTCTTTTGTAAGGAAGCAACGgtaatgtgcaaactcctcctttaattgtgtttttttttttttttgggggggagtctatcatacaattgttttgagcactgtaattgtgtgccttgtgggg...

Basic information

species Vitis vinifera
transcript Vv16s0013g00860.t01
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0013g00860.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: PP1S57_97V6.1 (Physcomitrella patens), 5'ss of exon 18
ATGCTTGATGATTTTGTGGATGTGACTAAAGATGAGAAGCAACTAATGCATCTATGGAACTCTTTTGTAAGGAAGCAACGgtaatgtgcaaactcctcctttaattgtgtt-------tttttttttttttgggggggagtctatcatacaattgttttgagcactgtaattg-tgtgccttgtgggg-----------------------
||||| || |||||||||||||| |||   ||||||||| || | |||||||||||||| || |||||  ||||||| ||||| ||| | |  || |     || ||||||       || | |   || ||    ||| |||    || || | | | |    ||  | ||| | ||    |    |                       
ATGCTAGAAGATTTTGTGGATGTAACTGCGGATGAGAAGGAAATCATGCATCTATGGAATTCGTTTGTGCGGAAGCAGCGgtattgttcta--tcgtgaagaaactgtgttgcaaactttatgtagcttgtgcttaggaatctgatttagaact-tctagtatgctcgatttgatatgtggagcaatggctaattgtgctcgcacatgcag
















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|352768737|gb|FQ467949.1|FQ467949
EST:     GATGAGAAGCAACTAATGCATCTATGGAACTCTTTTGTAAGGAAGCAACG                         GGTGTTAGCAGATGGGCACATTCCTTGGGCATGTGAGGCATTTTCAAGATT
genomic: GATGAGAAGCAACTAATGCATCTATGGAACTCTTTTGTAAGGAAGCAACGgtaatgtgca ... gtgatggcagGGTGTTAGCAGATGGGCACATTCCTTGGGCATGTGAGGCATTTTCAAGATT
EST: gi|349826707|gb|FQ418798.1|FQ418798
EST:     GATGAGAAGCAACTAATGCATCTATGGAACTCTTTTGTAAGGAAGCAACG                         GGTGTTAGCAGATGGGCACATTCCTTGGGCATGTGAGGCATTTTCAAGATT
genomic: GATGAGAAGCAACTAATGCATCTATGGAACTCTTTTGTAAGGAAGCAACGgtaatgtgca ... gtgatggcagGGTGTTAGCAGATGGGCACATTCCTTGGGCATGTGAGGCATTTTCAAGATT
EST: gi|352773492|gb|FQ472274.1|FQ472274
EST:     GATGAGAAGCAACTAATGCATTTATGGAACTCTTTTGTAAGGAAGCAACG                         GGTGTTAGCAGATGGGCACATTCCTTGGGCATGTGAGGCATTTTCAAGATT
genomic: GATGAGAAGCAACTAATGCATCTATGGAACTCTTTTGTAAGGAAGCAACGgtaatgtgca ... gtgatggcagGGTGTTAGCAGATGGGCACATTCCTTGGGCATGTGAGGCATTTTCAAGATT
EST: gi|110406617|gb|EC972196.1|EC972196
EST:     GATGAGAAGCAACTAATGCATCTATGGAACTCTTTTGTAAGGAAGCAACG                         GGTGTTAGCAGATGGGCACATTCCTTGGGCATGTGAGGCATTTTCAAGATT
genomic: GATGAGAAGCAACTAATGCATCTATGGAACTCTTTTGTAAGGAAGCAACGgtaatgtgca ... gtgatggcagGGTGTTAGCAGATGGGCACATTCCTTGGGCATGTGAGGCATTTTCAAGATT
EST: gi|46909877|gb|CN545252.1|CN545252
EST:     GATGAGAAGCAACTAATGCATCTATGGAACTCTTTTGTAAGGAAGCAACG                         GGTGTTAGCAGATGGGCACATTCCTTGGGCATGTGAGGCATTTTCAAGATT
genomic: GATGAGAAGCAACTAATGCATCTATGGAACTCTTTTGTAAGGAAGCAACGgtaatgtgca ... gtgatggcagGGTGTTAGCAGATGGGCACATTCCTTGGGCATGTGAGGCATTTTCAAGATT
EST: gi|77579006|gb|DV218336.1|DV218336
EST:     GATGAGAAGCAACTAATGCATCTATGGAACTCTTTTGTAAGGAAGCAACG                         GGTGTTAGCAGATGGGCACATTCCTTGGGCATGTGAGGCATTTTCAAGATT
genomic: GATGAGAAGCAACTAATGCATCTATGGAACTCTTTTGTAAGGAAGCAACGgtaatgtgca ... gtgatggcagGGTGTTAGCAGATGGGCACATTCCTTGGGCATGTGAGGCATTTTCAAGATT
EST: gi|352774234|gb|FQ474757.1|FQ474757
EST:     GATGAGAAGCAACTAATGCATCTATGGAACTCTTTTGTAAGGAAGCAACG                         GGTGTTAGCAGATGGGCACATTCCTTGGGCATGTGAGGCATTTTCAAGATT
genomic: GATGAGAAGCAACTAATGCATCTATGGAACTCTTTTGTAAGGAAGCAACGgtaatgtgca ... gtgatggcagGGTGTTAGCAGATGGGCACATTCCTTGGGCATGTGAGGCATTTTCAAGATT
EST: gi|349824453|gb|FQ413120.1|FQ413120
EST:     GATGAGAAGCAACTAATGCATCTATGGAACTCTTTTGTAAGGAAGCAACG                         GGTGTTAGCAGATGGGCACATTCCTTGGGCATGTGAGGCATTTTCAAGATT
genomic: GATGAGAAGCAACTAATGCATCTATGGAACTCTTTTGTAAGGAAGCAACGgtaatgtgca ... gtgatggcagGGTGTTAGCAGATGGGCACATTCCTTGGGCATGTGAGGCATTTTCAAGATT
EST: gi|351027451|gb|FQ444700.1|FQ444700
EST:     GATGAGAAGCAACTAATGCATCTATGGAACTCTTTTGTAAGGAAGCAACG                         GGCGTTAGCAGATGGGCACATTCCTTGGGCATGTGAGGCATTTTCAAGATT
genomic: GATGAGAAGCAACTAATGCATCTATGGAACTCTTTTGTAAGGAAGCAACGgtaatgtgca ... gtgatggcagGGTGTTAGCAGATGGGCACATTCCTTGGGCATGTGAGGCATTTTCAAGATT
EST: gi|110406834|gb|EC972420.1|EC972420
EST:     GATGAGAAGCAACTAATGCATCTATGGAACTCTTTTGTAAGGAAGCAACG                         GGTGTTAGCAGATGGGCACATTCCTTGGGCATGTGAGGCATTTTCAAGATT
genomic: GATGAGAAGCAACTAATGCATCTATGGAACTCTTTTGTAAGGAAGCAACGgtaatgtgca ... gtgatggcagGGTGTTAGCAGATGGGCACATTCCTTGGGCATGTGAGGCATTTTCAAGATT
EST: gi|352772283|gb|FQ469808.1|FQ469808
EST:     GATGAGAAGCAACTAATGCATCTATGGAACTCTTTTGTAAGGAAGCAACG                         GGTGTTAGCAGATGGGCACATTCCTTGGGCATGTGAGGCATTTTCAAGATT
genomic: GATGAGAAGCAACTAATGCATCTATGGAACTCTTTTGTAAGGAAGCAACGgtaatgtgca ... gtgatggcagGGTGTTAGCAGATGGGCACATTCCTTGGGCATGTGAGGCATTTTCAAGATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCTTGATGATTTTGTGGATGTGACTAAAGATGAGAAGCAACTAATGCATCTATGGAACTCTTTTGTAAGGAAGCAACGgtaatgtgcaaactcctcctttaattgtgtttttttttttttttgggggggagtctatcatacaattgttttgagcactgtaattgtgtgccttgtgggg

- - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggggag