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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCAGAgtaagtttgaagtctgctagaaattgttaaggtggttttgaattttggtagggtgaaaaattgtgtccccccaccccaccaaaaaaggagaaaactttgg...

Basic information

species Vitis vinifera
transcript Vv18s0001g06010.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g06010.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os01g66240.1 (Oryza sativa), 5'ss of exon 8
TTGTCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCAGAgtaagtttgaagtctgctagaaattgttaaggtggttttgaattttggtagggtgaaaaattgtgtccccccaccccaccaaaaaaggagaaaactttgg--
| |   |||||||||| ||||||||||||||||| |||||||| || ||||| ||||   |||   ||  |   ||| |||   ||| |    | | | |||    |    |||  | |   |  |    |      |    |    |  |    
TGGCTCTGAGCATGGTAGAACAAGCTGCAAAACCGCTTGCACGTCCTGTCAGGgtaatcatgagtacttttctgaatggttttagtg-tgacaattatgggtgatatttctaatctt-ttgtctaagtttattctgtatattgtgtcccctaaag

upper sequence: Vv18s0001g06010.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA01G44190.1 (Glycine max), 5'ss of exon 8
TTGTCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCAGAgtaagtttgaagtctgctagaaattgttaaggtggttttgaattttggtagggtgaaaaattgtgtccccccaccccaccaaaaaa--ggagaaaactttgg------
|||| ||||||||||| || ||||||||||| |||||||| || ||||| ||||||||||  || || | |     ||| |    |||  | ||    ||   | |  | || ||    | |     |  |  | || |  ||   | |  | ||      
TTGTTTTGAGCATGGTAGACCAAGCTGCAAAGCCTCTTGCTCGGCCAGTGAGAgtaagttcaaattcagtttctgtttgct----tggggtaga----tgaaggtgccagaagttactcctctttctcagaaaataatattggttcatatgtgggatctat

upper sequence: Vv18s0001g06010.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA11G01670.1 (Glycine max), 5'ss of exon 8
TTGTCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCAGAgtaagtttgaagtctgctagaaattg-ttaaggtggttttgaattttggtagggtgaaaaattgtgtccccccaccccaccaaaaaaggagaaaactttgg-
|||| |||||||||||||| ||||||||||| || ||||| || ||||| ||||||||||  || || | |     ||| || || | |       |    | ||        |||         ||       | |||   |||     |  | 
TTGTTTTGAGCATGGTGGACCAAGCTGCAAAGCCACTTGCTCGGCCAGTGAGAgtaagttcaaattcagtttctgtttgcttgagatagacgaaggtgccagaagtcaccctcattacagtgtatcatgta--tagaaattaagatgttctcaga

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|30295766|gb|CB972560.1|CB972560
EST:     TCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCAGA                         GTTTGGGTTCTAGATGCAACTCCTGGGAAGGTTCGTCCTGGTGGAGATGGA
genomic: TCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCAGAgtaagtttga ... tttttattagGTTTGGGTTCTAGATGCAACTCCTGGGAAAGTTCGTCCTGGTGGAGATGGA
EST: gi|352776833|gb|FQ472720.1|FQ472720
EST:     TCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCAGA                         GTTTGGGTTCTAGATGCAACTCCTGGGAAAGTTC
genomic: TCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCAGAgtaagtttga ... tttttattagGTTTGGGTTCTAGATGCAACTCCTGGGAAAGTTC
EST: gi|352773576|gb|FQ472358.1|FQ472358
EST:     TCTTGAGCATGGTGGAACAAGCTGCNAAACCTCTTGCACGACCAGTCAGA                         GTTTGGGTTCTAGATGCAACTCCTGGGAAAGTTC
genomic: TCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCAGAgtaagtttga ... tttttattagGTTTGGGTTCTAGATGCAACTCCTGGGAAAGTTC
EST: gi|352769737|gb|FQ468665.1|FQ468665
EST:     TCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCAGA                         GTTTGGGTTCTAGATGCAACTCCTGGGAAAGTTCGTCCTGGTGGAGATGGA
genomic: TCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCAGAgtaagtttga ... tttttattagGTTTGGGTTCTAGATGCAACTCCTGGGAAAGTTCGTCCTGGTGGAGATGGA
EST: gi|352781488|gb|FQ468332.1|FQ468332
EST:     TCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCAGA                         GTTTGGGTTCTAGATGCAACTCCTGGAAAAGTTCGTCCTGGTGGAGATGGA
genomic: TCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCAGAgtaagtttga ... tttttattagGTTTGGGTTCTAGATGCAACTCCTGGGAAAGTTCGTCCTGGTGGAGATGGA
EST: gi|352776761|gb|FQ472648.1|FQ472648
EST:     TCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCAGA                         GTTTGGGTTCTAGATGCAACTCCTGGGGAAAGTTCGTCCTG
genomic: TCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCAGAgtaagtttga ... tttttattagGTTTGGGTTCTAGATGCAACTCCTGGG-AAAGTTCGTCCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCAGAgtaagtttgaagtctgctagaaattgttaaggtggttttgaattttggtagggtgaaaaattgtgtccccccaccccaccaaaaaaggagaaaactttgg

- - - - - - TGGTGG
- - - - - -  GGTGGA
- - - - - - - - - - CAAGCT
- - - - - - - - - -  AAGCTG
- - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagaaaa