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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACCCCATTTTAATCCACTGAAGAAAGATCATGGCGCTCCTACAGATAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATGgtgtgtaatgtatcttttatctgtatgtaatttgggaattgcgaagagataatatcgcttctttgacaggcttatttcaatgttgtag

Basic information

species Vitis vinifera
transcript Vv08s0007g07280.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g07280.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA16G27020.2 (Glycine max), 5'ss of exon 3
GACCCCATTTTAATCCACTGAAGAAAGATCATGGCGCTCCTACAGATAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATGgtgtgtaatgtatcttttatctgtatgtaatttgggaattgcgaagagataatatcgcttctttg-acaggcttat----------ttcaatgttgtag
| || || || |||||  | ||||| |||||||| |||||| ||||| |  |||||||||||||||||||||| ||||| | ||| || || |||||| | ||   | | | || |   ||| || ||||  | ||   |  |     ||    || | || ||||   | |          |||  | ||||||
GTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATAAGCGCCATGCTGGTGATTTGGGCAACATTGCTGCAGGCCCTGATGgtat-tatcttctttctttttcatatttattttgatatttcttactattctttacgagttgtctgcacagaaatttccaaagagctttctgttttgtag

upper sequence: Vv08s0007g07280.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA16G27020.1 (Glycine max), 5'ss of exon 3
----GACCCCATTTTAATCCACTGAAGAAAGATCATGGCGCTCCTACAGATAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATGgtgtgtaatgtatcttttatctgtatgtaatttgggaattgcgaagagataatatcgcttctttg-acaggcttat----------ttcaatgttgtag
    | || || || |||||  | ||||| |||||||| |||||| ||||| |  |||||||||||||||||||||| ||||| | ||| || || |||||| | ||   | | | || |   ||| || ||||  | ||   |  |     ||    || | || ||||   | |          |||  | ||||||
CCAGGTCCTCACTTCAATCCGTTCAAGAAGGATCATGGGGCTCCTTCAGATGATAAGCGCCATGCTGGTGATTTGGGCAACATTGCTGCAGGCCCTGATGgtat-tatcttctttctttttcatatttattttgatatttcttactattctttacgagttgtctgcacagaaatttccaaagagctttctgttttgtag
















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|349825158|gb|FQ415705.1|FQ415705
EST:     TAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATG                         GAGTTGCTGAGGTTTCAATTAAAGATATGCAG
genomic: TAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATGgtgtgtaatg ... aatgttgtagGAGTTGCTGAGGTTTCAATTAAAGATATGCAG
EST: gi|26263916|gb|CA814979.1|CA814979
EST:     TAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATG                         GAGTTGCTGAGGTT-CAATTAAAGATATGCAG
genomic: TAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATGgtgtgtaatg ... aatgttgtagGAGTTGCTGAGGTTTCAATTAAAGATATGCAG
EST: gi|71870823|gb|DT019878.1|DT019878
EST:     TAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATG                         GAGTTGCTGAGGTTTCAATTAAAGATATGCAG
genomic: TAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATGgtgtgtaatg ... aatgttgtagGAGTTGCTGAGGTTTCAATTAAAGATATGCAG
EST: gi|110429247|gb|EC995737.1|EC995737
EST:     TAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATG                         GAGTTGCTGAGGTTTCAATTAAAGATATGCAG
genomic: TAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATGgtgtgtaatg ... aatgttgtagGAGTTGCTGAGGTTTCAATTAAAGATATGCAG
EST: gi|110392958|gb|EC957655.1|EC957655
EST:     TAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATG                         GAGTTGCTGAGGTTTCAATTAAAGATATGCAG
genomic: TAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATGgtgtgtaatg ... aatgttgtagGAGTTGCTGAGGTTTCAATTAAAGATATGCAG
EST: gi|32456166|gb|CD797340.1|CD797340
EST:     TAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATG                         GAGTTGCTGAGGTTCCAATTAAAGATATGCAG
genomic: TAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATGgtgtgtaatg ... aatgttgtagGAGTTGCTGAGGTTTCAATTAAAGATATGCAG
EST: gi|351040393|gb|FQ434526.1|FQ434526
EST:     TAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATG                         GAGTTGCTGAGGTTTCAATTAAAGATATGCAG
genomic: TAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATGgtgtgtaatg ... aatgttgtagGAGTTGCTGAGGTTTCAATTAAAGATATGCAG
EST: gi|71867553|gb|DT016608.1|DT016608
EST:     TAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATG                         GAGTTGCTGAGGTTTCAATTAAAGATATGCAG
genomic: TAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATGgtgtgtaatg ... aatgttgtagGAGTTGCTGAGGTTTCAATTAAAGATATGCAG
EST: gi|110389316|gb|EC954144.1|EC954144
EST:     TAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATG                         GAGTTGCTGAGGTTTCAATTAAAGATATGCAG
genomic: TAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATGgtgtgtaatg ... aatgttgtagGAGTTGCTGAGGTTTCAATTAAAGATATGCAG
EST: gi|110414987|gb|EC980855.1|EC980855
EST:     TAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATG                         GAGTTGCTGAGGTTTCAATTAAAGATATGCAG
genomic: TAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATGgtgtgtaatg ... aatgttgtagGAGTTGCTGAGGTTTCAATTAAAGATATGCAG
EST: gi|37184575|gb|CF603929.1|CF603929
EST:     TAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATG                         GAGTTGCTGAGGTTTCAATTAAAGATATGCAG
genomic: TAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATGgtgtgtaatg ... aatgttgtagGAGTTGCTGAGGTTTCAATTAAAGATATGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACCCCATTTTAATCCACTGAAGAAAGATCATGGCGCTCCTACAGATAAAGAGCGCCATGCTGGTGATTTGGGAAACATCGTTGCCGGTCCAGATGgtgtgtaatgtatcttttatctgtatgtaatttgggaattgcgaagagataatatcgcttctttgacaggcttatttcaatgttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG