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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCCACGTCTGGACCACTTCGACCTATTGTCCATGGGCAAACTCTGAAGTACAATATGAAAGTTAGGGCTGGCAGAGGATTTTCTCTTGAAGAGCTAAAGgtgtgatgtgctgtcttatgttttggaaattttggaatgatagtttcatttggtcactgtgtttatattattttcccatttaactttttgttctctagaa...

Basic information

species Vitis vinifera
transcript Vv14s0006g00820.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0006g00820.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA09G34760.2 (Glycine max), 5'ss of exon 3
GCCCACGTCTGGACCACTTCGACCTATTGTCCATGGGCAAACTCTGAAGTACAATATGAAAGTTAGGGCTGGCAGAGGATTTTCTCTTGAAGAGCTAAAGgtgtgatgtgctgtcttatgttttggaaattttggaatgatagtttcatttggtcactgtgt-ttatattattttc---ccatttaactttttgttctctagaa
 || ||| ||||||| ||  | || ||||| ||||| |||||| |||| ||||| |||||||| || | ||| || ||||||||||||||||| || |||||   |  || | | |  | ||||       ||   ||     ||  | ||  | |||   |  || || |  ||      | | |||       || ||    
ACCTACGGCTGGACCTCTCAGGCCCATTGTACATGGTCAAACTTTGAAATACAACATGAAAGTGAGAGGTGGAAGGGGATTTTCTCTTGAAGAACTCAAGgtaaaacttg-tatatcctattttaatgtaattattatccagcttgaaatttataactccatgctacatgaagtttgaggtactaaacccaaacctccctg---

upper sequence: Vv14s0006g00820.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA16G08090.1 (Glycine max), 5'ss of exon 3
GCCCACGTCTGGACCACTTCGACCTATTGTCCATGGGCAAACTCTGAAGTACAATATGAAAGTTAGGGCTGGCAGAGGATTTTCTCTTGAAGAGCTAAAGgtgtgatgtgctgtcttatgttttggaaattttggaatgatagtttcatttggtcactgtgtttatattattttcccatttaactttttgttctctagaa------
||| ||  ||||||| ||  | || ||||| ||||| || |||||||| ||||| |||||||| ||  |||| |||||||||||||| |||||| | |||||   ||    |||  |       || | | |    |    |  |    |  || |      ||  | |   | |    ||       || | || |         
GCCTACTGCTGGACCTCTCAGGCCAATTGTTCATGGCCAGACTCTGAAATACAACATGAAAGTCAGATCTGGGAGAGGATTTTCTCTCGAAGAGTTGAAGgtaaaattacttgttctgc----cggcactctccctaaagcaactgttgtgagttatgac--ttgcaatggatccttgattggtggggtgatatcaatgttgtcaa

upper sequence: Vv14s0006g00820.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA16G17370.2 (Glycine max), 5'ss of exon 2
GCCCACGTCTGGACCACTTCGACCTATTGTCCATGGGCAAACTCTGAAGTACAATATGAAAGTTAGGGCTGGCAGAGGATTTTCTCTTGAAGAGCTAAAGgtgtgatgtgctgtcttatgttttggaaattttggaatgatagtttcatttggtcactgtgtttatattattttcccatttaactttttgttctctagaa-----
||| ||  ||||| | ||  | |||||||| ||||| || |||||||| ||||| |||||||| || || || ||||||||||| || |||||  | |||||   |||   | |  |          | | ||| ||    |  |    |  || | ||  ||  |||   |    ||||       |  | |  |||       
GCCTACTGCTGGATCTCTCAGGCCTATTGTTCATGGCCAGACTCTGAAATACAACATGAAAGTCAGAGCCGGGAGAGGATTTTCACTGGAAGAATTGAAGgtaaaatgacttattctgacccc----attcttgcaaaagcaactgttatgagtta-tgacttgctatggatcattcattggtggggtaatacaataggcttgac

upper sequence: Vv14s0006g00820.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT5G23900.1 (Arabidopsis thaliana), 5'ss of exon 3
GCCCACGTCTGGACCACTTCGACCTATTGTCCATGGGCAAACTCTGAAGTACAATATGAAAGTTAGGGCTGGCAGAGGATTTTCTCTTGAAGAGCTAAAGgtgtgatgtgctgtcttatgttttggaaattttggaatgatagtttcatttggtcactgtgtttata--ttattttcccatttaactttttgttctctagaa-
 ||||| ||||| || || |||||| |||| ||||| || || || |||||||| ||||||||||| ||||| | ||||||  ||||||||||||| ||||| ||   |     |||   ||||  ||  ||   | || |   |   | | |  | |  | | | |  | ||  |  | |    ||||||||| | |   | 
TCCCACCTCTGGTCCTCTCCGACCTGTTGTTCATGGTCAGACACTTAAGTACAACATGAAAGTTAGAGCTGGAAAAGGATTCACTCTTGAAGAGCTTAAGgtttggatt-----cttgaatttttcaatgttctaagtgttctctctttatagatattaagatgaaagctcatagttgcttgcttctttttgtttttttttag

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|110372767|gb|EC936956.1|EC936956
EST:     ACAATATGAAAGTTAGGGCTGGCAGAGGATTTTCTCTTGAAGAGCTAAAG                         GCGGCAGGTATTCCNNNNNNNCTTGCTCCGACCATTGGTATTGCTGTTGAT
genomic: ACAATATGAAAGTTAGGGCTGGCAGAGGATTTTCTCTTGAAGAGCTAAAGgtgtgatgtg ... tacattccagGTGGCAGGTATTCCAAAAAAACTTGCTCCGACCATTGGTATTGCTGTTGAT
EST: gi|26256908|gb|CA807971.1|CA807971
EST:     ACAATATGAAAGTTAGGGCTGGCAGAGGATTTTCTCTTGAAGAGCTAAAG                         GTGGCAGGTATTCCNNNNNNNCTTGCTCCGACCATTGGTATTGCTGTTGAT
genomic: ACAATATGAAAGTTAGGGCTGGCAGAGGATTTTCTCTTGAAGAGCTAAAGgtgtgatgtg ... tacattccagGTGGCAGGTATTCCAAAAAAACTTGCTCCGACCATTGGTATTGCTGTTGAT
EST: gi|29781900|gb|CB346727.2|CB346727
EST:     ACAATATGAAAGTTAGGGCTGGCAGAGGATTTTCTCTTGAAGAGCTAAAG                         GCGGCAGGTATTCCNNNNNNNCTTGCTCCGACCATTGGTATTGCTGTTGAT
genomic: ACAATATGAAAGTTAGGGCTGGCAGAGGATTTTCTCTTGAAGAGCTAAAGgtgtgatgtg ... tacattccagGTGGCAGGTATTCCAAAAAAACTTGCTCCGACCATTGGTATTGCTGTTGAT
EST: gi|30303531|gb|CB980325.1|CB980325
EST:     ACAATATGAAAGTTAGGGCTGGCAGAGGATTTTCTCTTGAAGAGCTAAAG                         GCGGCAGGTATTCCNNNNNNNCTTGCTCCGACCATTGGTATTGCTGTTGAT
genomic: ACAATATGAAAGTTAGGGCTGGCAGAGGATTTTCTCTTGAAGAGCTAAAGgtgtgatgtg ... tacattccagGTGGCAGGTATTCCAAAAAAACTTGCTCCGACCATTGGTATTGCTGTTGAT
EST: gi|26256977|gb|CA808040.1|CA808040
EST:     ACAATATGAAAGTTAGGGCTGGCAGAGGATTTTCTCTTGAAGAGCTAAAG                         GCGGCAGGTATTCCNNNNNNNCTTGCTCCGACCATTGGTATTGCTGTTGAT
genomic: ACAATATGAAAGTTAGGGCTGGCAGAGGATTTTCTCTTGAAGAGCTAAAGgtgtgatgtg ... tacattccagGTGGCAGGTATTCCAAAAAAACTTGCTCCGACCATTGGTATTGCTGTTGAT
EST: gi|110387515|gb|EC952187.1|EC952187
EST:     ACAATATGAAAGTTAGGGCTGGCAGAGGATTTTCTCTTGAAGAGCTAAAG                         GTGGCAGGTATTCCNNNNNNNCTTGCTCCGACCATTGGTATTGCTGTTGAT
genomic: ACAATATGAAAGTTAGGGCTGGCAGAGGATTTTCTCTTGAAGAGCTAAAGgtgtgatgtg ... tacattccagGTGGCAGGTATTCCAAAAAAACTTGCTCCGACCATTGGTATTGCTGTTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCCACGTCTGGACCACTTCGACCTATTGTCCATGGGCAAACTCTGAAGTACAATATGAAAGTTAGGGCTGGCAGAGGATTTTCTCTTGAAGAGCTAAAGgtgtgatgtgctgtcttatgttttggaaattttggaatgatagtttcatttggtcactgtgtttatattattttcccatttaactttttgttctctagaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttggaaa