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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGCTAGAGATGCAAAATGCTCAGGGACTCGCAGATGTATTAATGGAAATGCTTGGTGCTGTGGATCCACGGAAGCCAGAGgtagttattttgtcttctgtcccatttaaaggatcatgaaacagcttcatgtagccagttccattctgaacttagacaagttgcttgcaccatatggctt...

Basic information

species Vitis vinifera
transcript Vv18s0001g01180.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g01180.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA04G42250.1 (Glycine max), 5'ss of exon 7
CTTGCTAGAGATGCAAAATGCTCAGGGACTCGCAGATGTATTAATGGAAATGCTTGGTGCTGTGGATCCACGGAAGCCAGAGgtag--ttattttgtcttctgtcccatttaaaggatcatgaaacagcttcatgtagccagttccattctgaacttagacaagttgcttgcaccatatggctt--
 ||||||||||| ||||||||||| ||||| || |||||||| |||||||||||| | ||  ||  |||     | |  |||||    ||| | |   |  | |    | |      |  |     ||||||||   |  |  ||  || |     |  |  |  |  | |    |    ||||  
TTTGCTAGAGATTCAAAATGCTCAAGGACTAGCTGATGTATTGATGGAAATGCTTAGCGCCTTGAGTCCTAAAGACCGTGAGgtgatattagtattattattattatttctcgttccttttctgctagcttcattctggaacctctgtttttcttgtttatgaagtattggtttga----gctttg

upper sequence: Vv18s0001g01180.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA06G12570.1 (Glycine max), 5'ss of exon 7
CTTGCTAGAGATGCAAAATGCTCAGGGACTCGCAGATGTATTAATGGAAATGCTTGGTGCTGTGGATCCACGGAAGCCAGAGgtagttattttgtcttctgtcccatttaaaggatcatgaaacagcttcatgtagccagttccattctgaacttagacaagttgcttgcaccatatggctt---
 ||||||||||| ||||||||||| ||||| || |||||||| |||||||||||| | ||  || ||||     | |  ||||||  |||| |  ||  | || ||||       |  ||       |         | |||   |  ||    |  |  | | | |||  |  |     |    
TTTGCTAGAGATTCAAAATGCTCAAGGACTAGCTGATGTATTGATGGAAATGCTTAGCGCCTTGAATCCTAAAGACCGTGAGgta--tattattactatt-tctcattctttttctgctggcttcattctggaacctctgtttattcttgtttatgaagtattagtttgagctttgaaattgctg
















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|110697681|gb|EE074884.1|EE074884
EST:     CAGATGTATTAATGGAAATGCTTGGTGCTGTGGATCCACGGAAGCCAGAG                         AGTGTGAAGGACGAAGTGATTGTTGACCTTGTTGACCAGTGCCGCAATTAC
genomic: CAGATGTATTAATGGAAATGCTTGGTGCTGTGGATCCACGGAAGCCAGAGgtagttattt ... atcttggcagAGTGTGAAGGACGAAGTGATTGTTGACCTTGTTGACCAGTGCCGCAATTAC
EST: gi|110724482|gb|EE100348.1|EE100348
EST:     CAGATGTATTAATGGAAATGCTTGGTGCTGTGGATCCACGGAAGCCAGAG                         AGTGTGAAGGACGAAGTGATTGTTGACCTTGTTGACCAGTGCC
genomic: CAGATGTATTAATGGAAATGCTTGGTGCTGTGGATCCACGGAAGCCAGAGgtagttattt ... atcttggcagAGTGTGAAGGACGAAGTGATTGTTGACCTTGTTGACCAGTGCC
EST: gi|32269534|gb|CD718693.1|CD718693
EST:     CAGATGTATTAATGGAAATGCTTGGTGCTGTGGATCCACGGAAGCCAGAG                         AGTGTGAAGGACGAAGTGATTGTTGACCTTGTTGACCAGTGCCGCAATTAC
genomic: CAGATGTATTAATGGAAATGCTTGGTGCTGTGGATCCACGGAAGCCAGAGgtagttattt ... atcttggcagAGTGTGAAGGACGAAGTGATTGTTGACCTTGTTGACCAGTGCCGCAATTAC
EST: gi|110696101|gb|EE074878.1|EE074878
EST:     CAGATGTATTAATGGAAATGCTTGGTGCTGTGGATCCACGGAAGCCAGAG                         AGTGTGAAGGACGAAGTGATTGTTGACCTTGTTGACCAGTGCCGCAATTAC
genomic: CAGATGTATTAATGGAAATGCTTGGTGCTGTGGATCCACGGAAGCCAGAGgtagttattt ... atcttggcagAGTGTGAAGGACGAAGTGATTGTTGACCTTGTTGACCAGTGCCGCAATTAC
EST: gi|294966615|gb|GW839606.1|GW839606
EST:     GGAAATGCTTGGTGCTGTGGATCCACGGAAGCCAGAG                         AGTGTGAAGGACGAAGTGATTGTTGACCTTGTTGACCAGTGCCGCAATTAC
genomic: GGAAATGCTTGGTGCTGTGGATCCACGGAAGCCAGAGgtagttattt ... atcttggcagAGTGTGAAGGACGAAGTGATTGTTGACCTTGTTGACCAGTGCCGCAATTAC
EST: gi|110686103|gb|EE063415.1|EE063415
EST:     CAGATGTATTAATGGAAATGCTTGGTGCTGTGGATCCACGGAAGCCAGAG                         AGTGTGAAGGACGAAGTGATTGTTGACCTTGTTGACCAGTGCCGCAATTAC
genomic: CAGATGTATTAATGGAAATGCTTGGTGCTGTGGATCCACGGAAGCCAGAGgtagttattt ... atcttggcagAGTGTGAAGGACGAAGTGATTGTTGACCTTGTTGACCAGTGCCGCAATTAC
EST: gi|110721049|gb|EE097599.1|EE097599
EST:     CAGATGTATTAATGGAAATGCTTGGTGCTGTGGATCCACGGAAACCAGAG                         AGTGTGAAGGACGAAGTGATTGTTGACCTTGTTGACCAGTGCCCCCATTTA
genomic: CAGATGTATTAATGGAAATGCTTGGTGCTGTGGATCCACGGAAGCCAGAGgtagttattt ... atcttggcagAGTGTGAAGGACGAAGTGATTGTTGACCTTGTTGACCAGTGCCGCAATT-A
EST: gi|161717089|gb|FC069551.1|FC069551
EST:     CAGATGTATTAATGGAAATGCTTGGTGCTGTGGATCCACGGAAGCCAGAG                         AGTGTGAAGGACGAAGTGATTGTTGACCTTGTTGACCAGTGCCGCAATTAC
genomic: CAGATGTATTAATGGAAATGCTTGGTGCTGTGGATCCACGGAAGCCAGAGgtagttattt ... atcttggcagAGTGTGAAGGACGAAGTGATTGTTGACCTTGTTGACCAGTGCCGCAATTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGCTAGAGATGCAAAATGCTCAGGGACTCGCAGATGTATTAATGGAAATGCTTGGTGCTGTGGATCCACGGAAGCCAGAGgtagttattttgtcttctgtcccatttaaaggatcatgaaacagcttcatgtagccagttccattctgaacttagacaagttgcttgcaccatatggctt

- - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaagga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaacag