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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGTTGAAACTGATGGTATGGTGAACTGGGATCTGTTGAATGGGGCTTATGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGGgtactttctcatttttgcctctgctctctccagccataatacccatatcagtcactgttcttgtgtacatgttttcacactgaataatttcttttttcag...

Basic information

species Vitis vinifera
transcript Vv12s0028g00960.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0028g00960.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os12g43130.1 (Oryza sativa), 5'ss of exon 1
CCTGTTGAAACTGATGGTATGGTGAACTGGGATCTGT---TGAATGGGGCTTATGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGGgt--actttctcatttttgcctctgctctctccagccataatacccatatcagtcactgttct-tgtgtacatgttttcacactgaataat-ttcttttttcag
   |  | |   || |     ||  ||||||  ||     |    |  || ||  |  | ||||| |||||||| || ||||||||||||||||||||| | |||   |   | ||   ||| ||    ||  || |    |  |     |  | || | |  | | |   | ||    |  |  ||   || | ||| |||  || 
-TGGGCGGAG--GAGGACGCCGTCGACTGGGGCCTCCTCCTCGGCGACGCCTACCACCGCTGCGGCGAGGTCTGCGCCGAGTACGCCAAGACCTTCTACCTAGgtcagccaacccaacattgact--aatcattcaatt--ttgtttttgtcaccgttattactttatcatttcacaggtgaaagctagctactattcgtttgccac

upper sequence: Vv12s0028g00960.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA14G03500.1 (Glycine max), 5'ss of exon 1
---CCTGTTGAAACTGATGGTATGGTGAACTGGGATCTGTTGAATGGGGCTTATGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGGgtactttctcatttttgcctctg---ctctctccagccataatacccatatcagtcactgttcttgtgtacatgttttcacactgaataatttcttttttcag
     ||||||  |||||   |     ||   |||||||||||||| |||||||||| |||| ||||| || ||||||||||| |||||||| || ||||| ||||||| ||  | |||   | ||   || |   ||  ||| ||  |    |||       || | |    | | ||||    |   || || |||   |    
AAAGATGTTGAGGCTGATTTCAAC---AATGTGGATCTGTTGAATGCGGCTTATGATCGGTGTGGTGAAGTTTGTGCTGAGTATGCCAAGACATTTTACTTAGgtacttgctgctcttttgttttgagccttttctcattcattatttctgattcaaatga-attttagccctcttattttttttccccatcatatctaaataa--

upper sequence: Vv12s0028g00960.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA02G45270.1 (Glycine max), 5'ss of exon 1
---CCTGTTGAAACTGATGGTATGGTGAACTGGGATCTGTTGAATGGGGCTTATGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGGgtactttctcatttttgcctctg---ctctctccagccataatacccatatcagtcactgttcttgtgtacatgttttcacactgaataatttcttttttcag
      ||||||   | || | |    ||   ||||||||||||||  ||||||||| |||| ||||| |||||||||||||| |||||||| || ||||| |||||||  | || |||   | ||   ||     ||  ||| ||  |  | |||       || ||||   | | ||||  |||   |||| |   |  |    
AAAGACGTTGAA---GGTGATTTCACCAATGTGGATCTGTTGAATGCAGCTTATGATCGGTGTGGTGAAGTCTGTGCTGAGTATGCCAAGACATTTTACTTAGgtacttgtttatcttttgatttgagccttatctcattcattatttctgtttcaaattgaatttttgtcctcttcttttaccacatcataactaaataatg---

upper sequence: Vv12s0028g00960.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA18G13700.1 (Glycine max), 5'ss of exon 1
-CCTGTTGAAACTGATGGTATGGTGAACTGGGATCTGTTGAATGGGGCTTATGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGGgtactttctcat--ttttgcctctgctctctccagccataatacccatatcagtcactgttcttgtgtacatgttttcacactgaataatttcttttttcag
 ||    |     | || | |     |  |||||||||||| ||  |||||||||||||| ||||| ||||||||||| || |||||||| || ||  | |||||| ||||    |  ||  |  |  || |       |  ||  ||| |    |  |||||   ||    | | | ||   |    || ||| || |    
ACCAACAGTTGAAGGTGATTTAACCCATGGGGATCTGTTGAGTGCTGCTTATGATAGGTGTGGTGAAGTCTGTGCTGAATATGCCAAGACATTTTATCTTggtactctctctctgtcctgttttggtcctttttgtttttcttaatcatttt--cccttgttccaatgagtttttgtgcatttttttaaagttcattataat-

upper sequence: Vv12s0028g00960.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA08G41890.1 (Glycine max), 5'ss of exon 2
CCTGTTGAAACTGATGGTATGGTGAACTGGGATCTGTTGAATGGGGCTTATGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGGgtactttctcatttttgcctctgctctctccagccataatacccatatcagtcactgttcttgtgtacatgttttcacactgaataatttcttttttcag--
||          | || | |    ||  |||||||||||| ||  |||||||||||||| ||||| ||||||||||| || |||||||| || ||  | |||||| ||||  | |  |      | | ||  |   |    ||  |    ||   | ||  |       | || |  || ||| |   | | ||||| |   
CCAACAATTGAAGGTGATTTAACCAATGGGGATCTGTTGAGTGATGCTTATGATAGGTGTGGTGAAGTCTGTGCTGAATATGCCAAGACATTTTATCTAGgtactctctctctctctctgtatgtgtgtcttgttttgg--ccttttcttgtttttcttaatcatcgtctcttgttccaatgagtttgtgcatttttaaagt

upper sequence: Vv12s0028g00960.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S196_120V6.1 (Physcomitrella patens), 5'ss of exon 2
CCTGTTGAAACTGATGGTATGGTGAACTG-GGATCTGTTGAATGGGGCTTATGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGGgtactttctcatttttgcctctgctctctccag---ccataatacccatatcagtcactgttcttgtgtacatgttttcacactgaataatttcttttttcag
 | |    | ||||  |   |     ||| |||  ||||  | | ||| || | | | ||||| ||||| ||||||||||| || |||||||||||||||||||   | ||    | | ||  | |||||  ||   |     || ||    |   | |    |      | |                               
-CGGCCTGACCTGAATGCTGGCACTGCTGCGGAGTTGTTAGACGAGGCATACGTTCGCTGCGGCGAGGTGTGTGCTGAGTATGCGAAGACCTTCTACTTGGgtaagctttc---ctcggcttcgatctctttagtgtcttctgtagcccccccccccccccccccaaaaaaaaaannnnnnnnnnnnnnnnnnnnnnnnnnnnn

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|351022225|gb|FQ438810.1|FQ438810
EST:     TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGG                         GAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
genomic: TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGGgtactttctc ... ctctcctcagGAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
EST: gi|110712808|gb|EE088180.1|EE088180
EST:     TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGG                         GAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
genomic: TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGGgtactttctc ... ctctcctcagGAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
EST: gi|349819154|gb|FQ412048.1|FQ412048
EST:     TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGG                         GAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
genomic: TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGGgtactttctc ... ctctcctcagGAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
EST: gi|349811692|gb|FQ409689.1|FQ409689
EST:     TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGG                         GAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
genomic: TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGGgtactttctc ... ctctcctcagGAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
EST: gi|351029870|gb|FQ427710.1|FQ427710
EST:     TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGG                         GAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
genomic: TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGGgtactttctc ... ctctcctcagGAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
EST: gi|351027652|gb|FQ446819.1|FQ446819
EST:     TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGG                         GAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
genomic: TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGGgtactttctc ... ctctcctcagGAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
EST: gi|349828503|gb|FQ417245.1|FQ417245
EST:     TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGG                         GAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
genomic: TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGGgtactttctc ... ctctcctcagGAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
EST: gi|349830020|gb|FQ420280.1|FQ420280
EST:     TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGG                         GAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
genomic: TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGGgtactttctc ... ctctcctcagGAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
EST: gi|294967171|gb|GW840046.1|GW840046
EST:     TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGG                         GAACCCTACTTATGACTCCAGAGCGACGGAGAGCTGTATGGGCAATTTATG
genomic: TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGGgtactttctc ... ctctcctcagGAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
EST: gi|28959461|gb|CB339731.1|CB339731
EST:     TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGG                         GAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
genomic: TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGGgtactttctc ... ctctcctcagGAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
EST: gi|349822698|gb|FQ412962.1|FQ412962
EST:     TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGG                         GAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
genomic: TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGGgtactttctc ... ctctcctcagGAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
EST: gi|349824582|gb|FQ413249.1|FQ413249
EST:     TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGG                         GAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
genomic: TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGGgtactttctc ... ctctcctcagGAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
EST: gi|349819472|gb|FQ412366.1|FQ412366
EST:     TGATAGGTGCGGTGAGGTCTGTGCTGAGTACCCCCAGACCTTCTACTTGG                         GAACCCTACTTATGACTCCCGAGCGGCGGAGAGCTGTATGGGC
genomic: TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGGgtactttctc ... ctctcctcagGAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGC
EST: gi|29785565|gb|CB342700.2|CB342700
EST:     TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGG                         GAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
genomic: TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGGgtactttctc ... ctctcctcagGAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
EST: gi|351014636|gb|FQ437638.1|FQ437638
EST:     TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGGCCTTCTACTTGG                         GAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
genomic: TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGGgtactttctc ... ctctcctcagGAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
EST: gi|110711026|gb|EE087755.1|EE087755
EST:     TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGG                         GAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG
genomic: TGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGGgtactttctc ... ctctcctcagGAACCCTACTTATGACTCCAGAGCGGCGGAGAGCTGTATGGGCAATTTATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGTTGAAACTGATGGTATGGTGAACTGGGATCTGTTGAATGGGGCTTATGATAGGTGCGGTGAGGTCTGTGCTGAGTACGCCAAGACCTTCTACTTGGgtactttctcatttttgcctctgctctctccagccataatacccatatcagtcactgttcttgtgtacatgttttcacactgaataatttcttttttcag

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