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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttttagaaattttgagttagttctggacttcttttggctgtgggatgtgttgtttccattaatttgtacctcgggcctgaacttctttcttggactttggtcagTCACCCATCTCCTTCTGTTCTCATTCCTGCACTTCGCACGGTTGGAAACATTGTCACTGGAGATGATATGCAAACCCAG

Basic information

species Vitis vinifera
transcript Vv14s0060g01510.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g01510.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G29000.1 (Glycine max), 3'ss of exon 6
gtgagtttttagaaattttgagttagttctggacttct----tttggctgtg-ggatgtgt-tgtttccat--taatttgtacctcgggc-ctgaacttctttcttggactttggtcagTCACCCATCTCCTTCTGTTCTCATTCCTGCACTTCGCACGGTTGGAAACATTGTCACTGGAGATGATATGCAAACCCAG
                     || ||| ||   |||||    | ||||| ||   |  | | || | ||||  | ||||  |   |   | || ||  |  | ||      ||  |||| |||||||| ||||| || || |||||||| ||||| || |||||||| ||||||||||||||||||||||| || |||
---------------------gtgagtactctgcttctcaaatatggctatgcaaaaatatatgctcccatgttcattttaatgccaaacactaaatgtgctactc-----ttattcagGCACCCATCCCCTTCAGTGCTAATTCCTGCTCTTCGAACTGTTGGAAATATTGTCACTGGAGATGATATGCAGACACAG

upper sequence: Vv14s0060g01510.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G38320.1 (Glycine max), 3'ss of exon 6
gtgagtttttagaaattttgagttagttctggacttcttttggctgtgggatgtgttgtttccattaatttgtacctcgggcctgaacttctttcttggactttggtcagTCACCCATCTCCTTCTGTTCTCATTCCTGCACTTCGCACGGTTGGAAACATTGTCACTGGAGATGATATGCAAACCCAG
||||||  |  |    |   |  | | | || |    | |  |||     ||||||  |||  ||          |      || ||  || | ||      ||  |||| |||||||| ||||| || || |||||||| ||||| || |||||||| ||||||||||||||||||||||| || |||
gtgagtactctgcttctcgaatatggctatgcaaaaatatatgctccc--atgtgtcattttaatg---------ccaaatactaaatgtcctactc-----ttattcagGCACCCATCCCCTTCAGTGCTAATTCCTGCTCTTCGAACTGTTGGAAATATTGTCACTGGAGATGATATGCAGACTCAG

upper sequence: Vv14s0060g01510.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA19G41770.1 (Glycine max), 3'ss of exon 6
gtgagtttttagaaattttgagttagttctggacttcttttggctgtgggatgtgttgtttccattaatttgtacc-tcgggcctgaacttctttcttggactttggtcagTCACCCATCTCCTTCTGTTCTCATTCCTGCACTTCGCACGGTTGGAAACATTGTCACTGGAGATGATATGCAAACCCAG
                              |    |  | ||  ||        | |||    |   ||  |||   ||       || |  | |  |   |||   |||| ||||| || ||||| || || |||||||| ||||| || |||||||| ||||| |||||||||||| |||| ||  ||
------------------------------gtgagtactatgaatgcaaatatggatgtgcagaaatatacgtattgtcaaattctaaatattattctactcttct-tcagGCACCCTTCCCCTTCAGTGCTTATTCCTGCTCTTCGTACCGTTGGAAATATTGTTACTGGAGATGATTTGCAGACAGAG

upper sequence: Vv14s0060g01510.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ31557 (Selaginella moellendorffii), 3'ss of exon 6
gtgagtttttagaaattttgagttagttctggacttcttttggctgtgggatgtgttgtttccattaatttgtacctcgggcctgaacttctttcttggactttggtcagTCACCCATCTCCTTCTGTTCTCATTCCTGCACTTCGCACGGTTGGAAACATTGTCACTGGAGATGATATGCAAACCCAG
                                             ||  |  ||||  ||  |  | | || || ||  || ||||  ||| |  ||          |||  | || || ||   ||||||||||||||| ||||| ||||| ||||||||||| ||||| || ||| | ||||| |||
---------------------------------------------gtaagtcgtgtctttagctgtgacttttaact--gggctgacgttcctggtt---------ccagGTATCCTTCACCGAATGTTCTCATTCCTGCTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAG

upper sequence: Vv14s0060g01510.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ31559 (Selaginella moellendorffii), 3'ss of exon 2
gtgagtttttagaaattttgagttagttctggacttcttttggctgtgggatgtgttgtttccattaatttgtacctcgggcctgaacttctttcttggactttggtcagTCACCCATCTCCTTCTGTTCTCATTCCTGCACTTCGCACGGTTGGAAACATTGTCACTGGAGATGATATGCAAACCCAG---------------------
                                             ||  |  ||||  ||  |  | | || || ||  |||||||  ||| |  ||          |||  | || || ||   |||||| |||||||| ||||| ||||| ||||||||||| ||||| || ||| | ||||| |||                     
---------------------------------------------gtaagtcgtgtctttagctctgacttttaact--ggcctgacgttcctggtt---------ccagGTATCCTTCACCGAATGTTCTTATTCCTGCTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAGGAAAACTTGAAACGGAACAAC

upper sequence: Vv14s0060g01510.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ38593 (Selaginella moellendorffii), 3'ss of exon 6
gtgagtttttagaaattttgagttagttctggacttcttttggctgtgggatgtgttgtttccattaatttgtacctcgggcctgaacttctttcttggactttggtcagTCACCCATCTCCTTCTGTTCTCATTCCTGCACTTCGCACGGTTGGAAACATTGTCACTGGAGATGATATGCAAACCCAG
                                             ||  |  ||||  ||  |  | | || || ||  |||||||  ||| |  ||          |||  | || || ||   |||||| |||||||| ||||| ||||| ||||||||||| ||||| || ||| | ||||| |||
---------------------------------------------gtaagtcgtgtctttagctctgacttttaact--ggcctgacgttcctggtt---------ccagGTATCCTTCACCGAATGTTCTTATTCCTGCTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAG

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|110359173|gb|EC920237.1|EC920237
EST:     CAAGCTGTTATTGAAGCGGGTGTATGTCCTAGGCTTGTTGAGCTTTTACT                         TCACCCATCTCCTTCTGTTCTCATTCCTGCACTTCGCACGGTTGGAAACAT
genomic: CAAGCTGTTATTGAAGCGGGTGTATGTCCTAGGCTTGTTGAACTTTTACTgtgagttttt ... ctttggtcagTCACCCATCTCCTTCTGTTCTCATTCCTGCACTTCGCACGGTTGGAAACAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttccattaatttgtacctcgggcctgaacttctttcttggactttggtcagTCACCCATCTCCTTCTGTTCTCATTCCTGCACTTCGCACGGTTGGAAACATTGTCACTGGAGATGATATGCAAACCCAG
       cattaat  putative branch site (score: 3)
        attaatttgta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttttagaaattttgagttagttctggacttcttttggctgtgggatgtgttgtttccattaatttgtacctcgggcctgaacttctttcttggactttggtcagTCACCCATCTCCTTCTGTTCTCATTCCTGCACTTCGCACGGTTGGAAACATTGTCACTGGAGATGATATGCAAACCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG