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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattcatactttaatttgttagttattctgtatggtctgttctgcattgtcaattgagttagccatcctagtggtggtaacatgaatggattttatttttttccttaattaaaaagtctcttaaattttatttttttgcagGGTGTTCTTCTTTATGGGCCTCCTGGTACTGGGAAGACATTATTAGCTAGAGCAATTGCCAGTAATATAGATGCCAACTTCTTGAAG

Basic information

species Vitis vinifera
transcript Vv18s0001g13090.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g13090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G37220.1 (Glycine max), 3'ss of exon 4
-----gtgattcatacttta--atttgttagttattctgtatggtctgttct------gcattgtcaattgagt---tagccatcctagtggtggtaacatg-----aatggattttattttt--ttccttaattaaaaagtctcttaaattttatttttttgcagGGTGTTCTTCTTTATGGGCCTCCTGGTACTGGGAAGACATTATTAGCTAGAGCAATTGCCAGTAATATAGATGCCAACTTCTTGAAG
      |  ||   ||| ||  | ||| |  ||   || ||| || |||  |      |||||||||  | |||    |    | ||  |||||| |   ||     |   |   |  ||| |  ||   ||  | |  | | ||||     || || | |  |||||||||||||||||||||||||||||||||||||| ||||| |||||||| |||||||||||||| |||||||| ||||||||||| 
ggtgattacttttcactgtactacttggtctttggcctctattgtatgtgttttggcagcattgtcacctaagtatccacattttcttttggtggaagtgtgttttgaggagccatggtttatagttttgtatctgatcaatttcttctcaattcttgtctcccaGGGTGTTCTTCTTTATGGGCCTCCTGGTACTGGGAAAACATTGTTAGCTAGGGCAATTGCCAGTAACATAGATGCTAACTTCTTGAA-

upper sequence: Vv18s0001g13090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G07750.1 (Glycine max), 3'ss of exon 4
----gtgattcatacttta--atttgttagttattctgtatgg--tctgttctg----cattgtcaattgagttagcca----tcctagtggtggtaacatgaatgga-----ttttattttt--ttccttaattaaaaagtctcttaaattttatttttttgcagGGTGTTCTTCTTTATGGGCCTCCTGGTACTGGGAAGACATTATTAGCTAGAGCAATTGCCAGTAATATAGATGCCAACTTCTTGAAG
     |  ||   ||| ||  | ||| |  ||   || ||| |  | |||| ||    ||||||||  | ||| | |||    | ||  ||||||     ||  | ||       |  ||| |  ||   ||  | |    | ||||     || || | |  ||||||||||| ||||||||||||||||||||||| || ||||| |||||||| |||||||||||||| ||||| || ||||||||||||
gtgattacttttcactgtactacttggtctttggcctctattgtatttgttttggcagcattgtcacctaagt-atccacaatttcttttggtggatgtgtgtttagaggagccatggtttatagttttgtatctgatcgatttcttctcaattcttgtctcccagGGTGTTCTCCTTTATGGGCCTCCTGGTACTGGTAAAACATTGTTAGCTAGGGCAATTGCCAGTAACATAGAAGCTAACTTCTTGAAG

upper sequence: Vv18s0001g13090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G03180.1 (Glycine max), 3'ss of exon 4
------------------------------------------------gtgattcatactttaatttgttagttattctgt---atggtctgttctgcattgtcaattgagttagccatcctagtggtggtaacatgaatggattttatttttttccttaattaaaaagtctcttaaattttatttttttgcagGGTGTTCTTCTTTATGGGCCTCCTGGTACTGGGAAGACATTATTAGCTAGAGCAATTGCCAGTAATATAGATGCCAACTTCTTGAAG
                                                 | ||  ||  ||||  || |||||   | |||    |  | | |||| |||  |   ||     |  | |  | ||  |||    |    || ||||||  |||      ||| ||||  ||| || |||| || ||||   ||||||||||| ||||| ||||||||||||||||| || ||||| |||||||| |||||||| |||||||||||||| || ||| | |||
gtgatttacctttttactgctctttctagtctctgatttctattagtgttaatctatgttttagatttttagtagctttgttatgtcattttttctacatatttttttagtggaagcttatttgtaatggccgtacttttgaattttacattt------aatcaaaa--tcttttcaattctaatttt---cagGGTGTTCTCCTTTACGGGCCTCCTGGTACTGGTAAAACATTGTTAGCTAGGGCAATTGCAAGTAATATAGATGCAAATTTCCTAAAG

upper sequence: Vv18s0001g13090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G03230.1 (Glycine max), 3'ss of exon 4
------------------------------------------------gtgattcatactttaatttgttagttattctgt-atgg--tctgttctgcattgtcaattgagttagccatcctagtggtggtaacatgaatggattttatttttttccttaattaaaaagtctcttaaattttatttttttgcagGGTGTTCTTCTTTATGGGCCTCCTGGTACTGGGAAGACATTATTAGCTAGAGCAATTGCCAGTAATATAGATGCCAACTTCTTGAAG
                                                 | ||  ||  ||||  || |||||   | ||| |||   | | | || |||  |   ||     |  | | || ||  |||    |    || ||||||        ||| || ||||  ||| || |||| || ||||   ||||||||||| ||||| ||||||||||||||||| || ||||| ||||| || || |||||||||||||||||||| |||||| | |||
gtgatttaccctttcactgctctttctagtctctgacttctattagtgttaatctatgttttagatttttagtagctttgttatgacatttttcctacatatttttttagtggaagcttacttgtaatggctgtacttttgaattttaca------cttgatcaaaa--tcttttcaattctaatttt---cagGGTGTTCTCCTTTACGGGCCTCCTGGTACTGGTAAAACATTGTTAGCCAGGGCTATTGCCAGTAATATAGATGCTAACTTCCTAAAG

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|30128746|gb|CB914085.1|CB914085
EST:     CTCTAATGAATCCTGAACTCTTTCTTAGAGTTGGAATTAAACCTCCCAAG                         GGTGTTCTTCTTTATGGGCCTCCTGGTACTGGGAAGACATTATTAGCTAGA
genomic: CTCTAATGAATCCTGAACTCTTTCTTAGAGTTGGAATTAAACCTCCCAAGgtgattcata ... ttttttgcagGGTGTTCTTCTTTATGGGCCTCCTGGTACTGGGAAGACATTATTAGCTAGA
EST: gi|30136830|gb|CB922168.1|CB922168
EST:     CTCTAATGAATCCTGAACTCTTTCTTAGAGTTGGAATTANACCTCCCAAG                         GGTGTTCTTCTTTATGGGCCTCCTGGTACTGNGAAGACATTATTAGCTAGA
genomic: CTCTAATGAATCCTGAACTCTTTCTTAGAGTTGGAATTAAACCTCCCAAGgtgattcata ... ttttttgcagGGTGTTCTTCTTTATGGGCCTCCTGGTACTGGGAAGACATTATTAGCTAGA
EST: gi|71859476|gb|DT008531.1|DT008531
EST:     CTCTAATGAATCCTGAACTCTTTCTTAGAGTTGGAATTAAACCTCCCAAG                         GGTGTTCTTCTTTATGGGCCTCCTGGTACTGGGAAGACATTATTAGCTAGA
genomic: CTCTAATGAATCCTGAACTCTTTCTTAGAGTTGGAATTAAACCTCCCAAGgtgattcata ... ttttttgcagGGTGTTCTTCTTTATGGGCCTCCTGGTACTGGGAAGACATTATTAGCTAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggattttatttttttccttaattaaaaagtctcttaaattttatttttttgcagGGTGTTCTTCTTTATGGGCCTCCTGGTACTGGGAAGACATTATTAGCTAGAGCAATTGCCAGTAATATAGATGCCAACTTCTTGAAG
                ccttaat  putative branch site (score: 4)
                                       ttttatttttttgc  putative PPT
     tttatttttttcctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattcatactttaatttgttagttattctgtatggtctgttctgcattgtcaattgagttagccatcctagtggtggtaacatgaatggattttatttttttccttaattaaaaagtctcttaaattttatttttttgcagGGTGTTCTTCTTTATGGGCCTCCTGGTACTGGGAAGACATTATTAGCTAGAGCAATTGCCAGTAATATAGATGCCAACTTCTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG