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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctattaactctagttgtgctgttctctagaggatttaactctgaatctgtgcagaccatgtgaagcttgaattgattttaatattgttaaatcttttcagGTCATCGAACCTGATGTTCAACCTAGCGATCTATGTACACGTCGTGAGTTTGCTCGTTGGTTGGTTTCTGCAAGTAGTGTTCTTTCAAG

Basic information

species Vitis vinifera
transcript Vv16s0050g00600.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g00600.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G30160.1 (Glycine max), 3'ss of exon 3
-------ctattaactctagttgtgctgttctctagaggatttaactctgaatctgtgcagaccatgtgaagcttgaattgattttaatattgttaaatcttttcagGTCATCGAACCTGATGTTCAACCTAGCGATCTATGTACACGTCGTGAGTTTGCTCGTTGGTTGGTTTCTGCAAGTAGTGTTCTTTCAAG
        | |    | ||||   | | ||   ||    || | | |||||   |  | | |   ||  |   |||  || | ||  | ||| ||| ||| ||  ||||||| || ||||||||||||||||| ||| |||||||||||||||| | |||||| |||||||||||||| || |||| |||||||||
taaacatatctctgatttagtgtggatatttgttaatatatattattctgatcataagtaaaggttgcta---ttg--ttcacttggacattattacatcctt--agGTCATTGAGCCTGATGTTCAACCTAGTGATTTATGTACACGTCGTGAATATGCTCGCTGGTTGGTTTCTGCTAGCAGTGCTCTTTCAAG

upper sequence: Vv16s0050g00600.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G25200.1 (Glycine max), 3'ss of exon 7
ctattaactctagttgtgctgttctctagaggatttaactctgaatctgtgcagaccatgtgaa------gcttgaattgattttaatattgttaaatcttttcagGTCATCGAACCTGATGTTCAACCTAGCGATCTATGTACACGTCGTGAGTTTGCTCGTTGGTTGGTTTCTGCAAGTAGTGTTCTTTCAAG
   | |||  |   | || | |  | | ||  ||||     |  || | | | || |||  |||      |||    || | ||  | ||||||| ||| ||  ||||||| || ||||||||||||||||| ||| |||||||||| ||||| | |||||| |||||||| ||||| || |||| |||||||||
---taaacattgtctctgatttagtgtggat-atttgttaatttatttattctgatcataagaaaaggttgctattgttcacttggaaattgttacatcctt--agGTCATTGAGCCTGATGTTCAACCTAGTGATTTATGTACACGCCGTGAATATGCTCGCTGGTTGGTGTCTGCTAGCAGTGCTCTTTCAAG

upper sequence: Vv16s0050g00600.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G37850.1 (Glycine max), 3'ss of exon 6
ctattaactctagttgtgctgttctctag-aggatttaactctgaatctgtgcagaccatgtgaagcttgaattgat--tttaatattgttaaatcttttcagGTCATCGAACCTGATGTTCAACCTAGCGATCTATGTACACGTCGTGAGTTTGCTCGTTGGTTGGTTTCTGCAAGTAGTGTTCTTTCAAG
             |||   | ||    || |  || |  |  |   ||||  ||    || | ||   |  | || |    | | | | |   |  |  ||||||||| |||||||||||||| || || ||| |||| ||||| ||||||| |||||| ||||| || ||||| ||||||| ||| |||||
-----------gtttggattttttcacagtaaaatattccagttggtctgatcat-taatataaaatgtctactgctcacctgaaaatttgctacataatcagGTCATTGAACCTGATGTTCAGCCCAGTGATTTATGCACACGCCGTGAGTATGCTCGATGGTTAGTGTCTGCTAGTAGTGCTCTATCAAG

upper sequence: Vv16s0050g00600.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G29970.1 (Glycine max), 3'ss of exon 2
ctattaactctagtt--gtgctgttctctagaggatttaactctgaatctgtgcagaccatgtgaagcttgaattgat--tttaatattgttaaatcttttcagGTCATCGAACCTGATGTTCAACCTAGCGATCTATGTACACGTCGTGAGTTTGCTCGTTGGTTGGTTTCTGCAAGTAGTGTTCTTTCAAG
    ||  | |||||  ||  | ||  |   |  || |  |  |   ||||  ||    || | ||  ||  | || |    | | | | |   |  |  ||||||||| |||||||||||||| || || ||| |||| ||||  | ||||| |||||  ||||| || ||||| ||||||| ||| |||||
---atagatatagtttggttttttttacagtaaaatattccagttggtctgatcat-taatataaaatttctactgttcacctgaaaatttgctacataatcagGTCATTGAACCTGATGTTCAGCCCAGTGATTTATGCACACACCATGAGTATGCTCAATGGTTAGTGTCTGCTAGTAGTGCTCTATCAAG

upper sequence: Vv16s0050g00600.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G52410.1 (Arabidopsis thaliana), 3'ss of exon 4
ctattaactctagttgtgctgttctctagaggatttaactctgaatctgtgcagaccatgtgaagcttgaattgattttaatattgttaaatcttttcagGTCATCGAACCTGATGTTCAACCTAGCGATCTATGTACACGTCGTGAGTTTGCTCGTTGGTTGGTTTCTGCAAGTAGTGTTCTTTCAAG
    | |||    |     | || |      ||   | || |  || |||| |||   ||   |      ||| ||   ||   | || |||  |||||||| || ||| | |||| ||  |||  |||| |||||||||| ||||| || ||||||||| ||||||||||||| | |  ||| || ||
---gttactgctttcagattatttt------gaccaatcttttgatgtgtgaagatactg---attgcatatttataa-aaccctatttaat--tttcagGTTATTGAATCCGATGCTCTGCCTTACGATTTATGTACACGCCGTGAATTCGCTCGTTGGGTGGTTTCTGCAAGCAATACTCTATCGAG

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|161719035|gb|FC067655.1|FC067655
EST:     TTGTTGATCAAGTCCAGGGACAGGCGCTAGCAGCATTGCAGGTTTTAAAG                         GTCATCGAACCTGATGTTCAACCTAGCGATCTATGTACACGTCGTGAGTTT
genomic: TTGTTGATCAAGTCCAGGGACAGGCGCTAGCAGCATTGCAGGTTTTAAAGgtaccattct ... atcttttcagGTCATCGAACCTGATGTTCAACCTAGCGATCTATGTACACGTCGTGAGTTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtgcagaccatgtgaagcttgaattgattttaatattgttaaatcttttcagGTCATCGAACCTGATGTTCAACCTAGCGATCTATGTACACGTCGTGAGTTTGCTCGTTGGTTGGTTTCTGCAAGTAGTGTTCTTTCAAG
                              ttttaat  putative branch site (score: 3)
                                              tcttttc  putative PPT
                     ttgaattgattttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctattaactctagttgtgctgttctctagaggatttaactctgaatctgtgcagaccatgtgaagcttgaattgattttaatattgttaaatcttttcagGTCATCGAACCTGATGTTCAACCTAGCGATCTATGTACACGTCGTGAGTTTGCTCGTTGGTTGGTTTCTGCAAGTAGTGTTCTTTCAAG

- - - - - - - - tgctgtt
- - - - - - - - - - - - - - - - - - - ctctgaa
- - - - - - - - - - - - - - - - - - - - - - - - -tgcagac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtga