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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaactgagataaatattgttcgcatataaaggatgggtataaattgtttttagcatgagaaatggaattaattatgtgttgtggaattttctttctacagGGTATTGATGGTTCTAGAGTTGAAAAGGTTCTTGAATCAGTTCACATTGCAGCCAATAAAAACACTGTTCCTGGGGATGTGTCTGCCATGGTTCCTGGTG

Basic information

species Vitis vinifera
transcript Vv18s0001g07960.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA14G36280.2 (Glycine max), 3'ss of exon 12
aaactgagataaatattgttcgcatataaaggatgggtataaattgtttttagcatgagaaatggaattaattatgtgttgtggaattttctttctacagGGTATTGATGGTTCTAGAGTTGAAAAGGTTCTTGAATCAGTTCACATTGCAGCCAATAAAAACACTGTTCCTGGGGATGTGTCTGCCATGGTTCCTGGTG------------
               ||||| |  |  |    ||| |||  | || | |||   |  |  || || |   |  | || |    ||  |    ||  ||||||||||||||||||||| ||||| ||||| || ||| ||||||| || || ||||||||||| || ||||| |||||||||||||| ||||||||||| |            
---------------ttgttgggtttgatttcatgagtagtatttatattttatagcatcaagggga--gagcaggtttcaatgatgtgctgtttgacagggtattgatggttctagGGTTGAGAAGGTACTGGAAGCAGTTCATATAGCTGCCAATAAAAATACCGTTCCAGGGGATGTGTCTGCTATGGTTCCTGGAGGCATTCGAATGG

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA02G38160.2 (Glycine max), 3'ss of exon 12
-----aaactgagataaatattgttcgcatataaaggatgggtataaattgtttttagcatgagaaatggaattaatt-atgtgttgtggaattttctttctacagGGTATTGATGGTTCTAGAGTTGAAAAGGTTCTTGAATCAGTTCACATTGCAGCCAATAAAAACACTGTTCCTGGGGATGTGTCTGCCATGGTTCCTGGTG
     |   | | ||   | |||    |   |  | ||   ||||  ||  ||  |||||| |   |  ||     || |  || ||||   |||       |||||| |||||||||||||| ||||| ||||| || ||| ||||||| || || ||||||||||| |||||||| |||||||||||||| ||||||||||| |
gaaagatgttaatatttttgttgggttcgatttcatgagtagtatttatatttcatagcatcaaggagagagcagttttacatgctgtgctgtttg------acagGGCATTGATGGTTCTAGGGTTGAGAAGGTACTGGAAGCAGTTCATATAGCTGCCAATAAAAATACTGTTCCAGGGGATGTGTCTGCTATGGTTCCTGGAG

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA14G36280.1 (Glycine max), 3'ss of exon 12
--aaactgagataaatattgttcgcatataaaggatgggtataaattgtttttagcatgagaaatggaattaattatgtgttgtggaattttctttctacagGGTATTGATGGTTCTAGAGTTGAAAAGGTTCTTGAATCAGTTCACATTGCAGCCAATAAAAACACTGTTCCTGGGGATGTGTCTGCCATGGTTCCTGGTG
  ||  ||  |  | | ||||| |  |  |    ||| |||  | || | |||   |  |  || || |   |  | || |    ||  |    ||  ||||||||||||||||||||| ||||| ||||| || ||| ||||||| || || ||||||||||| || ||||| |||||||||||||| ||||||||||| |
gaaagatgttaatatttttgttgggtttgatttcatgagtagtatttatattttatagcatcaagggga--gagcaggtttcaatgatgtgctgtttgacagGGTATTGATGGTTCTAGGGTTGAGAAGGTACTGGAAGCAGTTCATATAGCTGCCAATAAAAATACCGTTCCAGGGGATGTGTCTGCTATGGTTCCTGGAG

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT5G26780.3 (Arabidopsis thaliana), 3'ss of exon 12
aaactgagataaatattgttcgcatataaaggatgggtataaattgtttt---tagcatgagaaatggaattaattatgtgttgt-ggaattttctttctacagGGTATTGATGGTTCTAGAGTTGAAAAGGTTCTTGAATCAGTTCACATTGCAGCCAATAAAAACACTGTTCCTGGGGATGTGTCTGCCATGGTTCCTGGTG
    | | ||   || | || | |     |   |  |||  || || ||    ||||      | |    | || ||| || ||| ||||  |   || | ||||| || ||||| || ||||| ||||| ||  | |||| ||| || |||||||| || || || ||||||||||| ||||| |||||||||||||| ||||
----taaaatgtttaatttttgtactgttaaccttagtaggaagtgcttagaatagctaatttactcttgtaaaatatttgatgttggaaaatgggttttgcagGGAATAGATGGATCAAGAGTGGAAAAAGTATTAGAATTAGTACATATTGCAGCAAACAAGAATACTGTTCCTGGTGATGTTTCTGCCATGGTTCCCGGTG

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|161709499|gb|FC058863.1|FC058863
EST:     TATCTGGTGGAACTGATAACCATTTAGTCTTGGTGAATTTAAAAAACAAG                         GGTATTGATGGTTCTAGAGTTGAAAAGGTTCTTGAATCAGTTCACATTGCA
genomic: TATCTGGCGGAACTGATAACCATTTAGTCTTGGTGAATTTGAAAAACAAGgtaataggag ... ctttctacagGGTATTGATGGTTCTAGAGTTGAAAAGGTTCTTGAATCAGTTCACATTGCA
EST: gi|110383662|gb|EC948045.1|EC948045
EST:     TATCTGGCGGAACTGATAACCATTTAGTCTTGGTGAATTTGAAAAACAAG                         GGTATTGATGGTTCTAGAGTTGAAAAGGTTCTTGAATCAGTTCACATTGCA
genomic: TATCTGGCGGAACTGATAACCATTTAGTCTTGGTGAATTTGAAAAACAAGgtaataggag ... ctttctacagGGTATTGATGGTTCTAGAGTTGAAAAGGTTCTTGAATCAGTTCACATTGCA
EST: gi|110361032|gb|EC924482.1|EC924482
EST:     TATCTGGCGGAACTGATAACCATTTAGTCTTGGTGAATTTGAAAAACAAG                         GGTATTGATGGTTCTAGAGTTGAAAAGGTTCTTGAATCAGTTCACATTGCA
genomic: TATCTGGCGGAACTGATAACCATTTAGTCTTGGTGAATTTGAAAAACAAGgtaataggag ... ctttctacagGGTATTGATGGTTCTAGAGTTGAAAAGGTTCTTGAATCAGTTCACATTGCA
EST: gi|351022221|gb|FQ438806.1|FQ438806
EST:     TATCTGGCGGAACTGATAACCATTTAGTCTTGGTGAATTTGAAAAACAAG                         GGTATTGATGGTTCTAGAGTTGAAAAGGTTCTTGAATCAGTTCACATTGCA
genomic: TATCTGGCGGAACTGATAACCATTTAGTCTTGGTGAATTTGAAAAACAAGgtaataggag ... ctttctacagGGTATTGATGGTTCTAGAGTTGAAAAGGTTCTTGAATCAGTTCACATTGCA
EST: gi|351043008|gb|FQ434449.1|FQ434449
EST:     TATCTGGCGGAACTGATAACCATTTAGTCTTGGTGAATTTGAAAAACAAG                         GGTATTGATGGTTCTAGAGTTGAAAAGGTTCTTGAATCAGTTCACATTGCA
genomic: TATCTGGCGGAACTGATAACCATTTAGTCTTGGTGAATTTGAAAAACAAGgtaataggag ... ctttctacagGGTATTGATGGTTCTAGAGTTGAAAAGGTTCTTGAATCAGTTCACATTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttagcatgagaaatggaattaattatgtgttgtggaattttctttctacagGGTATTGATGGTTCTAGAGTTGAAAAGGTTCTTGAATCAGTTCACATTGCAGCCAATAAAAACACTGTTCCTGGGGATGTGTCTGCCATGGTTCCTGGTG
                    aattaat  putative branch site (score: 3)
                                         ttttctttctac  putative PPT
              aaatggaattaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaactgagataaatattgttcgcatataaaggatgggtataaattgtttttagcatgagaaatggaattaattatgtgttgtggaattttctttctacagGGTATTGATGGTTCTAGAGTTGAAAAGGTTCTTGAATCAGTTCACATTGCAGCCAATAAAAACACTGTTCCTGGGGATGTGTCTGCCATGGTTCCTGGTG

- - - agataaa
- - - - - - - - - - - - - - - ggatggg
- - - - - - - - - - - - - - - - - - - - - - - - - - -catgaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatggaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtgga