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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgacactctcaacttttgtttatattctttttcctttaattggtttgtgggatttccatttcttttaattgtaaccattttaacatgtaattctcagGAAAGAGATGTGAGTGAAGAGTCTGGCTGGAAGCTTGTTCATGGGGATGTTTTCCGGCCTCCTCCCAATTTAGTTCTACTTTCAGCTGTTGTTGGCACAG

Basic information

species Vitis vinifera
transcript Vv12s0035g00280.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os02g34690.1 (Oryza sativa), 3'ss of exon 7
gtgacactctcaacttttgtttatattctttttcctttaattggtttgtgggatttccatttcttttaattgtaaccattttaacatgtaattctcagGAAAGAGATGTGAGTGAAGAGTCTGGCTGGAAGCTTGTTCATGGGGATGTTTTCCGGCCTCCTCCCAATTTAGTTCTACTTTCAGCTGTTGTTGGCACAG
  |  | |  | |  | | || | ||  | |       ||||   || || | ||   |  || | |   ||    |||||| |    | | | ||||||||||||||| |||||||| ||||| ||||||||||| ||||||||||||||||||||||||| || ||| | ||| ||||||||  |||||||    |
--gtgattgactatctatattcaaataatgtaca----aattctgttatgcgcttcatacatcctcttgctga---catttttat---tcaatatcagGAAAGAGATGTCAGTGAAGAATCTGGATGGAAGCTTGTCCATGGGGATGTTTTCCGGCCTCCTCGCAGTTTGGCTCTTCTTTCAGCCCTTGTTGGTGTTG

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os11g07910.1 (Oryza sativa), 3'ss of exon 7
gtgacactctcaacttttgtttatattctttttcctttaattggtttgtgggatttccatttcttttaattgtaaccattttaacatgtaattctc-------agGAAAGAGATGTGAGTGAAGAGTCTGGCTGGAAGCTTGTTCATGGGGATGTTTTCCGGCCTCCTCCCAATTTAGTTCTACTTTCAGCTGTTGTTGGCACAG
|||||      || | || |  |||||| |        |||   ||||    |||| ||| |  | |  |  ||    | ||||| | || || ||       ||||||||||||| ||||| || ||||| ||||||||||| ||||| |||||||||||||||||||  |  || ||  | ||||| ||| ||||||| |  |
gtgactggacgaattatt-tgaatattcatagca----aatcattttgcattattttcatctaatctcttgatagttttgttaacttatatttttcttttatcagGAAAGAGATGTTAGTGAGGAATCTGGTTGGAAGCTTGTCCATGGAGATGTTTTCCGGCCTCCTCGTAGCTTGGTGTTTCTTTCTGCTTTTGTTGGTATTG

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 3'ss of exon 7
gtgacactctcaacttttgttta--tattctttttcctttaattggtttgtgggatttccattt---------cttttaattgtaacc----attttaacatgtaattc-tcagGAAAGAGATGTGAGTGAAGAGTCTGGCTGGAAGCTTGTTCATGGGGATGTTTTCCGGCCTCCTCCCAATTTAGTTCTACTTTCAGCTGTTGTTGGCACAG
     |     | ||||||||||  | |  | ||  || ||     |  || ||||||   ||          |  |  ||||  |||     | || | ||    ||  | |||| |||||||| | ||| || ||||| ||||||||||||||||| ||||| || || |||||||  | ||| |   | ||||| || ||||||||||  |
---gtatatctaccttttgtttaattgtattcttagctctagcatctaagttggatttgttttcacctagtgccactcgattgggacctcaagtcttgatattccttttgttagGAGAGAGATGTTAATGAGGAATCTGGATGGAAGCTTGTTCATGGTGATGTATTTCGCCCTCCTCGAAGTTTGGCCTTTCTTTCTGCAGTTGTTGGCATCG

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G165631_T01 (Zea mays), 3'ss of exon 6
gtgacactctcaacttttgtttatattctttttcc--------tttaattggtttgtggg-----atttccatttcttt-taattgtaaccatt-ttaacatgtaat------tctcagGAAAGAGATGTGAGTGAAGAGTCTGGCTGGAAGCTTGTTCATGGGGATGTTTTCCGGCCTCCTCCCAATTTAGTTCTACTTTCAGCTGTTGTTGGCACAG
||||   |||  |  | || | ||  | || ||||        ||||||   | ||  ||     ||||  |||  ||| || ||||| || ||  | | ||  | |      | | ||||| ||||||| | |||||| ||||| ||||||||||| ||||| ||||||||||||||||||  |||| ||||||| ||||||||| ||||||| |  |
gtgagtttctatatatatgatcatggtgttattccagtagcgttttaatatttatgcaggttctgattttaattagtttatacttgtatcctttgctgatatacattagtttgtattagGAACGAGATGTCAATGAAGAATCTGGATGGAAGCTTGTACATGGTGATGTTTTCCGGCCTCCTTGCAATCTAGTTCTTCTTTCAGCTCTTGTTGGTATTG

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G087212_T01 (Zea mays), 3'ss of exon 7
-------gtgacactctcaacttttgtttatattctttttcctttaattggtttgtgggatttccatttcttttaattgtaaccattttaacatgtaattctcagGAAAGAGATGTGAGTGAAGAGTCTGGCTGGAAGCTTGTTCATGGGGATGTTTTCCGGCCTCCTCCCAATTTAGTTCTACTTTCAGCTGTTGTTGGCACAG
        |||  |   ||| ||     ||    |   |  |   || |  ||  | |  |       || ||||    |||    |  |   |    || ||||||  ||||||| | |||||| || || ||||||||||| ||||| ||||| |||||||||||||        ||  | ||||| ||  | ||||| |  |
aataaaattgaatcatacaagttccaagtaacaacaagtaac---aagtttttctttgactcgatggatcgtttaggattaa--gatacagttttcctttttcagGAGCGAGATGTTAATGAAGAATCCGGGTGGAAGCTTGTCCATGGTGATGTGTTCCGGCCTCCTCGTGGCCAGGTGTTTCTTTCTGCCCTAGTTGGTATTG

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 7
-----------gtgacact---ctcaact-tttgtt---tat-attctttttcctttaattggtttgtgggatttccatttcttttaattgtaaccattt-taacatgtaattctcagGAAAGAGATGTGAGTGAAGAGTCTGGCTGGAAGCTTGTTCATGGGGATGTTTTCCGGCCTCCTCCCAATTTAGTTCTACTTTCAGCTGTTGTTGGCACAG
           |||||  |   || || | |||||    ||| | || |||     ||  |      | |   ||| | || ||  |  | |   ||||| |  ||||    |  ||||| |||||||| |||||||| ||||||||||| ||||| ||||| |||||||| |||||||||| ||| |||||| | |||||||||||||||||||| |
gtgatggtttcgtgacttttatcttaattatttgtggaatatgaatcctttcttactagataaagcattgtggttctaattgttgaatatttggtcatttcttccatgc---ttacagGAGAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAACTTAGTTATTCTTTCAGCTGTTGTTGGCACTG

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 7
-----------gtgacactc-tcaacttttgtttatattctttttcctttaattggtttgtgggat-----ttccatttc-------------------ttttaattgtaa---ccattttaacatgtaa---ttctcagGAAAGAGATGTGAGTGAAGAGTCTGGCTGGAAGCTTGTTCATGGGGATGTTTTCCGGCCTCCTCCCAATTTAGTTCTACTTTCAGCTGTTGTTGGCACAG
            |||   |  ||   |  | ||  |||| || ||  |  ||||  | ||||| |      |||  |||                    || | ||||| |   |   || |||    ||   ||  |||||||||||||| |||||||| ||||||||||| ||||| ||||| |||||||| |||||||||| || ||| ||| | ||||||||||||||||| ||||
gttaggctttcttgatgtttgtctgttactattattattattatttttaaaatttatgtgtggaacatagattctgttttcctggaaagttcattgtggttctgattgtcaattcttgttcaacccccaaatatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTGTTGTTGGTACAG

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 7
------------------------gtgacactctcaacttttgtttatattctttttcctttaattgg--------tttgtgggatttccatttc--ttttaattgtaa---ccattttaacatgta---attctcagGAAAGAGATGTGAGTGAAGAGTCTGGCTGGAAGCTTGTTCATGGGGATGTTTTCCGGCCTCCTCCCAATTTAGTTCTACTTTCAGCTGTTGTTGGCACAG
                        || ||  |    ||| || |||| | | | | |     |  | |        ||  ||| |  | ||||    || | ||||| |   |   || |||    |   |||  |||||||||||||| |||||||| ||||||||||| ||||| ||||| |||||||| |||||||||| || ||| ||| | ||||||||| ||||||| ||||
gtgaggctttcttgatgtttgtctgttactattattactattttttaaaatttatgtgtggaacatagattctactttcctggaaaattcattgtggttctgattgtcaattcttgttcaacccccatacatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTATTGTTGGTACAG

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 7
gtgacactctca--acttttgtttatattctttttc---ctttaa---ttggtttgtgggatttccatttc--ttttaattgt-aaccattttaacatgta------attctcagGAAAGAGATGTGAGTGAAGAGTCTGGCTGGAAGCTTGTTCATGGGGATGTTTTCCGGCCTCCTCCCAATTTAGTTCTACTTTCAGCTGTTGTTGGCACAG
||||   | |||  |||||| | | || |  |||      | | |   ||  ||  | |      ||||    || |||||||  |  ||||   ||| |         |  ||||| |||||||| |||||||| ||||||||||| ||||| ||||| |||||||| || || |||| ||| |||||| | ||||||||||||||||||||||
gtgatggtttcatgacttttatctttaataatttgtggaatatgaacctttcttcctagagaaatcattgtggttctaattgtcgaatatttggtcatttcttccatgcttacagGAGAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGACCGCCTCGCAACTTAGTTATTCTTTCAGCTGTTGTTGGCACAG

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ37593 (Selaginella moellendorffii), 3'ss of exon 7
gtgacactctcaacttttgtttatattctttttcctttaattggtttgtgggatttccatttcttttaattgtaaccattttaacatgtaattctcagGAAAGAGATGTGAGTGAAGAGTCTGGCTGGAAGCTTGTTCATGGGGATGTTTTCCGGCCTCCTCCCAATTTAGTTCTACTTTCAGCTGTTGTTGGCACAG
                                                  | |  |  || |     | ||| |     |  || |  |  ||  |||||||| || ||||||||||||||||| ||||||||||| || || ||||| ||| | || || | | || | ||| | || ||  |  ||||||| || |
--------------------------------------------------gtacgtttatgttgcgca-ttgcagtggctgaaagaact--tttccagGAAAGGGACGTGAGTGAAGAGTCTGGATGGAAGCTTGTCCACGGTGATGTCTTCAGACCGCCACGCTATCTTGTTTTGCTGTCTTCGCTTGTTGGTACCG

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ15096 (Selaginella moellendorffii), 3'ss of exon 7
gtgacactctcaacttttgtttatattctttttcctttaattggtttgtgggatttccatttcttttaattgtaaccattttaacatgtaattctc-agGAAAGAGATGTGAGTGAAGAGTCTGGCTGGAAGCTTGTTCATGGGGATGTTTTCCGGCCTCCTCCCAATTTAGTTCTACTTTCAGCTGTTGTTGGCACAG
                                                       | | ||| | ||     |  |  | ||   | | | || || ||||||| || ||||||||||||||||| ||||||||||| || || ||||| ||| | || || | | || | ||| | || ||  |  ||||||| || |
------------------------------------------------------gtacgtttatgttgcgcattgcagtgtttgaaagaacttttccagGAAAGGGACGTGAGTGAAGAGTCTGGATGGAAGCTTGTCCACGGTGATGTCTTCAGACCGCCACGCTATCTTGTTTTGCTGTCTTCGCTTGTTGGTACTG

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|351023401|gb|FQ432784.1|FQ432784
EST:     GAAATGACTATGCTAAATGTGCTCGGGAAGATGATGATCTGGAGACTCTG                         GAAAGAGATGTGAGTGAAGAGTCTGGCTGGAAGCTTGTTCATGGGGATGTT
genomic: GAAATGACTATGCTAAATATGCTCGGGAAGATGATGATCTGGAGACTCTGgtgacactct ... taattctcagGAAAGAGATGTGAGTGAAGAGTCTGGCTGGAAGCTTGTTCATGGGGATGTT
EST: gi|28959529|gb|CB339765.1|CB339765
EST:     GAAATGACTATGCTAAATATGCTCGGGAAGATGATGATCTGGAGACTCTG                         GAAAGAGATGTGAGTGAAGAGTCTGGCTGGAAGCTTGTTCATGGGGATGTT
genomic: GAAATGACTATGCTAAATATGCTCGGGAAGATGATGATCTGGAGACTCTGgtgacactct ... taattctcagGAAAGAGATGTGAGTGAAGAGTCTGGCTGGAAGCTTGTTCATGGGGATGTT
EST: gi|110708664|gb|EE086465.1|EE086465
EST:     GAAATGACTATGCTAAATATGCTCGGGAAGATGATGATCTGGAGACTCTG                         GAAAGAGATGTGAGTGAAGAGTCTGGCTGGAAGCTTGTTCATGGGGATGTT
genomic: GAAATGACTATGCTAAATATGCTCGGGAAGATGATGATCTGGAGACTCTGgtgacactct ... taattctcagGAAAGAGATGTGAGTGAAGAGTCTGGCTGGAAGCTTGTTCATGGGGATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgtgggatttccatttcttttaattgtaaccattttaacatgtaattctcagGAAAGAGATGTGAGTGAAGAGTCTGGCTGGAAGCTTGTTCATGGGGATGTTTTCCGGCCTCCTCCCAATTTAGTTCTACTTTCAGCTGTTGTTGGCACAG
                                   ttttaac  putative branch site (score: 2)
                                                ttctc  putative PPT
                    ttttaattgtaaccat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgacactctcaacttttgtttatattctttttcctttaattggtttgtgggatttccatttcttttaattgtaaccattttaacatgtaattctcagGAAAGAGATGTGAGTGAAGAGTCTGGCTGGAAGCTTGTTCATGGGGATGTTTTCCGGCCTCCTCCCAATTTAGTTCTACTTTCAGCTGTTGTTGGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT