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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcaatatttagttgctgaattagaaatacaatgatctaatcttgtttcctgatatatttttctggttgctgtagATCCTGGGAAGTGGCATGTCAAATAAGATGTGGGAGGCTCTTATAGAGCATGCAAAGACTTGCACCATGAGTGGAAAGTTCTATGTTTATTATTCTGATG

Basic information

species Vitis vinifera
transcript Vv11s0052g01380.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 6
gtaagtgcaatatttagttgctgaattagaaatacaatgatctaatcttgtttcctgatatatttttctggttgctgtagATCCTGGGAAGTGGCATGTCAAATAAGATGTGGGAGGCTCTTATAGAGCATGCAAAGACTTGCACCATGAGTGGAAAGTTCTATGTTTATTATTCTGATG
|||||   | |   || |       ||     |    |  | |  | |||  | || | |||| | |   ||  |   ||||||| |||||||| ||||| ||||||||||||||   |||| | || ||||||||||||||   | | |||||||| |  ||  | |||||||| || |
gtaagattatttcctattcagcatttttcttctttttttcttttgt-ttgagttctaacatatatgttctgtccc---agATCCTTGGAAGTGGTATGTCTAATAAGATGTGGGATATTCTTGTCGAACATGCAAAGACTTGTGTCTTAAGTGGAAAATATTACATATATTATTCAGACG

upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 6
gtaagtgcaatattta--gttgctgaattagaaatacaatgatctaatcttgtttcctgatatatttttctggttgctgtagATCCTGGGAAGTGGCATGTCAAATAAGATGTGGGAGGCTCTTATAGAGCATGCAAAGACTTGCACCATGAGTGGAAAGTTCTATGTTTATTATTCTGATG
|||||| | | | ||   |||  |   ||  || ||   |  | |||| |  |   |  |||  | ||| |   |  | ||||| || || ||||| ||||||||||||||||||||    ||| | |||||||||||||||||   | | |||||||||  |||||| |||||| ||  ||
gtaagttctacaattgttgttaataggttgtaattaatgtagtttaat-tgatgatcaaatacctcttttt---tcttttagATTCTTGGCAGTGGAATGTCAAATAAGATGTGGGAAAGCCTTGTTGAGCATGCAAAGACTTGTGTCTTAAGTGGAAAGCACTATGTATATTATGCTATTG

upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G054109_T01 (Zea mays), 3'ss of exon 6
gtaagtgcaatatttagttgctgaattagaaatacaatgatctaatcttgtttcctgatatatttttctggttgctgtagATCCTGGGAAGTGGCATGTCAAATAAGATGTGGGAGGCTCTTATAGAGCATGCAAAGACTTGCACCATGAGTGGAAAGTTCTATGTTTATTATTCTGATG
|||||| | ||  |   ||  ||     ||  ||   |  |       || ||  ||| |    ||  |  ||  ||||||| ||||| ||||| ||||||||||||||||||||    ||| | || ||||||||||| ||   | | |||||||||   ||||| || ||| ||   |
gtaagttctatgataccttattgt----gatttatggtatttcctatatgatt--tgacaccccttgttcttttttgtagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGATCATGCAAAGACGTGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG

upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G113453_T01 (Zea mays), 3'ss of exon 6
gtaagtgcaatatttagttgctgaattagaaatacaatgatctaatcttgtttcctgatatatttttctgg---------ttgctgtagATCCTGGGAAGTGGCATGTCAAATAAGATGTGGGAGGCTCTTATAGAGCATGCAAAGACTTGCACCATGAGTGGAAAGTTCTATGTTTATTATTCTGATG
|||||| | ||  |   |   |    |    |||   |||| || |  | || ||| ||||  |||    |         ||  | ||||| ||||| ||||| ||||||||||||||||||||    ||| | |||||||||||||| ||   | | |||||||||   ||||| || ||| ||   |
gtaagttctatgatacctgtttttgcttactatattgtgattta-tggtattccct-atatggtttgacagcccttgttctttttatagATTCTGGGCAGTGGAATGTCAAATAAGATGTGGGACAGCCTTGTTGAGCATGCAAAGACATGTGTCTTAAGTGGAAAGCATTATGTATACTATGCTAGAG

upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AC202073.4_FGT001 (Zea mays), 3'ss of exon 5
gtaagtgcaatatttagttgctgaattagaa--atacaatgatctaatcttgtttcc----------tgatatatttttctggttgct--gtagATCCTGGGAAGTGGCATGTCAAATAAGATGTGGGAGGCTCTTATAGAGCATGCAAAGACTTGCACCATGAGTGGAAAGTTCTATGTTTATTATTCTGATG
||||||  |  || |      | | |  |    || ||    | || ||||||  ||          |  |   | | ||||||| ||  | |||| || || |||  ||||||||||| |||||||||   |||||| |||||||||||||| ||     ||||||| ||    ||| | ||||| ||   ||
gtaagtttagcatctctactttaactatgtttcatccacctctgtagtcttgtgaccaataccattttatttcttctctctggttactctgcagATTCTTGGCAGTAACATGTCAAATAGGATGTGGGAAAGTCTTATTGAGCATGCAAAGACATGTGTTTTGAGTGGCAACCATTATATATATTACTCAAGTG

upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 6
gtaagtgcaatatttagttgctgaattagaaat-acaatgatctaatcttgtttcctgatatatttttctggttgctgtagATCCTGGGAAGTGGCATGTCAAATAAGATGTGGGAGGCTCTTATAGAGCATGCAAAGACTTGCACCATGAGTGGAAAGTTCTATGTTTATTATTCTGATG
||||||  |   |||   |  | |  | ||| | |      | |    |||||| ||  |||||  |||      ||||||||||| || ||||| |||||||| |||||||||||||||||| |||| |||||||| || ||     | ||||| ||| |||||||||||||| | || |
gtaagtttaggttttgcatcttaatcttgaagttaggcctttttccagttgttttct--tatatcattcaa----ctgtagATCCTTGGGAGTGGTATGTCAAACAAGATGTGGGAGGCTCTTTTAGACCATGCAAAAACATGTGTTCTAAGTGGGAAGCTCTATGTTTATTATCCAGAAG

upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G07290.1 (Glycine max), 3'ss of exon 7
gtaagtgcaatatttagttgctgaattagaaatacaatgatctaatc-ttgtttcctgatatatttttctggttgctgtagATCCTGGGAAGTGGCATGTCAAATAAGATGTGGGAGGCTCTTATAGAGCATGCAAAGACTTGCACCATGAGTGGAAAGTTCTATGTTTATTATTCTGATG
||||||  |   |||   |  | |  | ||| |    |  | |     |||||| ||  |||||  |||      ||||||||||| || ||||| |||||||| |||||||||||||||||| |||| |||||||| || ||     | ||||| ||| |||||||||||||| | || |
gtaagtttaggttttgcgtcttaatcttgaagttaggtcttttcccagttgttttct--tatatcattcaa----ctgtagATCCTTGGGAGTGGTATGTCAAACAAGATGTGGGAGGCTCTTTTAGACCATGCAAAAACATGTGTTCTAAGTGGGAAGCTCTATGTTTATTATCCAGAAG

upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------gtaagtgcaatatttagttgctgaattagaaatacaatgatctaat-cttgtttcctgatatatttttctggttgctgt--agATCCTGGGAAGTGGCATGTCAAATAAGATGTGGGAGGCTCTTATAGAGCATGCAAAGACTTGCACCATGAGTGGAAAGTTCTATGTTTATTATTCTGATG
               || ||  |     | |||| || || ||||   || | ||  ||| ||  |       |||  || | || |   |||  |||| || |||||||||||||||||||||||||||||    ||  | ||||||||||| || ||   | | || || ||| | ||| | || ||| |||| |
gtgagtgcctcctattacgtcaagctcattgttgttggatgagaa---cattcattcaatgctcatgagtaattatgattatttgatatttgtctagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGATTTGCTAGTGGAGCATGCAAAAACATGTGTCCTAAGCGGTAAGCTTTATATCTACTATACTGAAG

upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ34469 (Selaginella moellendorffii), 3'ss of exon 5
gtaagtgcaatatttagttgctgaattagaaatacaatgatctaatcttgtttcctgatatatttttctggttgctgtagATCCTGGGAAGTGGCATGTCAAATAAGATGTGGGAGGCTCTTATAGAGCATGCAAAGACTTGCACCATGAGTGGAAAGTTCTATGTTTATTATTCTGATG
          ||  || |     | ||||   |    |  |||     |||   || || || ||    |  ||  | |||| || ||||||||||||||||||||||||||||| |      | |||||||| || || |||  | | || |||||| | ||||| |||||| | || |
---------gtaagtaatga--aagttagttttttctttctctctctctgtcagctcatgtagttg---gtctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG

upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ05811 (Selaginella moellendorffii), 3'ss of exon 5
gtaagtgcaatatttagttgctgaattagaaatacaatgatctaatcttgtttcctgatat-atttttctggt-tgctgtagATCCTGGGAAGTGGCATGTCAAATAAGATGTGGGAGGCTCTTATAGAGCATGCAAAGACTTGCACCATGAGTGGAAAGTTCTATGTTTATTATTCTGATG
              ||  |  ||| ||       |  |  |    |||  ||   | |  | || |   |||| ||  | |||| || ||||||||||||||||||||||||||||| |      | |||||||| || || |||  | | || |||||| | ||||| |||||| | || |
-------------gtaagtaatgagtttttttctctctctttctctctctttctttcagctcatgtagttggtctggcgcagATTCTTGGAAGTGGCATGTCAAATAAGATGTGGGAAGGAACAGTGGAGCATGCTAAAACGTGCGTCCTCAGCGGAAAGCTGTATGTCTATTATGCCGACG

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|161709162|gb|FC061372.1|FC061372
EST:     TGGAAGATTTCCTCCGGCTTGTGGTTAGAGACTCCCAAAAATTGCGGAGT                         ATCCTGGGAAGTGGCATGTCAAATGAGATGTGGGAGGCTCTTATAGAGCAT
genomic: TGGAAGATTTCCTCCGGCTTGTGGTTAGAGACTCCCAAAAATTGCGGAGTgtaagtgcaa ... gttgctgtagATCCTGGGAAGTGGCATGTCAAATAAGATGTGGGAGGCTCTTATAGAGCAT
EST: gi|71883679|gb|DT032734.1|DT032734
EST:     TGGAAGATTTCCTCCGGCTTGTGGTTAGAGACTCCCAAAAATTGCGGAGT                         ATCCTGGGAAGTGGCATGTCAAATAAGATGTGGGAGGCTCTTATAGAGCAT
genomic: TGGAAGATTTCCTCCGGCTTGTGGTTAGAGACTCCCAAAAATTGCGGAGTgtaagtgcaa ... gttgctgtagATCCTGGGAAGTGGCATGTCAAATAAGATGTGGGAGGCTCTTATAGAGCAT
EST: gi|110719043|gb|EE096564.1|EE096564
EST:     TGGAAGATTTCCTCCGGCTTGTGGTTAGAGACTCCCAAAAATTGCGGAGT                         ATCCTGGGAAGTGGCATGTCAAATAAGATGTGGGGGGCTCTTATAGAGCAT
genomic: TGGAAGATTTCCTCCGGCTTGTGGTTAGAGACTCCCAAAAATTGCGGAGTgtaagtgcaa ... gttgctgtagATCCTGGGAAGTGGCATGTCAAATAAGATGTGGGAGGCTCTTATAGAGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagaaatacaatgatctaatcttgtttcctgatatatttttctggttgctgtagATCCTGGGAAGTGGCATGTCAAATAAGATGTGGGAGGCTCTTATAGAGCATGCAAAGACTTGCACCATGAGTGGAAAGTTCTATGTTTATTATTCTGATG
                           tcctgat  putative branch site (score: 3)
                              tgatatatttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgcaatatttagttgctgaattagaaatacaatgatctaatcttgtttcctgatatatttttctggttgctgtagATCCTGGGAAGTGGCATGTCAAATAAGATGTGGGAGGCTCTTATAGAGCATGCAAAGACTTGCACCATGAGTGGAAAGTTCTATGTTTATTATTCTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA