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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgttcctccagttatagttgtgaatgggtatttttactttccccagaatttgcttttcaagtagttgaccattttttcttctttgctgcattcagATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCGTGTGAAGGAAGGAGATCATGTTATTATTGGCCAGTGCAG

Basic information

species Vitis vinifera
transcript Vv11s0118g00680.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os08g10608.1 (Oryza sativa), 3'ss of exon 4
gcatgttcctccagttatagttgtgaatgggtatttttactttccccagaatttgcttttcaagtagttgaccattttttcttctttgctgcattcagATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCGTGTGAAGGAAGGAGATCATGTTATTATTGGCCAGTGCAG
| | ||    | |   |    | ||||     |||| |  | ||           ||| |  || || |||  | || ||| ||||          |||||||| ||||||||||| |||||||| |||||||  || |||||||||||||| |||||||| || ||||| || ||||||||||||||
gtaagtaaagcaatggaggactatgaacttacatttct--tatctgtgatggcatcttatttagaaggtga--acttgttcatcttg--------tagATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAG

upper sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g42380.1 (Oryza sativa), 3'ss of exon 4
gcatgttcctccagttatagttgtgaatgggtatttttactttccccagaatttgcttttcaagtagttgaccattttttcttctttgctgcattcagATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCGTGTGAAGGAAGGAGATCATGTTATTATTGGCCAGTGCAG
||| |||   |  |||   | || | ||  ||  | | |     |   |   |   | ||||   | || |      |||  |   ||||| || ||| || |||||||||||||| || |||||||||||||  || || ||||||||||| |||||||||||||| || || ||||||||||||||
gcaagttaacctggtt---gctgggtatcagttctataatgcctcattgggctgtttgttcataaaattaa------ttttattgatgctg-atgcagGTACGAGAAGAGGCACTCCAATATTCCTGCTCACATTTCACCGTGCTTCCGTGTTAAGGAAGGAGATCACGTGATCATTGGCCAGTGCAG

upper sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g52361.1 (Oryza sativa), 3'ss of exon 4
gcatgttcctccagttatagttgtgaatgggtatttttactttccccagaatttgcttttcaagtagttgaccattttttcttctttgctgcattcagATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCGTGTGAAGGAAGGAGATCATGTTATTATTGGCCAGTGCAG
                      |  | |    | || |   |||  |  |  || ||||||   |  ||  ||  ||| |    |  | ||||    | |||||||||||||| || |||||||| ||||||   || |||||||||||||| |||||||| || ||||| || ||||||||||||||
----------------------gcaagtaaacaattatggattctacttatgtttcttttccttttttttccccatttctgacttgggttgca----gGTATGAGAAGAGGCATTCCAACATTCCGGCTCACGTCTCCCCATGCTTCCGTGTCAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAG

upper sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os07g37780.1 (Oryza sativa), 3'ss of exon 4
gcatgttcctccagttatagttgtgaatgggtatttttactttccccagaatttgcttttcaagtagttgaccattttttcttctttgctgcattcagATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCGTGTGAAGGAAGGAGATCATGTTATTATTGGCCAGTGCAG
           |    || | | |  ||   ||| ||| ||||||      | | | ||  ||      |  ||    | |  | ||||       || |||||||||||||| || |||||||| ||||||   || |||||||||||||| |||||||| || ||||| || |             
------gtaaactaccatggat-tatatacttatgtttcctttccttt---tctccgttctaacatagGGTGCAAACCTCCCACCTTGC-------AGGTATGAGAAGAGGCATTCCAACATTCCGGCTCACGTCTCCCCATGCTTCCGTGTCAAGGAAGGTGACCATGTCATCA-------------

upper sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G044800_T01 (Zea mays), 3'ss of exon 4
gcatgttcctccagttatagttgtgaatgggtatttttactttccccagaatttgcttttcaagtag-----ttgaccattttttcttctttgctgcattcagATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCGTGTGAAGGAAGGAGATCATGTTATTATTGGCCAGTGCAG
                 ||  || || ||  | |     ||   | ||   ||||  ||||||   |     |  | |||||  |      ||   | | ||| ||||||||||||||||| ||||||||||||||||  || ||||||||||||||||||||||| || ||||| || ||||||||||||||
----------------gtaagtg-gactgtttgtggaacctagactcatggtttgtctttcaaaatgaactttctaacatttagttactcgtgtcccttgcagGTATGAGAAGAGGCACTCCAACATTCCTGCTCACATCTCCCCATGCTTCCGTGTGAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAG

upper sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G019325_T01 (Zea mays), 3'ss of exon 4
gcatgttcctccagttatagttgtgaatgggtatttttactttccccagaatttg-cttttcaagtagttgaccattttttcttctttgctgcatt-cagATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCGTGTGAAGGAAGGAGATCATGTTATTATTGGCCAGTGCAG
                 ||  || || |   | |     ||   | ||   |||| |||   ||| | ||      |||||  | |  | | |||  ||| ||||| ||||||||||| |||||||| |||||||  || ||||||||||||||||||||||| || ||||| || ||||||||||||||
----------------gtaagtg-gactctttgtggaacctaggctcatgctttgtcttcctaaggaattttgttgtttttaatataagttacatcacagGTATGAAAAGAGGCACTCCAACATTCCAGCTCACATCTCCCCATGCTTCCGTGTGAAGGAAGGCGACCATGTCATCATTGGCCAGTGCAG

upper sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G086486_T02 (Zea mays), 3'ss of exon 6
gcatgtt--cctccagttatagttgtgaatgggtatttttactttccccagaatttgcttttcaagtagttgaccattttttcttctttgctgcattcagATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCGTGTGAAGGAAGGAGATCATGTTATTATTGGCCAGTGCAG
||| | |   || || |  | | |   | |   |  |       | ||   |  |||  | |     |  |||  |||| ||  | ||||     |  || ||||||||||| ||||| ||||| ||||| ||||  || |||||||| ||||| ||||||||||||||||| || ||||||||||||||
gcaagctaatcttcaatattggcttgtatttactgatcgcttcgtgccttcatgttgtctgttcgccaactgataatttgttggtgtttg-----tgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG

upper sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G086486_T01 (Zea mays), 3'ss of exon 6
---------gcatgtt--cctccagttatagttgtgaatgggtatttttactttccccagaatttgcttttcaagtagttgaccattttttcttctttgctgcattcagATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCGTGTGAAGGAAGGAGATCATGTTATTATTGGCCAGTGCAG
         ||| | |   || || |  | | |   | |   |  |       | ||   |  |||  | |     |  |||  |||| ||  | ||||     |  || ||||||||||| ||||| ||||| ||||| ||||  || |||||||| ||||| ||||||||||||||||| || ||||||||||||||
gtaccagaggcaagctaatcttcaatattggcttgtatttactgatcgcttcgtgccttcatgttgtctgttcgccaactgataatttgttggtgtttg-----tgtagGTATGAGAAGAGACACTCCAACATCCCTGCGCACATTTCACCATGCTTTCGTGTCAAGGAAGGAGATCATGTGATCATTGGCCAGTGCAG

upper sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G12430.1 (Glycine max), 3'ss of exon 4
gcatgttcctccagttatagttgtgaatgggtatttttactttccccagaatttgcttttcaagtagttgaccattttttcttctttgctgcattcagATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCGTGTGAAGGAAGGAGATCATGTTATTATTGGCCAGTGCAG
| ||   ||| |  |     | ||||   | |||| ||  || |      |          |||||  | |   || ||  ||  |   |  ||| |||||||| ||| |||| ||||| |||||| | |||| ||| || || |||||||| ||||||||||||||||||||||||||||| |||||
gtattccccttccatacctttggtgagcagttattgttgtttacatggacag---------aagtaactaatgtttcttctttgctcattctatttagATATGAAAAGCGGCATTCAAATATTCCTTCACACATATCACCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAG

upper sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G23400.1 (Glycine max), 3'ss of exon 4
gcatgttcctccagttatagttgtgaatgggtatttttactttccccagaatttgcttttcaagtagttgaccattttttcttctttgctgcattcagATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCGTGTGAAGGAAGGAGATCATGTTATTATTGGCCAGTGCAG
   | ||| ||| |  ||  || | |        ||||  |||     | || |   |   ||     | || |||   | ||  ||  |   ||||| || ||||||||||||||||| ||||||||||| | ||| ||   |||||||||||||||||| ||||| ||||||||||| || |||||
--gtattc-tcctgccatcctttttagc-----ctttttttttgtttggtatgtttgtagaaacataattacaattccatttttatttttttgttcagGTACGAGAAGAGGCACTCAAATATTCCTGCTCATATATCACCTGCCTTCCGTGTGAAGGAAGGGGATCACGTTATTATTGGTCAATGCAG

upper sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G11430.1 (Glycine max), 3'ss of exon 4
gcatgttcctccagttatagttgtgaatgggtatttttactttccccagaatttgcttttcaagtagt--tgaccattttttcttctttgctgcattcagATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCGTGTGAAGGAAGGAGATCATGTTATTATTGGCCAGTGCAG
| ||  | |||| |  ||  || ||  |   | || ||   || |      | || ||    |    |  | |  |||   | ||| ||  |    |||| || ||||| |||||||| |||||||||||||| | ||| ||    ||||||||||||||||||||||| ||||||||||| || |||||
gtattattctcctgcaatccttttgtgttcattttgttttgtttcgttttgtatgtttggagaaacataattataattccattttcatttttatgctcagGTACGAGAAAAGGCACTCCAACATTCCTGCTCATATATCACCTGCTTTCCGTGTGAAGGAAGGAGATCACGTTATTATTGGTCAATGCAG

upper sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G12420.1 (Glycine max), 3'ss of exon 4
gcatgttcctccagttatagttgtgaatgggtatttttactttccccagaatttgcttttcaagtagttgaccattttttcttctttgctgcattcagATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCGTGTGAAGGAAGGAGATCATGTTATTATTGGCCAGTGCAG
| ||   ||| |  |     | ||||   | |||| ||  || |      |          |||||  | |   || ||  ||  |   |  ||| |||||||| ||| | || || || |||||||| || ||||| || || |||||||| || |||||||||||||||||||||||||| |||||
gtattccccttccatacctttggtgagcagttattgttgtttacatggacag---------aagtaactaatgtttcttctttgctcattctatttagATATGAAAAGCGACATTCCAATATTCCTGCACATACATCACCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG

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|71878095|gb|DT027150.1|DT027150
EST:     ACCATAATTGTTCGAAGGAACTACCTTCACTATGTGAAGAAATACCAAAG                         ATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCG
genomic: ACCATAATTGTTCGAAGGAACTACCTTCACTATGTGAAGAAATACCAAAGgcatgttcct ... ctgcattcagATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCG
EST: gi|71878876|gb|DT027931.1|DT027931
EST:     ACCATAATTGTTCGAAGGAACTACCTTCACTATGTGAAGAAATACCAAAG                         ATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCG
genomic: ACCATAATTGTTCGAAGGAACTACCTTCACTATGTGAAGAAATACCAAAGgcatgttcct ... ctgcattcagATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCG
EST: gi|71879179|gb|DT028234.1|DT028234
EST:     ACCATAATTGTTCGAAGGAACTACCTTCACTATGTGAAGAAATACCAAAG                         ATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCG
genomic: ACCATAATTGTTCGAAGGAACTACCTTCACTATGTGAAGAAATACCAAAGgcatgttcct ... ctgcattcagATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCG
EST: gi|71871214|gb|DT020269.1|DT020269
EST:     ACCATAATTGTTCGAAGGAACTACCTTCACTATGTGAAGAAATACCAAAG                         ATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCG
genomic: ACCATAATTGTTCGAAGGAACTACCTTCACTATGTGAAGAAATACCAAAGgcatgttcct ... ctgcattcagATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccccagaatttgcttttcaagtagttgaccattttttcttctttgctgcattcagATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCGTGTGAAGGAAGGAGATCATGTTATTATTGGCCAGTGCAG
                      agttgac  putative branch site (score: 4)
                               ttttttcttctttgct  putative PPT
                              attttttcttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgttcctccagttatagttgtgaatgggtatttttactttccccagaatttgcttttcaagtagttgaccattttttcttctttgctgcattcagATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCGTGTGAAGGAAGGAGATCATGTTATTATTGGCCAGTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA