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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcttacgtctttgtcttagattcagcttgtgtctttttctaacacttgcagttacctagaatttttctttcatatgccaactccagGTTGTGATTAGGAAACAGAGAACTGCATTTCCACCAAATTTTGTTCACTCACTTGATGGTTCACACATGATGATGACCGCTGTTGCCTGCAGGGATGCTG

Basic information

species Vitis vinifera
transcript Vv11s0037g00630.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0037g00630.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 16
gtgagcttacgtctttgtcttagattcagcttgtgtctttttctaacacttgcagttacctagaatttttctttcatatgccaactccagGTTGTGATTAGGAAACAGAGAACTGCATTTCCACCAAATTTTGTTCACTCACTTGATGGTTCACACATGATGATGACCGCTGTTGCCTGCAGGGATGCTG
|| ||  ||   |    |  | |||| |  ||     | |||||  || || | |  |     ||| |  || ||| |    |  ||||| |||   |   |   || |   | || ||||| ||||||||||| ||||| |||||| ||||||||||||||||||| ||| |||| ||||   | ||||
gtaag--taaaaccaatttctggattgatttttccgttctttctttca-ttactgcgatt---aatatcgctgtcaca----atttccagATTGCACTCCAGCGGCAAAAGGCAGCTTTTCCCCCAAATTTTGTGCACTCTCTTGATAGTTCACACATGATGATGACTGCTATTGCATGCAAAAAGGCTG

upper sequence: Vv11s0037g00630.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GRMZM2G115564_T02 (Zea mays), 3'ss of exon 16
gtgagcttacgtctttgtcttagattcagcttgtgtctttttctaacacttgcagttacctagaatttttctttcatatgccaactccagGTTGTGATTAGGAAACAGAGAACTGCATTTCCACCAAATTTTGTTCACTCACTTGATGGTTCACACATGATGATGACCGCTGTTGCCTGCAGGGATGCTG
||||| | |  | |||  |  |   |   | ||| |||||| | |   |||| || ||  ||          || | ||   |  | ||| |||  ||    |  || |   | || ||||||||||||||||| |||||||| ||| ||||||| ||||||||||| ||  |||| |||| |||  |||
gtgagttcagctattt--caaaacgttttcctgtttcttttcccatt-cttgtagctaattaa---------ttgacata--attttcagATTGCAATCCAAAGGCAAAAGGCAGCTTTTCCACCAAATTTTGTGCACTCACTGGATAGTTCACATATGATGATGACAGCGATTGCTTGCAAGGAGTCTG

upper sequence: Vv11s0037g00630.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA17G07940.1 (Glycine max), 3'ss of exon 16
gtgagcttacgtctttgtcttagattcagcttgtgtctttttctaacacttgcagttacctagaatttttctttcatatgccaactccagGTTGTGATTAGGAAACAGAGAACTGCATTTCCACCAAATTTTGTTCACTCACTTGATGGTTCACACATGATGATGACCGCTGTTGCCTGCAGGGATGCTG
|| ||   || |  |  ||||   | ||||||   | | ||||| |    |     |   || || |  ||||          | ||||||| |     | |||||||||| |||||||||| ||||| || || || ||||| ||||||||||||||||||||||| ||| ||||||| ||||||||||
gtaagtggacatagtcctcttttttgcagctttcctttctttctgaactatattcgttattaaaactactctt----------attccagGTAGATGCCAAGAAACAGAGATCTGCATTTCCTCCAAACTTCGTACATTCACTGGATGGTTCACACATGATGATGACTGCTCTTGCCTGTAGGGATGCTG

upper sequence: Vv11s0037g00630.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA04G24350.1 (Glycine max), 3'ss of exon 11
gtgagcttacgtctttgtcttagattcagcttgtgtctttttctaacacttgcagttacctagaatttttctttcatatgccaactccagGTTGTGATTAGGAAACAGAGAACTGCATTTCCACCAAATTTTGTTCACTCACTTGATGGTTCACACATGATGATGACCGCTGTTGCCTGCAGGGATGCTG
|| ||  ||  |  |    ||| ||||  ||| | | || ||     |||             | |||   | | |       | |||||||     | | ||| ||||||| ||||||||| ||||| ||||| || ||| | ||| ||||||||||||||||||| ||| | || ||||  || ||||
gtaagtatagataatc--tttatattccacttttcttttctttctgaact-------------attttcattattaagactgtattccagGTATCTGTCAAGAAGCAGAGAAGTGCATTTCCTCCAAACTTTGTACATTCATTGGATAGTTCACACATGATGATGACTGCTCTAGCTTGCAATGACGCTG

upper sequence: Vv11s0037g00630.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA06G24890.1 (Glycine max), 3'ss of exon 9
gtgagcttacgtctttgtcttagattcagcttgtgtctttttct--aacacttgcagttacctagaatttttctttcatatgccaactccagGTTGTGATTAGGAAACAGAGAACTGCATTTCCACCAAATTTTGTTCACTCACTTGATGGTTCACACATGATGATGACCGCTGTTGCCTGCAGGGATGCTG
|| ||  ||| |  |  | | | ||||  ||| | | || ||    |||  ||   ||||   ||| | | |             | |||||||     | | ||| ||||||| ||||||||| || || ||||| || ||| | ||| ||||||||||||||||||| ||| | |||||||  |||||||
gtaagtatacataatcttttcatattccacttttcttttctttctgaactattttcgttattaagactgtgt-------------attccagGTATCTGTCAAGAAGCAGAGAAGTGCATTTCCTCCTAACTTTGTACATTCATTGGATAGTTCACACATGATGATGACTGCTCTAGCCTGCAATGATGCTG

upper sequence: Vv11s0037g00630.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: AT2G24120.1 (Arabidopsis thaliana), 3'ss of exon 16
gtgagcttacgtctttgtcttagattcagcttgtgtctttttctaacacttgcagttacctagaatttttctttcata-tgccaactc-cagGTTGTGATTAGGAAACAGAGAACTGCATTTCCACCAAATTTTGTTCACTCACTTGATGGTTCACACATGATGATGACCGCTGTTGCCTGCAGGGATGCTG
      | | | |  | | || | |||    | | ||  |    || |||  ||||      |   ||| |||  | | |  ||| || ||||| |   |||||||||| |||||||||||||| || || ||||| ||||| || || ||  | |||||||||||||| |||||||| ||  | || || |
-----gtaaagccgatttgtttgtttctttgttt-tcactgagcaagactatcagt-----gggtctttgcttaaagactatcaattcgcagGTCGATGTTAGGAAACAAAGAACTGCATTTCCTCCCAACTTTGTGCACTCGCTGGACGGCACTCACATGATGATGACTGCTGTTGCATGTCGAGAGGCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttttctaacacttgcagttacctagaatttttctttcatatgccaactccagGTTGTGATTAGGAAACAGAGAACTGCATTTCCACCAAATTTTGTTCACTCACTTGATGGTTCACACATGATGATGACCGCTGTTGCCTGCAGGGATGCTG
     ttctaac  putative branch site (score: 1)
                            aatttttctttcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcttacgtctttgtcttagattcagcttgtgtctttttctaacacttgcagttacctagaatttttctttcatatgccaactccagGTTGTGATTAGGAAACAGAGAACTGCATTTCCACCAAATTTTGTTCACTCACTTGATGGTTCACACATGATGATGACCGCTGTTGCCTGCAGGGATGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG