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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actttttctctaagaggcagtgcatagaatatgtgcgggctcagtttttttgttgtcacattatggttaatgacttttgtttttttggttttaatttcagAGTTTGAAGCACAATTCTAATGGAAGGTCTGTTGTTGTTTGTGGGGATGGGGAATACATAATATACACATCTTTGGCATGGAGAAATAGATCATTTGGCT

Basic information

species Vitis vinifera
transcript Vv11s0016g04180.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 11
-actttttctctaagaggcagtgcatagaatatgtgcgggctcagtttttttgttgtcacattatggttaatgacttttgtttttttggttttaatttcagAGTTTGAAGCACAATTCTAATGGAAGGTCTGTTGTTGTTTGTGGGGATGGGGAATACATAATATACACATCTTTGGCATGGAGAAATAGATCATTTGGCT
   ||||    |   |      |  |  ||||  || |       ||| |  ||| |    ||||| ||      | ||  |  |   || || |||||||||||| | ||||||| | |||||||| | ||||||||| ||||| ||||| ||||||||||| |||||  | ||||||||||||||||||||||| || |
cggttttgaaattgtacttgtcgggttaaataaatgtgatgaacttttctacgttctggt-ttatgtttgcatgttattaataatagtgtattcatttcagAGTTTAAGGCACAATCCAAATGGAAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACCGCATTGGCATGGAGAAATAGATCATTCGGGT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 2
-actttttctctaagaggcagtgcatagaatatgtgcgggctcagtttttttgttgtcacattatg-gttaatgacttttgtttttttggtt--ttaatttcagAGTTTGAAGCACAATTCTAATGGAAGGTCTGTTGTTGTTTGTGGGGATGGGGAATACATAATATACACATCTTTGGCATGGAGAAATAGATCATTTGGCT
 | | | |   |       | |   || | ||    |      ||| |  | ||  | | | | |  |||| | | | | ||  || | ||   || ||||||||| || | ||||||| | ||||| || | ||||||||| ||||| ||||| ||||||||||| |||||  | || |||||||||||||||||||| || |
gattctgttgttgtagtaaaat---taaattaatctcaaatctagtatagt-gtaattatagtgtatgttagtaattatagtaattatagtgtattcatttcagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 11
----actttttctctaagaggcagtgcatagaatatgtgcgggctcagtttttttgttgtcacattatggttaatgacttttgtttttttggttttaatttcagAGTTTGAAGCACAATTCTAATGGAAGGTCTGTTGTTGTTTGTGGGGATGGGGAATACATAATATACACATCTTTGGCATGGAGAAATAGATCATTTGGCT
       || ||   |      |   | |    | ||  |  |   |  |||||||| |     |||   ||| | |  | |  |  | || | ||  |||||||| || |  |||||| | ||||| || | ||||||||| ||||| ||||| |||||||||||||||||| | || ||||||||||||||||||||||| |
gtttgaattatcatgattttttaaaacttgttttgtggtcatgtatatcttttttgt-gctggtttaca-ttattaa--tatactggtgtgatatttgtttcagAGCTTAAGACACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATATACACAGCATTAGCATGGAGAAATAGATCATTTGGGT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 11
----actttttctctaagaggcagtgcatagaatatgtgcgggctcagtttttttgttgtcacattatggttaatgacttttgtttttttggttttaatttcagAGTTTGAAGCACAATTCTAATGGAAGGTCTGTTGTTGTTTGTGGGGATGGGGAATACATAATATACACATCTTTGGCATGGAGAAATAGATCATTTGGCT
       |||| | ||| |     |   |   ||   | |  ||  |  || ||||| |  |  ||| |||||||||  | |  |  | || | ||  ||||||||||| | ||||||| | ||||| || | ||| ||||| ||||| ||||| |||||||||||||||||| | || ||||||||||| ||||||||||| |
atcatgattttttttaaaacttgttttgtgtcatgcataccagcatatcttatttgt-gctagttta-ggttaatga--tatactggtgtgatatttgtttcagAGTTTAAGGCACAATCCGAATGGGAGATTTGTAGTTGTATGTGGAGATGGAGAATACATAATATACACAGCCTTAGCATGGAGAAACAGATCATTTGGGT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 12
actttttctctaagaggcagtgcatagaatatgtgcgggctcagttt---ttttgttgtcacattatggttaatgacttttgtttttttggttttaatttcagAGTTTGAAGCACAATTCTAATGGAAGGTCTGTTGTTGTTTGTGGGGATGGGGAATACATAATATACACATCTTTGGCATGGAGAAATAGATCATTTGGCT
  ||||| |  |||    |  |||  |  | | |    | |   | |   || || |   | |||      |  |    |  |  |||  ||| |   | ||||||||   ||||||| | ||||| |||| ||||| ||| ||||| ||||| || ||||| || |||||| |  | ||||||||||||||||| ||||| |
tttttttatggaaggaaaaaggcaccggttttttaaaagttagttctaacttatgctaggatatttaaaaaacagtaactaatcctttctgttct---tccagAGTTTACGGCACAATCCAAATGGGAGGTTTGTTGCTGTATGTGGAGATGGAGAGTACATTATCTACACAGCGCTAGCATGGAGAAATAGATCCTTTGGGT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 11
actttttctctaagaggcagtgcatagaatatgtgcgggctcagtttttttgttgtcacattatggttaatgacttttgtttt-tttggttttaatttcagAGTTTGAAGCACAATTCTAATGGAAGGTCTGTTGTTGTTTGTGGGGATGGGGAATACATAATATACACATCTTTGGCATGGAGAAATAGATCATTTGGCT
|  |||    ||| |  | |  | |    | |         || ||||||| ||    |||  ||  |  || ||    | |  |||  ||||| | ||||||| | | ||||||| | ||||| ||||  |||||||||||||| ||||||||||| || ||||||||  |||||||||||||||||||||||||||| |
agctttaaaataataatctgccccttagttttaattatttccacttttttttttaa-gcatgttgactggtgtctgacttgtgatttacttttattctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 11
---actttttctctaagaggcagtgcatagaatatgtgcgggctcagtttttttgttgtcacattatggttaatgacttttgtttttttggttttaatttcagAGTTTGAAGCACAATTCTAATGGAAGGTCTGTTGTTGTTTGTGGGGATGGGGAATACATAATATACACATCTTTGGCATGGAGAAATAGATCATTTGGCT
   | |  |  || |      |||    |  ||     |    | | ||||||  |          ||||   |||||| || |||  |  |||  | |  ||||||| | ||||||| | ||||| |||| ||||||||||||||| |||||||| || || ||||||||   ||||||||||||||||||||||||||| |
taaaataataatccaccccttagttttaattatcaccacttattta-ttttttcatgcatgttgactggtgtctgacttgtgatttact--tttatactcaagAGTTTAAGGCACAATCCGAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGGGAGTATATTATATACACTGGTTTGGCATGGAGAAATAGATCATTTGGTT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 11
---actttttctctaagaggcagtgcatagaatatgtgcgggctcagttttt--ttgttgtcacattatggttaatgactt-ttgtttttttggttttaatttcagAGTTTGAAGCACAATTCTAATGGAAGGTCTGTTGTTGTTTGTGGGGATGGGGAATACATAATATACACATCTTTGGCATGGAGAAATAGATCATTTGGCT
   | |   | |  ||     ||| | ||       ||| || ||| || |      |  |    | |||| |  |||||| |||||  |||  |||    | |||| ||| ||||||||| | ||||| |||| ||||||||| ||||| ||||| || ||||| ||||||||  | ||||||||||||||||| |||||||| |
agaagtgagttttaaaacaatagtccttat------tgctggttcaattatcaacaatatttgtttcatgggtggtgacttattgttgatttaatttgttgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 11
---actttttctctaagaggcagtgcatagaatatgtgcgggctcagttttt--ttgttgtcacattatggttaatgactt-ttgtttttttggttttaatttcagAGTTTGAAGCACAATTCTAATGGAAGGTCTGTTGTTGTTTGTGGGGATGGGGAATACATAATATACACATCTTTGGCATGGAGAAATAGATCATTTGGCT
   | |   | |  ||     ||| | ||       |||||| ||| || |      |  |    |||||| |  || ||  |||||  |||  |||    | |||| ||| ||||||||| | ||||| |||| ||||||||| ||||| ||||| || ||||| ||||||||  | ||||||||||||||||| |||||||| |
agaagtgagttttaaaataatagtccttat------tgcgggttcaattatcagcaatatttgttttatgggtggtggctgattgttgatttcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
-actttttctctaagaggcagtgcatagaatatgtgcgggctcagtttttttgtt--gtcacattatggttaatgacttttgtttttttggttttaatttcagAGTTTGAAGCACAATTCTAATGGAAGGTCTGTTGTTGTTTGTGGGGATGGGGAATACATAATATACACATCTTTGGCATGGAGAAATAGATCATTTGGCT
 | |   |    || | | |   | |     || ||  | | ||    | | ||   |    ||||||  |  || ||    | |   |  | | | | |||||| |||||||||||  ||||||| |||| ||| || || || || ||||| || |||||||| |||||  ||||||| |||||||||||||| ||||| |
taatagatgataaaaatgaaactc-tgtttcatatgaagtcccaagagtgtggtccagaataattatgtct--tgcctcacatatagctattctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 11
actttttctctaagaggcagtgcatagaatatgtgcgggctcagtttttttgt-tgtcacattatggttaatgacttttgtttttttggtttt-aatttcagAGTTTGAAGCACAATTCTAATGGAAGGTCTGTTGTTGTTTGTGGGGATGGGGAATACATAATATACACATCTTTGGCATGGAGAAATAGATCATTTGGCT
    |  ||| |||     | | || |   |   |||   ||||  | | | | |||       || |   || ||  | | |   |  | || ||| |||||| |||||||||||  ||||||| |||| ||| || || ||||| || || ||||| ||||| |||||  ||||||| ||||||||||| |||||||| |
-aagtgcctcaaagttatgg-gtatcgctaagccgcgtcttcagaatatatatctgttctcacttgatctgtgtctcatatgtgggtactcttgaatctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGACGGAGAATATATAATCTACACGGCTTTGGCTTGGAGAAATAGGTCATTTGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttgttgtcacattatggttaatgacttttgtttttttggttttaatttcagAGTTTGAAGCACAATTCTAATGGAAGGTCTGTTGTTGTTTGTGGGGATGGGGAATACATAATATACACATCTTTGGCATGGAGAAATAGATCATTTGGCT
                                           ttttaat  putative branch site (score: 3)
                             ttttgtttttttggtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actttttctctaagaggcagtgcatagaatatgtgcgggctcagtttttttgttgtcacattatggttaatgacttttgtttttttggttttaatttcagAGTTTGAAGCACAATTCTAATGGAAGGTCTGTTGTTGTTTGTGGGGATGGGGAATACATAATATACACATCTTTGGCATGGAGAAATAGATCATTTGGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - tgcatag
- - - - - - - - - - - - - - -tatgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - tgttgtc