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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagtcagaaagagtgtagagttatgttggcgatcctttgtatggaatttttttaaacagtgatttgggttctgttgattagtgctaattttcttgtgcagGAAGAGATTGTTTTTGTCTCATGCCAACAGGAGGAGGAAAGTCAATGTGTTATCAGATTCCTGCACTGGCAAAACCAGGGATTGTGCTCGTGGTTTGTCC

Basic information

species Vitis vinifera
transcript Vv11s0016g00850.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g00850.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g54020.1 (Oryza sativa), 3'ss of exon 2
----------------------------------------------------------------cagtcagaaagagtgtag--agttatgttggcgatcctttgtatggaatttttttaaacagtgatttgggttctgttgat-tagtgctaattttcttgtgcagGAAGAGATTGTTTTTGTCTCATGCCAACAGGAGGAGGAAAGTCAATGTGTTATCAGATTCCTGCACTGGCAAAACCAGGGATTGTGCTCGTGGTTTGTCC
                                                                  |||| ||  | | | |    | ||    |   |    ||| || || |||| |  ||  ||     | |||| || || ||      | ||| || |  |||||| ||||| |||||| | |||||||| ||||| ||||| |||||||| |||||||||||||| || |  ||  |||| ||||| || ||  | |  ||
gtgctcttcccgtctgtgtttgtgcttgtagtctttatttctttttagttttgctgaatatttctggtcaaaagaacttttgttgctgatcactgaagtatgctgtctgaaacttttgtgcaccatg-----gattctattaatgtaacaagcaatttatt-tctagGAAGGGATTGCTTTTGTTTGATGCCAACTGGAGGTGGAAAATCAATGTGCTATCAGATTCCTGCTCTAGTGAAGTCAGGCATTGTTCTTGTTATCTCACC

upper sequence: Vv11s0016g00850.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G039683_T01 (Zea mays), 3'ss of exon 2
---------cagtcagaaagagtgtagagttatgttggcgatcctttgtatggaatttttttaaacagtgatt------tgggttctgttgatta-gtgctaattttcttgtgcagGAAGAGATTGTTTTTGTCTCATGCCAACAGGAGGAGGAAAGTCAATGTGTTATCAGATTCCTGCACTGGCAAAACCAGGGATTGTGCTCGTGGTTTGTCC
         |   | |     ||||    |||| |  |  ||   |||       | ||  | |   ||  |       |||||| |||| | || ||  ||   ||  |||||||| |||||||| |||||| | |||||||| || || |||||||| ||||| ||||||||||| || ||||  ||| |||| ||||| || ||  |||  ||
gtctgctcgcttgctgcgctcgtgtgttcttatatctgtaattggttggcacctgtgttgctgagatgttttcaacgtatgggttttgtttaatatgttatacaatttatgtgcagGGAGAGATTGCTTTTGTTTGATGCCAACTGGTGGTGGAAAGTCCATGTGCTATCAGATTCCAGCTCTGGTGAAAACAGGCATTGTTCTTGTCATTTCACC

upper sequence: Vv11s0016g00850.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G08180.1 (Glycine max), 3'ss of exon 1
cagtcagaaagagtgtagagttatgttggcgatcctt-tgtatggaatttt---tttaaacagtgatttgggttctgttgattagtgctaattttcttgtgcagGAAGAGATTGTTTTTGTCTCATGCCAACAGGAGGAGGAAAGTCAATGTGTTATCAGATTCCTGCACTGGCAAAACCAGGGATTGTGCTCGTGGTTTGTCC
    |||   |  |     ||| | ||  |   |||    | ||| | |||   ||| |    |   |||  |   | |  ||| |  || ||||    |||||| | ||||||||||||||| |||||||| |||||||| ||||| |||||||||||||| |||||| |||||||| |||| |||||||| || ||||| ||
----cagtttggtttgtttgtttttttcacacccctagcatgtggtaatttaagtttgatttttccattgattgtggctctttatttttattttttggctgcagGGAAAGATTGTTTTTGTCTTATGCCAACTGGAGGAGGCAAGTCGATGTGTTATCAGATCCCTGCATTGGCAAAAGCAGGCATTGTGCTTGTCGTTTGCCC

upper sequence: Vv11s0016g00850.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G35740.1 (Arabidopsis thaliana), 3'ss of exon 1
cagtcagaaagagtgtagagttatgttggcgatcctttg-tatggaatttttttaaacagt-gatttgggttctgttgattagtgctaattttcttgtgcagGAAGAGATTGTTTTTGTCTCATGCCAACAGGAGGAGGAAAGTCAATGTGTTATCAGATTCCTGCACTGGCAAAACCAGGGATTGTGCTCGTGGTTTGTCC
              ||| |||  |  |     || |||  |  |||     ||  ||   | | ||| |  |    || || |||   |||     |   |||||| ||||| |||||  | |||||||| ||||||||||| || || ||||||||||| |||||| | || ||||| || || || || || || | |||
--------------gta-agtcgtaatttttctcttttactccggagaaaattagaatgattgttttagaattctctgttttgtg---attgatgagattagGAAGGGATTGCTTTTGCTTGATGCCAACGGGAGGAGGAAAATCGATTTGTTATCAGATACCTGCATTAGCTAAACCTGGAATCGTCCTTGTTGTGTCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttttaaacagtgatttgggttctgttgattagtgctaattttcttgtgcagGAAGAGATTGTTTTTGTCTCATGCCAACAGGAGGAGGAAAGTCAATGTGTTATCAGATTCCTGCACTGGCAAAACCAGGGATTGTGCTCGTGGTTTGTCC
                                    tgctaat  putative branch site (score: 2)
                                          ttttcttgt  CT-rich tract
                                       taattttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagtcagaaagagtgtagagttatgttggcgatcctttgtatggaatttttttaaacagtgatttgggttctgttgattagtgctaattttcttgtgcagGAAGAGATTGTTTTTGTCTCATGCCAACAGGAGGAGGAAAGTCAATGTGTTATCAGATTCCTGCACTGGCAAAACCAGGGATTGTGCTCGTGGTTTGTCC

- - -agaaaga
- - - - - - - - - - - -tgttggc
- - - - - - - - - - - - - - - - - - -tgtatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - -aaacagt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgttga