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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatctgcaggaaccatttcctgtacattcctttattttcaataaaggcatgtgtcatggctataatcacatcacttagttgattgattttttctttacagGTTACTACAGTTGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTGTCTCTTGTTCGTACTCGCTTCGTGGGTCACCTTCGTGATGTTAGAAGAC

Basic information

species Vitis vinifera
transcript Vv08s0056g01110.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0056g01110.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os03g26960.1 (Oryza sativa), 3'ss of exon 13
aatctgcaggaaccatttcctgtacattcctttattttcaataaaggcatgtgtcatggctataatcacatcacttagttgattgattttttctttac-----agGTTACTACAGTTGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTGTCTCTTGTTCGTACTCGCTTCGTGGGTCACCTTCGTGATGTTAGAAGAC
              ||||  ||      |  |  |||| ||   ||   | | ||||   |         |  || |  ||     |||| | |  |      ||||||| ||||| || ||||| || ||||| ||||||||||| || ||| | |||||||| || || || || ||||| || ||||||||||| |||||||
------------gtatttattgcttgagctatgttttttaagctagtattttatcattctttctgctttgt-gctgacatgtacccttttctatgcatcatgtagGTTACCACAGTGGACAAGTTCCAGGGTCAACAAAATGATTTCATTTTATTATCTCTTGTCCGCACCCGTTTTGTGGGGCATCTTCGTGATGTCAGAAGAC

upper sequence: Vv08s0056g01110.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G410479_T01 (Zea mays), 3'ss of exon 14
aatctgcaggaaccatttcctgtacattcctttattttcaataaaggcatgtgtcatggctataatcacatcacttagttgattgattttttctttacagGTTACTACAGTTGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTGTCTCTTGTTCGTACTCGCTTCGTGGGTCACCTTCGTGATGTTAGAAGAC
              ||||||  ||  |    |  | ||   |||  |  ||     ||||| || |    |   |    |||      | |  | |  ||||||| || || || ||||| || || |||||||||||||| || ||||| |||||||| ||||| || || |||||||| ||||||||||| |||||||
-----------gtaatttccaataagta---tggtgtttgctaacagtttgc----tggctttatttttttgggt--actgacatccatgtcatatctagGTTACCACTGTGGACAAGTTCCAGGGCCAGCAAAATGATTTCATTTTACTTTCTCTTGTCCGTACCCGTTTTGTGGGTCATCTTCGTGATGTCAGAAGAC

upper sequence: Vv08s0056g01110.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA20G00260.1 (Glycine max), 3'ss of exon 12
--aatctgcagga-accatttcctgtacattcctttattttcaataaaggcatgtgtcatggctataatcacatcacttagttgattgattttttctttacagGTTACTACAGTTGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTGTCTCTTGTTCGTACTCGCTTCGTGGGTCACCTTCGTGATGTTAGAAGAC
   || |   ||| |  |       ||     |  ||||||   | |||   ||  ||     || | | |  ||  ||   | ||  ||  || || | |||||||||||||| |||||||||||||||||||||||||||||||| || || |||||||| |||||||| || || |||||||| |||||||| |||||| 
atgatgttttggacagtagagtaaatagccatcaatattttttttgaagttgtgattctcaatta-agttatctctgttttct-ataaatgattgctct-cagGTTACTACAGTGGATAAGTTTCAAGGTCAGCAAAATGATTTTATATTGCTATCTCTTGTGCGTACTCGATTTGTTGGTCACCTACGTGATGTAAGAAGAT

upper sequence: Vv08s0056g01110.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA0048S00340.1 (Glycine max), 3'ss of exon 12
----aatctgcagga-accatttcctgtacattcctttattttcaataaaggcatgtgtcatggctataatcacatcacttagttgattgattttttctttacagGTTACTACAGTTGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTGTCTCTTGTTCGTACTCGCTTCGTGGGTCACCTTCGTGATGTTAGAAGAC
     || |   ||| |  |        | | | ||| |||||   |||||   ||  ||     ||   |  | |   ||| |   |  ||  || || | |||||||||||||| |||||||||||||||||||||||||||||||| || || ||| |||| |||||||| || || |||||||| |||||||| |||||| 
gtatgatgttttggacagtagagtaaagagacttcttcattttt--taaagttgtgattctcaattaagttatctttgtttact--gtaaatgattgctct-cagGTTACTACAGTGGATAAGTTTCAAGGTCAGCAAAATGATTTTATATTGCTATCTATTGTGCGTACTCGATTTGTTGGTCACCTACGTGATGTAAGAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcatgtgtcatggctataatcacatcacttagttgattgattttttctttacagGTTACTACAGTTGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTGTCTCTTGTTCGTACTCGCTTCGTGGGTCACCTTCGTGATGTTAGAAGAC
                                   gattgat  putative branch site (score: 4)
                                     ttgattttttcttt  CT-rich tract
                                    attgattttttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatctgcaggaaccatttcctgtacattcctttattttcaataaaggcatgtgtcatggctataatcacatcacttagttgattgattttttctttacagGTTACTACAGTTGATAAGTTTCAAGGTCAGCAAAATGATTTTATCTTACTGTCTCTTGTTCGTACTCGCTTCGTGGGTCACCTTCGTGATGTTAGAAGAC

- - -gcaggaa
- - - - - - ccatttc
- - - - - - - - - - - -acattcc
- - - - - - - - - - - - - - - - - - - -aataaag
- - - - - - - - - - - - - - - - - - - - - - - gcatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - -tcatggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catcact