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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttggcttctcatgatatttatttaatcctttgttgtgttttcattatcctttagaaacttgaagtttatcatggcattgtttttttgcagGGCATTCTTTCTGATATTCTGAAATGCCTTGGTGACAATAAAAAGCATATGAGAGAATGCACATTGACTACTCTAGATGCTTGGCTTGCTGCTGTTCATC

Basic information

species Vitis vinifera
transcript Vv10s0116g00460.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0116g00460.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 27
gtttgttggcttctcatgatatttatttaatcctttgttgtgttttcattatcctttagaaacttgaagtttatcatggcattgtttttttgcagGGCATTCTTTCTGATATTCTGAAATGCCTTGGTGACAATAAAAAGCATATGAGAGAATGCACATTGACTACTCTAGATGCTTGGCTTGCTGCTGTTCATC
     ||||  | ||  | | |  |||  |   | | || |   ||     |  |   || ||  ||  |||   ||       || || || |||| ||| |  | ||| | || ||||| ||||| |||||||| ||||| ||||| ||||||||||||||| |||||||    ||| ||||||| | ||| |
---gtttggaatgtctagttttgcattatactttatattattcatttgcagttataatgacaca-gatattttctat-------ttgttatgaagGGTATTTTGGCAGATGTCCTAAAATGTCTTGGCGACAATAAGAAGCACATGAGGGAATGCACATTGACTGCTCTAGACTTATGGGTTGCTGCAGCTCAAC

upper sequence: Vv10s0116g00460.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM2G068755_T03 (Zea mays), 3'ss of exon 26
gtttgttggcttctcatgatatttatttaatcctttgttgtgttttcattatcctttagaaacttgaagtttatcatggcattgtttttt-tgcagGGCATTCTTTCTGATATTCTGAAATGCCTTGGTGACAATAAAAAGCATATGAGAGAATGCACATTGACTACTCTAGATGCTTGGCTTGCTGCTGTTCATC
|||||       |||      | | |||| ||||   | |  |||   |  ||  |   | |  |||    | |       |||||| || || |||| ||| |  | ||| | ||||| || |||||||||||||| ||||| ||| ||||||||||||||||| |||||||| | ||| ||||||| |  || |
gtttggaactaactcccatgttatctttactcctgcat-gcttttatttggtcgctaccataactgacaactgt-------ttgtttgttatgaagGGTATTTTGGCAGATGTGCTGAAGTGTCTTGGTGACAATAAGAAGCACATGCGAGAATGCACATTGACTGCTCTAGATTCATGGATTGCTGCAGCCCAAC

upper sequence: Vv10s0116g00460.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 9
gtttgttggcttctcatgatatttatttaatcctttgttgtgttttcattatcctttagaaacttgaagtttatcatggcattgtttttttgcagGGCATTCTTTCTGATATTCTGAAATGCCTTGGTGACAATAAAAAGCATATGAGAGAATGCACATTGACTACTCTAGATGCTTGGCTTGCTGCTGTTCATC
|||||  |   || |  |     ||| || |  | ||     || |  ||   |  || ||      | || |  |  |  |  || |  || |||| ||| |  | ||| | ||||| || |||||||||||||| ||||| ||| ||||||||||||||||| |||||||| | ||| ||||||| |  || |
gtttg--gaactcactcgcatgctatctatttttctgcatgcttatttttggtcactacaat-----aattaacaactgtttgtttgtcatgaagGGTATTTTGGCAGATGTGCTGAAGTGTCTTGGTGACAATAAGAAGCACATGCGAGAATGCACATTGACTGCTCTAGATTCGTGGGTTGCTGCAGCCCAAC

upper sequence: Vv10s0116g00460.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 29
------gtttgttggcttctcatgatatttatttaatcc-tttgttgtgttttcattatcctttagaaacttgaagtttatcatggcattgtttttttgcagGGCATTCTTTCTGATATTCTGAAATGCCTTGGTGACAATAAAAAGCATATGAGAGAATGCACATTGACTACTCTAGATGCTTGGCTTGCTGCTGTTCATC
      |  |  ||   | |  |  ||||| |||   || |||| |    |||   | |  | |      |||||  || || ||  || |||| || |||||| ||||| ||||||||  ||||||| ||||||||||| || ||||| |||||||||||   | ||| |||  ||||||||||||| |||||||| ||||
gtaagtggattctgttctgtttttgtattttttttccccatttggtactattttgctgttttctg----tttgaacatt-tcttgaaatggtttgtt-gcagGGTATTCTGTCTGATATATTGAAATGTCTTGGTGACAACAAGAAGCACATGAGAGAATGTGTACTGAATACCTTAGATGCTTGGCTGGCTGCTGTCCATC

upper sequence: Vv10s0116g00460.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 27
------gtttgttggcttctcatgatatttatttaatcctttgttgtgttttcattatcctttagaaacttgaagtttatcatggcattgtttttttgcagGGCATTCTTTCTGATATTCTGAAATGCCTTGGTGACAATAAAAAGCATATGAGAGAATGCACATTGACTACTCTAGATGCTTGGCTTGCTGCTGTTCATC
      |  |  ||   | |  |  ||||| |||     || ||  ||||||     |  | ||     ||  | | | || ||  || |||| || |||||| ||||| |||||| |  ||||||| ||||||||||| || ||||| |||||||||||     ||| |||  |||| |||||||| |||||||||||||
gtaagaggattctgttctgtttttgtatttttttcccatttggtactgtttt-gccgttttcta-----tttgaatatttcttgaaatggtttgtt-gcagGGTATTCTGTCTGATGTATTGAAATGTCTTGGTGACAACAAGAAGCACATGAGAGAATGTGTGCTGAATACATTAGACGCTTGGCTGGCTGCTGTTCATC

upper sequence: Vv10s0116g00460.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: AT2G35630.1 (Arabidopsis thaliana), 3'ss of exon 27
gtttgttggcttctcatgatatttatttaatcctttgt-tgtgttttcattatcctttagaaacttg--aagtttatcatggcattgtttttttg----cagGGCATTCTTTCTGATATTCTGAAATGCCTTGGTGACAATAAAAAGCATATGAGAGAATGCACATTGACTACTCTAGATGCTTGGCTTGCTGCTGTTCATC
    ||||| |   ||||  ||  ||| ||     | | |    | | || ||  | |       ||  |  |||| || |   |||  || |      ||||| ||||| |||||| ||||||||||||| |||||||| || ||||| |||||||| || || ||| || |||| ||    ||||||| |||||| ||||
----gttggttatacatgtcatgcattgaaaatagtatgtacactgtaatcatagtatcactgtctgccatttttaccaagtacttgagttatctacctcagGGAATTCTGTCTGATGTTCTGAAATGCCTCGGTGACAACAAGAAGCACATGAGAGAGTGTACCTTGGCTGCTCTTGACTTGTGGCTTGGTGCTGTGCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttcattatcctttagaaacttgaagtttatcatggcattgtttttttgcagGGCATTCTTTCTGATATTCTGAAATGCCTTGGTGACAATAAAAAGCATATGAGAGAATGCACATTGACTACTCTAGATGCTTGGCTTGCTGCTGTTCATC
                                         ttgttttttt  CT-rich tract
                                        attgttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttggcttctcatgatatttatttaatcctttgttgtgttttcattatcctttagaaacttgaagtttatcatggcattgtttttttgcagGGCATTCTTTCTGATATTCTGAAATGCCTTGGTGACAATAAAAAGCATATGAGAGAATGCACATTGACTACTCTAGATGCTTGGCTTGCTGCTGTTCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT