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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtctaatttttgaatttggagtaacttggataaaattccacggatatttgtaagacattttcccctatgattattatcaaatcttgttttcgtcttccagGCCATTGACACAAGAGATGCTTTGGCGAAATCAATTTATGCTTGTTTATTTGACTGGCTGGTCGAACAAATCAACAAGTCACTTGCTGTAGGAAAACGGC

Basic information

species Vitis vinifera
transcript Vv10s0071g00210.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 12
gtctaatttttgaatttggag--taacttgg-ataaaattccacggatatttgtaagacattttcccctatgattattatcaaatcttgttttcg--tcttccagGCCATTGACACAAGAGATGCTTTGGCGAAATCAATTTATGCTTGTTTATTTGACTGGCTGGTCGAACAAATCAACAAGTCACTTGCTGTAGGAAAACGGC
      ||  ||| ||| |    |||||      ||  |  ||   | |    | | |   ||       | |   || |  |  |   | || |  | || ||||| || |||||||||||||| ||||| || ||| | |||||  |||| ||||| ||||| || |||||||| |||||||| ||| | || || || || |
-----gttagtgagttttgttcttaactaaatgcaaggtagcaacaacagccatgaaagtattgttaaattcacagttctgcacccacctctttgaatattgcagGCAATCGACACAAGAGATGCGTTGGCCAAGTCACTCTATGCCAGTTTGTTTGAGTGGCTTGTTGAACAAATTAACAAGTCTCTTTCAGTTGGCAAGCGTC

upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 12
----------gtctaatttttgaatttggagtaacttggataaaattccacggatatttgtaagacattttcccctatgattattatcaaatcttgttttcgtcttccagGCCATTGACACAAGAGATGCTTTGGCGAAATCAATTTATGCTTGTTTATTTGACTGGCTGGTCGAACAAATCAACAAGTCACTTGCTGTAGGAAAACGGC
          ||||| ||  |  |||  |   |||     | |   |    |    |||  || | ||||     | ||||    ||| |  |||  |||  | || ||||| | |||||||||||||||| |||| |||||| | |||||  |||| ||||| ||||| || |||||||| || ||||| ||  | || || || || |
agccactcaagtctatttaatagatt--gcccaacccctgttagggttaggg----tttccaatatatttgtatatctgatg--catctaccctt--tttaatatttcagGCAACTGACACAAGAGATGCTCTGGCCAAATCAGTGTATGCCAGTTTGTTTGAGTGGCTTGTAGAACAAATTAATAAGTCTCTCTCAGTTGGCAAGCGTC

upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G139583_T02 (Zea mays), 3'ss of exon 12
gtctaatttttgaatttggagtaacttg-gataaaattccacggatatttgtaagacattttcccctatgattat-tatcaaatct---tgttttcgtcttccagGCCATTGACACAAGAGATGCTTTGGCGAAATCAATTTATGCTTGTTTATTTGACTGGCTGGTCGAACAAATCAACAAGTCACTTGCTGTAGGAAAACGGC
         ||   | |  |  |||||  | |||| |  ||   ||| ||||||||  |  |    | ||  ||| |     ||||     ||||  | || ||||| | |||||||||||||||| |||| |||||| | |||||  |||| ||||| ||||| || |||||||| || ||||| ||  | || || || || |
--------gtttgttgtttatcaacttatggtaaactatcaaccataattgtaagaagtactataatttgtatatatgatgcatctaccctttttaatatttcagGCAACTGACACAAGAGATGCTCTGGCCAAATCATTGTATGCCAGTTTGTTTGAATGGCTTGTAGAACAAATTAATAAGTCTCTCTCAGTTGGCAAGCGTC

upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA20G23660.1 (Glycine max), 3'ss of exon 13
-----gtctaatttttgaatttggagtaacttggataaaattccacggatatttgtaagacattttcccctatgattattatcaaatcttgttttcgtcttccagGCCATTGACACAAGAGATGCTTTGGCGAAATCAATTTATGCTTGTTTATTTGACTGGCTGGTCGAACAAATCAACAAGTCACTTGCTGTAGGAAAACGGC
        |   |  ||||  | |  | | ||||||     | |  ||| ||||  |    ||  |    |||||  || ||     ||| || |  ||   ||||| |||||  ||||||||||||||||||| ||||| ||||||||| | ||||| ||| |||| |||||||| ||| | || ||||| || || ||| | |
acacttcattggtgatgaacattgcttca-ttggattttccttcttgga-attttcactcaatcgttaaatatga--atgattgttgctt-ttcttatcacgcagGCTATTGATGCAAGAGATGCTTTGGCGAAGTCAATATATGCTTGTCTGTTTGATTGGTTGGTTGAACAAATAAACCAATCCCTTGCGGTTGGCAAAAGAC

upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 11
gtctaatttttgaatttggagtaacttggataaaattccac-ggatatttgta--agacattttccccta---tgattattatcaaatcttgttt---tcgtcttccagGCCATTGACACAAGAGATGCTTTGGCGAAATCAATTTATGCTTGTTTATTTGACTGGCTGGTCGAACAAATCAACAAGTCACTTGCTGTAGGAAAACGGC
            || ||         |||| |    | ||  |||| ||  |    |  |||| | |  |   | | ||| |   | | ||| ||   |  || |  |||| |||||  | ||||||||||||||||| ||||| ||||||||| | ||||| ||| |||| |||||||| ||||| || || || || || ||| | |
---------gaaaacttcattggtaatggacattgcttcattggattttccttcttggaatttccactcaatctaaatatgaatgattgttgcttgtcttatcatgtagGCTATTGATGCGAGAGATGCTTTGGCGAAGTCAATATATGCTTGTCTGTTTGATTGGTTGGTTGAACAAATAAACAAATCCCTCGCGGTTGGCAAAAGAC

upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 13
gtctaattt--ttgaatttggagtaacttggataaaattccacggatatttgtaagacattttcccctatgat-tattatcaaatcttgttttcgtcttccagGCCATTGACACAAGAGATGCTTTGGCGAAATCAATTTATGCTTGTTTATTTGACTGGCTGGTCGAACAAATCAACAAGTCACTTGCTGTAGGAAAACGGC
  |  ||||  ||| | ||    |     |   |  || ||||    ||   | |    |||||       || | |||   | | || |||| ||||| |||||||||||  |||||||||||||||| || ||||| ||||| ||  | ||||| ||| |||| ||||| || || || ||||||||||| || ||| | |
--cagatttggttggactttatttgtaaggtgcatgatgccactatcatg-atgattttttttctttctcaatatcttaaatagtattttttttgtcttgcagGCCATTGATGCAAGAGATGCTTTGGCAAAGTCAATATATGCATGCCTGTTTGATTGGTTGGTTGAACAGATAAATAAATCACTTGCTGTTGGCAAAAGAC

upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 11
gtctaatttttgaatttggagtaacttggataaaattcca-cggatatttgtaa-gacattttcccctatgattattatcaaatcttgttttcgtcttccagGCCATTGACACAAGAGATGCTTTGGCGAAATCAATTTATGCTTGTTTATTTGACTGGCTGGTCGAACAAATCAACAAGTCACTTGCTGTAGGAAAACGGC
   ||   | |   ||   | || |||| || |  |   |   ||| ||| ||| ||  ||||  | |   |    | | |||| || ||||  |||| ||||| |||||  |||||||||||||||| || ||||| ||||| ||  | ||||| ||| |||| ||||| || || || ||||||||||| || ||| | |
tggtagaatgtaggttc--aataccttgaatgatttggaaatagatgtttataatgattttttttctttccaaatatcttaaatattttttttttcttgcagGCAATTGATGCAAGAGATGCTTTGGCAAAGTCAATATATGCATGCCTGTTTGATTGGTTGGTTGAACAGATAAATAAATCACTTGCTGTTGGCAAAAGAC

upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 13
gtctaatttttgaat--ttggagtaacttggataaaattccacggatatttgtaagacattttcccctatg-attattatcaaatcttgttttcgtcttccagGCCATTGACACAAGAGATGCTTTGGCGAAATCAATTTATGCTTGTTTATTTGACTGGCTGGTCGAACAAATCAACAAGTCACTTGCTGTAGGAAAACGGC
     | |||| | |  |  ||  |   ||  |  | ||  |      |   |     | |||    | |  ||| |  | | ||  | ||||  | || |||||||||||  ||||||||||||| || |||||||| ||| | ||  | |||||||||||||| ||||| |||||||| || |||||||| |||||  |||
---agacttttaattcctccgaagacgatgattgtatttttagtcccgtccttcttttactttaaattttacattttcttgatattctttttttttttttcagGCCATTGATGCAAGAGATGCTTTAGCAAAATCAATCTATTCGTGCCTGTTTGACTGGCTGGTTGAACAGATCAACAAATCTCTTGCTGTGGGAAAGAGGC

upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT1G50360.1 (Arabidopsis thaliana), 3'ss of exon 13
----------------------------------------------------------------gtctaatttttgaatttggagtaacttggataaaattccacggatatttg----taagacattttcccctatgattattatcaaa--tcttgttttcgtcttccagGCCATTGACACAAGAGATGCTTTGGCGAAATCAATTTATGCTTGTTTATTTGACTGGCTGGTCGAACAAATCAACAAGTCACTTGCTGTAGGAAAACGGC
                                                                |  |  ||||   | |   |  |   |  ||       |     ||||||     ||| | | |||   |||  || |  | |||  | || || |   |||||||||||||||| ||||||||||||| || || ||||| ||||| ||  ||||||||||||| || ||||| || ||||| || ||||| || |||||  || 
gtaggccttttagaaagattttttttttcacttgattctttgtgtgtacttttattctgagtagggttggttttaacactgtaatcatgatctatgccccctcttacttatttggaatcaagccttgttcatttatttttgtggtgaaagtttttcttatttgcttccagGCCATTGACGCAAGAGATGCTTTAGCAAAGTCAATCTATGCCTGCCTATTTGACTGGCTAGTTGAACAGATTAACAAATCTCTTGCGGTGGGAAAGAGGA

upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: EFJ05534 (Selaginella moellendorffii), 3'ss of exon 11
gtctaatttttgaatttggagtaacttggataaaattccacggatatttgtaagacattttcccctatgattat-tatcaaatcttgttttcgtcttccagGCCATTGACACAAGAGATGCTTTGGCGAAATCAATTTATGCTTGTTTATTTGACTGGCTGGTCGAACAAATCAACAAGTCACTTGCTGTAGGAAAACGGC
                                         | ||  |    | |  |||      |||   || | | |  || | ||  |   |  |||||||| ||| |||||||||| ||||| ||| | || ||| | ||||||||||| |||||||| ||| | || ||||| || || |  |  ||||||    
-----------------------------------------gtatgctatggataggtttcatggaatggcaatatgttagctcgttttcgctcgtcacagGCCATCGACTCAAGAGATGCGTTGGCAAAAGCCATATATTCCTGTTTATTTGAGTGGCTGGTTGAAAAGATAAACAACTCTCTGGACGCCGGAAAAGCTT

upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: EFJ25955 (Selaginella moellendorffii), 3'ss of exon 11
gtctaatttttgaatttggagtaacttggataaaattccacggatatttgtaagacattttcccctatgattattatcaaatcttgttttcgtc--ttccagGCCATTGACACAAGAGATGCTTTGGCGAAATCAATTTATGCTTGTTTATTTGACTGGCTGGTCGAACAAATCAACAAGTCACTTGCTGTAGGAAAACGGC
                                         | ||  |    | |  |||      |||   || ||  || || |||||||    |  |||||||| ||| |||||||||| ||||| ||| | || ||| | ||||||||||| |||||||| ||| | || ||||| || || |  |  |||||     
-----------------------------------------gtatgctatggataggtttcatggaatggcaat-atgtaagctcgttttcgctcgtcacagGCCATCGACTCAAGAGATGCGTTGGCAAAAGCCATATATTCCTGTTTATTTGAGTGGCTGGTTGAAAAGATAAACAACTCTCTGGACGCCGGAAAGGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgtaagacattttcccctatgattattatcaaatcttgttttcgtcttccagGCCATTGACACAAGAGATGCTTTGGCGAAATCAATTTATGCTTGTTTATTTGACTGGCTGGTCGAACAAATCAACAAGTCACTTGCTGTAGGAAAACGGC
                                    tcttgttttcgtcttc  CT-rich tract
                        attattatcaaatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctaatttttgaatttggagtaacttggataaaattccacggatatttgtaagacattttcccctatgattattatcaaatcttgttttcgtcttccagGCCATTGACACAAGAGATGCTTTGGCGAAATCAATTTATGCTTGTTTATTTGACTGGCTGGTCGAACAAATCAACAAGTCACTTGCTGTAGGAAAACGGC

- - - - - - - - - - - - - -ggataaa
- - - - - - - - - - - - - - - - - - -ccacgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atcaaat