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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttttatgtcctgtatcttggttttttttgagggattgtttgctatatcttgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGGATTATTTGCATGGAAGATCTTATTCATGAAATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGACCAT

Basic information

species Vitis vinifera
transcript Vv09s0054g00090.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0054g00090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g51630.2 (Oryza sativa), 3'ss of exon 6
gtttttatgtcctgtatcttggttttttttgagggattgtttgctatatcttgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGGATTATTTGCATGGAAGATCTTATTCATGAAATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGACCAT
  |||     | || ||||   || || |      | ||| |    |      || |   | || | ||   ||   ||| |||||| |||  ||  || || ||||| || |||||| ||||||| |||||||||||||| || ||||| |||||||||||||||||||| || ||||
-gtttgccaccttgaatctcacttgttctgcttttactgtgtcaattggtaccttacagtcttggtgtttgtat--cagGGTTTGGGTAAGCATGACATCATCTGCATTGAGGATCTTGTTCATGAGATCATGACTGTTGGCCCACATTTCAAGGAGGCCAACAACTTCCTCTGGCCAT

upper sequence: Vv09s0054g00090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G094051_T05 (Zea mays), 3'ss of exon 5
--------------gtttttatgtcctgtatcttggttttttttgagggattgtttgctatatcttgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGGATTATTTGCATGGAAGATCTTATTCATGAAATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGACCAT
                 | ||  ||  ||  ||  ||| | ||| |   ||       || ||  || |    ||||  |  |||  |   |||  ||||| |||      || || ||||| || |||||| |||| || |||||||||||||| || || || |||||||||||||||||||| || ||||
gtttgtaaacttggaactctacatctggttcctgtgttctgttt-atatatgacaatttacatgatgatctccaccttttggtgttctatcagGGCTTGGGCAAGCACAACATCATCTGCATTGAGGATCTTGTTCACGAGATCATGACTGTTGGCCCACACTTCAAGGAGGCCAACAACTTCCTGTGGCCAT

upper sequence: Vv09s0054g00090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 6
------gtttttatgtcctgtatcttggttttttttgagg-gattgtttgctatatcttgt-tgctaacctgc----ttttgtga--tgatagGCTTTGGGGAAGTTTGGGATTATTTGCATGGAAGATCTTATTCATGAAATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGACCAT
        | ||  |  ||| | || | |  ||| |||   | |||| |   | |  ||   || | | || |    ||| |||   |   |||  ||||| |||      || |||||||| || |||||| ||||||| ||||||||||| || || || || |||||||| ||||||||||| || ||||
gtttgcaatcttgagctctgcacctggatcctttgtgatctgcttgtatttgacaatttacatgatgatctccaccatttggtgttctatcagGGCTTGGGCAAGCACAACATCATTTGCATTGAGGATCTTGTTCATGAGATCATGACTGTCGGCCCACACTTCAAGGAGGCGAACAACTTCCTTTGGCCAT

upper sequence: Vv09s0054g00090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 6
---------------------------gtttttatgtcctgtatcttggttttttttgagggattgtttgctatatcttgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGGATTATTTGCATGGAAGATCTTATTCATGAAATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGACCAT
                           |||  | ||| |||| |  |  || ||| |    ||   ||| |   ||  || |    ||||  | ||||  |   |||  ||||  |||      || || ||| | || |||||| |||| || |||||||||||||| || || || |||||||| ||||||||||| || ||||
gtttgtaaacttggaactgtacatctggttcctgtgttctgt-ttatatttgtttatatttgacaatttac---atgatgatctccaccttttgttgttctatcagGGCTTGGACAAGCAAAAAATCATCTGCGTCGAGGATCTTGTTCACGAGATCATGACTGTTGGCCCACACTTCAAGGAGGCGAACAACTTCCTGTGGCCAT

upper sequence: Vv09s0054g00090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G18170.1 (Glycine max), 3'ss of exon 6
gtttttatgtcctgtatcttggttttttttgaggg-----attgtttgctatatcttgttgctaacctgcttt-------------tgtgatgatagGCTTTGGGGAAGTTTGGGATTATTTGCATGGAAGATCTTATTCATGAAATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGACCAT
||   | ||  || |    | ||  | | | |        |||| ||| | | |  | || || |  |  |||             |   |||  || |||||||||||  |||||| |||||| | |||||||| || ||||| |||||||||||||||||||| || |||||||||||||| || || || || |
gtccgtgtggtctattctgtagtcctctgtaaacacttccattgcttgtt-tgttctattacttagtttttttccctgacataacattcaatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATCATGACTGTTGGACCTCACTTCAAGGAGGCCAACAATTTTCTGTGGCCTT

upper sequence: Vv09s0054g00090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 6
--------gtttttatgtcctgt-atcttggttttttttgagggattgtttgctatatc--------ttgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGGATTATTTGCATGGAAGATCTTATTCATGAAATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGACCAT
        | | |   | |  || |||||    | | |  |  | ||||||| | |||         || | ||| || |    ||   |||  || |||||||||||  |||||| |||||| | |||||||| || ||||| ||  ||||||||||||||||||| |||||||||||||| || || || || |
gtctgtctggtgtaccggctagtcatctttaaatatctccattgcttgtttgttctattactcagttttttcgctgacataacatt-caatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATATTGACTGTTGGACCTCATTTCAAGGAGGCCAACAATTTTCTGTGGCCTT

upper sequence: Vv09s0054g00090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G02270.1 (Glycine max), 3'ss of exon 6
gtttttatgtcctgtatcttggttttttttgagggattgt--ttgctatat--cttgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGGATTATTTGCATGGAAGATCTTATTCATGAAATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGACCAT
     |||    | | |     || ||  | |  |||| |  ||  |      | || | || || |||||    ||||| ||||| |||| |||| ||| || || | ||  |||||||| || ||||| ||||| |||||||||||||| ||||||||||| ||||||||||| || ||||
----gtattgtttattttacaattcttccttacagattttaattaattcgctacatgcttcttacttgcttg---gatgacagGCTCTGGGCAAGTATGGAATCATATCCACTGAAGATCTGATCCATGAGATCATCACTGTTGGACCTCACTTTAAGGAGGCTAACAACTTCCTTTGGCCAT

upper sequence: Vv09s0054g00090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G23750.2 (Glycine max), 3'ss of exon 6
--gtttttatgtcctgtatcttggttttttttgagggattgtttgctatatcttgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGGATTATTTGCATGGAAGATCTTATTCATGAAATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGACCAT
   || |||  |      |||   ||     |  |   |  ||  ||| ||   | | || || |||||    ||||| ||||  |||| || | ||| || |||| ||  |||||||| || ||||| ||||| |||||||| ||||| ||||||||||| ||||||||||| || ||||
gtattgttaatttacaattctgtattacaaatttgaattaattcactacat---gcttctgacttgcttg---gatgacagGCGCTGGGCAAATATGGAATCATTTCCACTGAAGATCTGATCCATGAGATCATCACTGTTGGGCCTCACTTTAAGGAGGCTAACAACTTCCTTTGGCCAT

upper sequence: Vv09s0054g00090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
----------------gtttttatgtcctgtatcttggttttttttgaggg--attgtttgctatatcttg--ttgctaacctgcttttgtgatg-atagGCTTTGGGGAAGTTTGGGATTATTTGCATGGAAGATCTTATTCATGAAATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGACCAT
                 ||   |     |  |  || ||      ||| |   ||  |||||  |   ||    || | |  |   ||  |  ||  |||||  | || ||||| || || || || || || ||||| |||||||| ||| | |||||||||||||| || ||||| |||||||||||  ||||  | |
tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgtatcctttgcagtgatttcacctgatgaattctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttgagggattgtttgctatatcttgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGGATTATTTGCATGGAAGATCTTATTCATGAAATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGACCAT
                              tgctaac  putative branch site (score: 1)
                                        cttttgt  putative PPT
                    tatatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttttatgtcctgtatcttggttttttttgagggattgtttgctatatcttgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGGATTATTTGCATGGAAGATCTTATTCATGAAATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGACCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG