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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcttatcatgagcttactaatctaagcaagctatcccattagaaaaatggagtgttctttgatgacataagatcttctcattcacttctttgaatacagATATTCAATGGGGTGTTTCTTAAAGTGAACAAAGCAACAATGAACAAGTTGCACAGGGTTGAGCCTTATGTGACTTATGG

Basic information

species Vitis vinifera
transcript Vv09s0054g00060.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0054g00060.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 4
ctcttatcatgagcttactaatctaagcaagctatcccattagaaaaatggagtgttctttgatgacataagatcttctcattcacttctttgaatacagATATTCAATGGGGTGTTTCTTAAAGTGAACAAAGCAACAATGAACAAGTTGCACAGGGTTGAGCCTTATGTGACTTATGG
         || | || | |||      | | | |  |  | |||  ||||    || |||| ||| |   ||  || | ||| | || ||      |||||||||||||| ||||| || ||||| ||||| || || || |||| | | | ||||||||||||||||||  | |||||
--------gtgggtttgccaatt-----acgttcttgctattgaattatggccgattgtttg-tgaaactggacatt-taatttaattttt------cagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG

upper sequence: Vv09s0054g00060.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G23750.2 (Glycine max), 3'ss of exon 4
--ctcttatcatg---agcttactaatctaagcaagctatcccattagaaaaatggagt-gttctttgatgacataagatcttctcattcacttctttgaatacagATATTCAATGGGGTGTTTCTTAAAGTGAACAAAGCAACAATGAACAAGTTGCACAGGGTTGAGCCTTATGTGACTTATGG
   | | | ||||   ||   || | | ||   ||  | |    ||  |   ||  ||  |   |||| |||        ||| ||      || ||  || |||||| |||||||| || ||||| ||||| |||||||| ||| |||||| | ||||||| |||||||| ||||||||||||||
atttttgagcatgcaaagagcaccattatactgaatatttgtatttgtattcatatagaagcaatttggtgatgctgatccttatc------tttttgtaaaacagATTTTCAATGGTGTATTTCTCAAAGTTAACAAAGCCACAGTGAACATGCTGCACAGAGTTGAGCCCTATGTGACTTATGG

upper sequence: Vv09s0054g00060.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G02270.1 (Glycine max), 3'ss of exon 4
ctcttatcatg---agcttactaatctaagcaagctat---cccattagaaaaatggagtgttctttgatgacataagatcttctcattcacttctttgaatacagATATTCAATGGGGTGTTTCTTAAAGTGAACAAAGCAACAATGAACAAGTTGCACAGGGTTGAGCCTTATGTGACTTATGG
 |   |  |||   ||   |||| | ||  |||  | |       ||   | |    |  |   ||||||||        ||| ||      || ||  || |||||| |||||||| || ||||| ||||| |||||||| ||| |||||| | ||||||| |||||||| ||||||||||||||
tttagaggatgcagaggaaactattatactcaatgtttgtatttgttttcatataaaaaagcaatttgatgatgctgatccttatc------tttttgtaaaacagATTTTCAATGGTGTATTTCTCAAAGTTAACAAAGCCACAGTGAACATGCTGCACAGAGTTGAGCCGTATGTGACTTATGG

upper sequence: Vv09s0054g00060.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 4
--ctcttatcatgagcttactaatctaa-gcaagctatcccattagaaaaatggagtgttctttgatgacataagatcttctcattcacttctttgaatacagATATTCAATGGGGTGTTTCTTAAAGTGAACAAAGCAACAATGAACAAGTTGCACAGGGTTGAGCCTTATGTGACTTATGG
  || |||| ||    | | | ||  |   |   ||| |    |   |    | ||     || ||    |||   |  |     |   |  ||||  | ||||| || ||||| || |||||||||||||||||||| ||  |||| | | |||| ||||| ||||||||||| || |||||
gacttttat-attctttcatttattgattaccttctagctttgtcatatgtcgaagcaaagttgga--gtatagctttattattatgtttattttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTGCATAGGGTAGAGCCTTATGTTACCTATGG

upper sequence: Vv09s0054g00060.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G18170.1 (Glycine max), 3'ss of exon 4
ctcttatcatgagcttactaatctaagcaagctatc--ccattagaaaaatggagtgttctttgatgacataagatcttctcattcacttc--tttgaatacagATATTCAATGGGGTGTTTCTTAAAGTGAACAAAGCAACAATGAACAAGTTGCACAGGGTTGAGCCTTATGTGACTTATGG
     ||  |||  ||  |  |    ||  ||| ||  || || |  | |||       |   | ||   ||    ||| |  ||   ||   ||||  | ||||| || ||||| || |||||||||||||||||||| ||| |||| | | | || ||||| ||||||||||| || |||||
--taaattttgattttgatgttgct-gctggctgtcttccctttgtcatatgtc-caagcaaagttggagtatatccttattgttatgtttattttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACAGTGAATATGCTCCATAGGGTAGAGCCTTATGTTACCTATGG

upper sequence: Vv09s0054g00060.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT2G44120.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------------------------------------------------------ctcttatcatgagctt--actaatctaagcaagctatcc---------cattagaaaaatggagtgttctttgatgacat-aagatcttctcattcacttctttgaatacagATATTCAATGGGGTGTTTCTTAAAGTGAACAAAGCAACAATGAACAAGTTGCACAGGGTTGAGCCTTATGTGACTTATGG
                                                                  || | ||  | |   |||||| |  |  || |  |            ||| || |  | ||    || |   |   | ||||  ||  | |||   |   |   | ||||| |||||||| ||||||||||| |||||||| |||||| | |||| | ||| | | ||||| || || |||||||| ||
gtaggtttcacagtttgttattttcatccagctatattagcctaacatatgattattgattaatatttgttatatgttcaaactaatatgtgatagttgcctgttcatcatttttaaaagagagtagaagactattgcgttgtcaagaagtttactttcgtatacatttgtgcagATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatggagtgttctttgatgacataagatcttctcattcacttctttgaatacagATATTCAATGGGGTGTTTCTTAAAGTGAACAAAGCAACAATGAACAAGTTGCACAGGGTTGAGCCTTATGTGACTTATGG
            ctttgat  putative branch site (score: 5)
                            tcttctcattcacttc  putative PPT
                                            tttgaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcttatcatgagcttactaatctaagcaagctatcccattagaaaaatggagtgttctttgatgacataagatcttctcattcacttctttgaatacagATATTCAATGGGGTGTTTCTTAAAGTGAACAAAGCAACAATGAACAAGTTGCACAGGGTTGAGCCTTATGTGACTTATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA