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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaagtctgcactttgtgttttcatttcctttatagggtgggaatgcatactattttctgagtctttgaccataccgctttttcttatataataatccagGAAGCTGATAAAATTGCACTTGCTGAAACAACGGGTCTGGACCAGAAGCAAATTAACAATTGGTTTATAAATCAACGAAAGCGGCACTGGAAACCATCAG

Basic information

species Vitis vinifera
transcript Vv01s0127g00210.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0127g00210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G04190.1 (Glycine max), 3'ss of exon 4
gtaagtctgcactttgtgttttcatttcctttatagggtggga-atgcatactattttctgagtctt-tgaccataccgctttttcttatataataatcc--agGAAGCTGATAAAATTGCACTTGCTGAAACAACGGGTCTGGACCAGAAGCAAATTAACAATTGGTTTATAAATCAACGAAAGCGGCACTGGAAACCATCAG
  |  |  |||       | ||  ||     |||    |   | |   |||  ||||| | | | || | |   |     ||| | |||  | || |||   ||||||||||||| |||| ||| ||| |  |||| || |||||||||||||||||||||||||||||||| || ||| |||| || || |||||||||||||
aaagataagcataaaaaatgttggttg----tatgaattattatacaaatatcatttttttaatattattaaacttgtattttgttttacttgatcatctatagGAAGCTGATAAGATTGAACTGGCTAAGTCAACAGGGCTGGACCAGAAGCAAATTAACAATTGGTTTATTAACCAAAGAAAACGTCATTGGAAACCATCAG

upper sequence: Vv01s0127g00210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G39170.1 (Glycine max), 3'ss of exon 4
gtaagtctgcactttgtgttttcatttcctt-tatagggtgg-gaatgcatactattttctgagtctttgaccataccgctttttcttatataataatccagGAAGCTGATAAAATTGCACTTGCTGAAACAACGGGTCTGGACCAGAAGCAAATTAACAATTGGTTTATAAATCAACGAAAGCGGCACTGGAAACCATCAG
 ||    |     | |      |||| | |   ||  | |   ||||  |    | | |  |  |   | | || |    | ||||||  || ||  | ||||||| |||||| |||||||| ||| || |||| ||  | |||||||||||||||||||| |||||||| |||||  ||||||| |||||||||||||| |
-tatagtttattataggaaaaacattgcttgacatcagttaatgaatataattaagtctacgcctacattatcaaaagcttgtttcttg-atgatctttcagGAAGGTGATAAGATTGCACTGGCTAAATCAACTGGGTTAGACCAGAAGCAAATTAACAACTGGTTTATTAATCAGAGAAAGCGTCACTGGAAACCATCTG

upper sequence: Vv01s0127g00210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA01G03450.1 (Glycine max), 3'ss of exon 5
--gtaagtctgcactttgtgttttcatttcctttatagggtgggaatgcatactattttctgagtctttgaccataccgctttttcttatataataatcc--agGAAGCTGATAAAATTGCACTTGCTGAAACAACGGGTCTGGACCAGAAGCAAATTAACAATTGGTTTATAAATCAACGAAAGCGGCACTGGAAACCATCAG
    ||   || |||      ||   ||   |  ||    |   |    ||| | |||| |   |  || | | |     ||| | |||  | || ||    ||||||||||||| |||| ||| ||| |  |||| || || |||||||||||||||||||||||||||||||| ||| |||| || || ||||||||||| |
tgaaaaaaatgtactaaaaaatt--gttggatgaattattttacagataatatt-ttttttatattattaaacttgt-attttgttttacttgatcatgtatagGAAGCTGATAAGATTGAACTGGCTAAGTCAACAGGGCTAGACCAGAAGCAAATTAACAATTGGTTTATAAACCAAAGAAAACGACATTGGAAACCATCCG

upper sequence: Vv01s0127g00210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G20460.1 (Glycine max), 3'ss of exon 1
gtaagtctgcactttgtgttttcatttcctttatagggtgggaatgcatactattttctgagtctt--tgaccataccgctttttcttatataataatccagGAAGCTGATAAAATTGCACTTGCTGAAACAACGGGTCTGGACCAGAAGCAAATTAACAATTGGTTTATAAATCAACGAAAGCGGCACTGGAAACCATCAG
 ||  |   ||     |  ||  |  |  ||  |    |  |   |   |||    ||| || ||   | | || |    | || ||| | | ||  | ||||||| |||||| |||||||| ||| || |||| ||  | |||||||||||||||||||| |||||||| |||||  |||||||  ||||||||||||| |
-tattttctcatggattacttgaaaatatttcttgacatcagttagtgaactgaagtcttagcctacattatcaaaagcttgttccttgt-tgatctttcagGAAGGTGATAAGATTGCACTGGCTAAATCAACTGGATTAGACCAGAAGCAAATTAACAACTGGTTTATTAATCAGAGAAAGCGCTACTGGAAACCATCTG

upper sequence: Vv01s0127g00210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ23803 (Selaginella moellendorffii), 3'ss of exon 4
--------------------gtaagtctgcactttgtgttttcatttcctttatag--ggtgggaatgc-ata-ctattttctgagtctttgaccat---accgctttttcttatataat--aatccagGAAGCTGAT-----------AAAATTGCA-CTTGCTGAAACAACGGGTCTGGACCAGAAGCAAATTAACAATTGGTTTATAAATCAACGAAAGCGGCACTGGAAACCATCAG
                        ||  ||| | ||||| |   ||  | |||| |   |||||  ||| ||  || | |||    | | || || |   | ||||||||  | |   ||    | |     ||||             ||| | | | || ||  || | || || |||||||  ||||| || ||||| ||||||||||| || ||||||||||||||||| ||    |
gtgagtacctttgtgttctttcttgttggcattctgtgtctct-ttctcgttatggctagtgggcgtgccatggctttgttccttctttgtgtccttttcatcgcttttttctttgacatttgcttcgttgtgctggacagGAGAACCAAAAGTCGAATCTCGCGCAATCCACCGGGCTGGACCCAAAGCAGATCAACAACTGGTTTATAAACCAGCGAAAGCGGCACTGGAATCCGCAGG

upper sequence: Vv01s0127g00210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ21443 (Selaginella moellendorffii), 3'ss of exon 5
--------------------gtaagtctgcactttgtgttttcatttcctttatag--ggtgggaatgc-ata-------ctattttctgagtctttgaccataccgctttttcttatat-------aataatccagGAAGCTGAT---AAAATTGCA-CTTGCTGAAACAACGGGTCTGGACCAGAAGCAAATTAACAATTGGTTTATAAATCAACGAAAGCGGCACTGGAAACCATCAG
                        ||  ||| |  |||| |   ||  | |||| |   |||||  ||| ||           || | || ||| ||  |  | |   ||| | | | ||         |   |  |  ||  ||    ||| | | | || ||  || | || || |||||||  ||||| || ||||| ||||||||||| || ||||||||||||||||| |||   |
gtgagtacctttgtgttctttcttgttggcattccgtgtctct-ttctcgttatggctagtgggcgtgccatggctttgttccttctttgtgtccttttcattgcttttttctttgacatttgcttcgctgtgctggacagGAGAACCAAAAGTCGAATCTCGCGCAATCCACCGGCCTGGACCCAAAGCAGATCAACAACTGGTTTATAAACCAGCGAAAGCGGCACTGGAATCCACAGG

upper sequence: Vv01s0127g00210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ07541 (Selaginella moellendorffii), 3'ss of exon 5
gtaagtctgcactttgtgttttcatttcctttatagggtgggaatgcatactattttctgagtctttgaccataccgctttttcttatataataatccagGAAGCTGATAAAATTGCACTTGCTGAAACAACGGGTCTGGACCAGAAGCAAATTAACAATTGGTTTATAAATCAACGAAAGCGGCACTGGAAACCATCAG
                                     ||  |     ||| | ||   ||| | | |   | ||    |||  ||  |       | ||||||   || |||  |   || ||       || || || |||||||||||||||||||| |||||||| || ||  ||||||| || ||||| || ||||
-------------------------------------gtatgttgtgatagttttcattgaatttatattcttagttgtttggctggt-------ttcagGAACAGGAGAAAGCTAACCTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG

upper sequence: Vv01s0127g00210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ10744 (Selaginella moellendorffii), 3'ss of exon 5
gtaagtctgcactttgtgttttcatttcctttatagggtgggaatgcatactattttctgagtctttgaccataccgctttttcttatataataatccagGAAGCTGATAAAATTGCACTTGCTGAAACAACGGGTCTGGACCAGAAGCAAATTAACAATTGGTTTATAAATCAACGAAAGCGGCACTGGAAACCATCAG
                                     ||  |     ||| | ||   ||| | | |   | ||    |||  ||  |       | ||||||   || |||  |   || ||       || || || ||||||||||||||||||||||||||||| || ||  ||||||| || ||||| || ||||
-------------------------------------gtatgttgtgatagttttcattgaatttatattcttagttgtttggctggt-------ttcagGAACAGGAGAAAGCTAACCTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAATTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatactattttctgagtctttgaccataccgctttttcttatataataatccagGAAGCTGATAAAATTGCACTTGCTGAAACAACGGGTCTGGACCAGAAGCAAATTAACAATTGGTTTATAAATCAACGAAAGCGGCACTGGAAACCATCAG
                  ctttgac  putative branch site (score: 4)
                                 tttttcttatataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtctgcactttgtgttttcatttcctttatagggtgggaatgcatactattttctgagtctttgaccataccgctttttcttatataataatccagGAAGCTGATAAAATTGCACTTGCTGAAACAACGGGTCTGGACCAGAAGCAAATTAACAATTGGTTTATAAATCAACGAAAGCGGCACTGGAAACCATCAG

- -agtctgc
- - - - - - - - - - - catttcc
- - - - - - - - - - - - - - - - - - - - -gaatgca