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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcatctttttgaagcacgtgtgatgattctttttaatttcattctattcaagttttgtcatttgaaagtggttctaagttctgtaatggaatgctgtagGATGCTGCTGCTTGGCTCGAGTACTTTGAGTCAAAGGCTTTTGAACAGCAAGAAGCTGCAAGAAATGGGACTCGAAAACCTGATGCATCCATAGCCAGCA

Basic information

species Vitis vinifera
transcript Vv15s0046g00740.t01
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 19
------atcatctttttgaagcacgtgtgatgattctttttaatttcattctattcaagttttgtcatttgaaagtggttctaagttctgtaatggaatgctgtagGATGCTGCTGCTTGGCTCGAGTACTTTGAGTCAAAGGCTTTTGAACAGCAAGAAGCTGCAAGAAATGGGACTCGAAAACCTGATGCATCCATAGCCAGCA
      |     ||||| ||  | || ||   |   |      |||   |  |||| | | |  ||  ||||   ||  |||   ||    | || |||||   |||| ||||| |||||||| || |||||||| ||||| | | | || || || ||||||||| | ||||| ||||| |||||||||||||| || || || |
ttcaacagttctttttttaaatatgtttgtacaaaataaactgtttg--ttaattccaatatcatc-cttgatcttgtgtctgttttgaaaattgaaatgc---agGACGCTGCCGCTTGGCTTGAATACTTTGAATCAAAAGTTATCGAGCAACAGGAAGCTGCACGCAATGGAACTCGGAAACCTGATGCATCAATTGCTAGTA

upper sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 21
--------atcatctttttgaagcacgtgtgatga-ttctttttaatttcattctattcaagttttgtcatttgaaagtggttctaagttctgtaatggaatgctgtagGATGCTGCTGCTTGGCTCGAGTACTTTGAGTCAAAGGCTTTTGAACAGCAAGAAGCTGCAAGAAATGGGACTCGAAAACCTGATGCATCCATAGCCAGCA
         || | || || ||  |    ||| || || |   |  || |||  | |  |  |||| | ||||         | ||  || | | ||  |||   | |||||||||| |||||||| ||||| ||||| || ||||||||||||||||||||||||||  ||||||| |||||||||||||||||||| ||||||||||
ctcaatttgtctttttcttaaaaaaatgatgaggaattataactgtttgcataatctatagttttttttattta--------tttacttttttttata-aatttggcagGATGCTGCGGCTTGGCTTGAGTATTTTGAATCCAAGGCTTTTGAACAGCAAGAAGCTGCTCGAAATGGTACTCGAAAACCTGATGCATCAATAGCCAGCA

upper sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 21
atcatctttttgaagcacgtgtgatgattctttttaatttcattctattca-agttttgtcatttgaaagtggttctaagttctgtaatggaatgctgtagGATGCTGCTGCTTGGCTCGAGTACTTTGAGTCAAAGGCTTTTGAACAGCAAGAAGCTGCAAGAAATGGGACTCGAAAACCTGATGCATCCATAGCCAGCA
||      |   |  | |   |  |  || | |||||    | |  ||    | || |  |  ||   |     | ||  || | |  |  |||     |||||||||| |||||||| ||||| |||||||| ||||||||||||||||||||||||||  ||||||| |||||||||||||||||||| ||||| ||||
attggtgctcc-agtctcaatttgtctttttctttaaaaaaaatgaatgaggaattataactgtttgcataatctatagttttttttttataatttgacagGATGCTGCGGCTTGGCTTGAGTATTTTGAGTCCAAGGCTTTTGAACAGCAAGAAGCTGCTCGAAATGGTACTCGAAAACCTGATGCATCAATAGCTAGCA

upper sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: AT1G01320.2 (Arabidopsis thaliana), 3'ss of exon 21
atcatctttttgaagcacgtgtgatgattctttttaatt--tcattctattcaagttt-tgtcatttgaaagtggt-tctaagttctgtaatgga----atgctgtagGATGCTGCTGCTTGGCTCGAGTACTTTGAGTCAAAGGCTTTTGAACAGCAAGAAGCTGCAAGAAATGGGACTCGAAAACCTGATGCATCCATAGCCAGCA
              | |  | | || ||  | |   ||    ||   || |||  ||| || ||  || | |   | | ||||||    ||| ||    ||| |  ||||||||||||||||||| || ||||||||||| |||||||||||||| |||||||||||  ||||||| ||||  || || || || || ||||||||||
--------------gtatatattatcatgatatcctatcagccaaattagtcatctttctgacaactgtatgcattctttaagtttgacaattgattatatggttcagGATGCTGCTGCTTGGCTAGAATACTTTGAGTCCAAGGCTTTTGAACAACAAGAAGCTGCGCGAAATGGTACTCCTAAGCCAGACGCGTCTATAGCCAGCA

upper sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: EFJ26424 (Selaginella moellendorffii), 3'ss of exon 20
atcatctttttgaagcacgtgtgatgattctttttaatttcattctattcaagttttgtcatttgaaagtggttctaagttctgtaatggaatgctgtagGATGCTGCTGCTTGGCTCGAGTACTTTGAGTCAAAGGCTTTTGAACAGCAAGAAGCTGCAAGAAATGGGACTCGAAAACCTGATGCATCCATAGCCAGCA
                               |  ||| ||  ||          | | | ||| ||   | |||||   |  |  | |       |||||||||| ||||||||||| || || || || ||||| ||| | || |||||||| |||||| ||| |||| | | |||||| ||||| || || |||||||
------------------------------gtactaacttatttgcgagtgcactattttattcga--tttgttctttttctttcatta------tgtagGATGCAGCTGCTTGGCTGGACTATTTCGACTCAAAAGCTGTAGAGCAGCAAGAGGCTGCACGAACTGGGGCACCAAAACCAGATGCTTCAATCGCCAGCA

upper sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: EFJ26734 (Selaginella moellendorffii), 3'ss of exon 20
atcatctttttgaagcacgtgtgatgattctttttaatttcattctattcaagttttgtcatttgaaagtggttctaagttctgtaatggaatgctgtagGATGCTGCTGCTTGGCTCGAGTACTTTGAGTCAAAGGCTTTTGAACAGCAAGAAGCTGCAAGAAATGGGACTCGAAAACCTGATGCATCCATAGCCAGCA
                               |  ||| ||  ||        | | | | ||| ||   | |||||   |  | | ||       |||||||||| ||||||||||| || || || || ||||| ||| | || |||||||| |||||| ||| |||| | | |||||| ||||| || || |||||||
------------------------------gtactaacttatttgcgagtgcgctattttattcga--tttgttctttttcttttcatta-----tgtagGATGCAGCTGCTTGGCTGGACTATTTCGACTCAAAAGCTGTAGAGCAGCAAGAGGCTGCACGAACTGGGGCACCAAAACCAGATGCTTCAATCGCCAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattcaagttttgtcatttgaaagtggttctaagttctgtaatggaatgctgtagGATGCTGCTGCTTGGCTCGAGTACTTTGAGTCAAAGGCTTTTGAACAGCAAGAAGCTGCAAGAAATGGGACTCGAAAACCTGATGCATCCATAGCCAGCA
               atttgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcatctttttgaagcacgtgtgatgattctttttaatttcattctattcaagttttgtcatttgaaagtggttctaagttctgtaatggaatgctgtagGATGCTGCTGCTTGGCTCGAGTACTTTGAGTCAAAGGCTTTTGAACAGCAAGAAGCTGCAAGAAATGGGACTCGAAAACCTGATGCATCCATAGCCAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - tgaagca