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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgattttctattattttaattatggtgtctcatcattttcactagtgtcgtttctgtattttttattctaactttcaattggagttctttgctttagGTTCAAATTTGATGATGAACGGGTGACAAAAGAAGATATTAAGAGGGCACTAGAGGAGCAGTATGGTGGTGAGGAAGAG

Basic information

species Vitis vinifera
transcript Vv13s0073g00610.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 11
-----ttttgattttctattattttaattatggtgtctcatcattttcactagtgtcgtttctgtattttttattctaactttcaattggagttctttgctttagGTTCAAATTTGATGATGAACGGGTGACAAAAGAAGATATTAAGAGGGCACTAGAGGAGCAGTATGGTGGTGAGGAAGAG
     |  | ||   ||    || ||  |    | | | | ||||  || | |    ||   |  ||   ||  | |||  ||   ||| | ||      ||||||| ||| |||||||||||||| |||||||||||||| || ||| ||||| |||||||||| || ||||| |||||||||
gttgctaataatgccctgcctttctatcttcaattttttagcattc-cattgg-acagtcatttgatgaatttatgtaatgtt---ttgtactttcacaatttagGTACAAGTTTGATGATGAACGAGTGACAAAAGAAGACATGAAGCGGGCATTAGAGGAGCAATACGGTGGCGAGGAAGAG

upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 7
ttttgatttt-ctattattttaattatggtgtctcatcattttcactagtgt-cgtttctgtattttttattctaactttcaattggagttctttgctttagGTTCAAATTTGATGATGAACGGGTGACAAAAGAAGATATTAAGAGGGCACTAGAGGAGCAGTATGGTGGTGAGGAAGAG
   ||||| | |  ||  |  || |||| |||   ||  |     ||||    |  |||   |||  ||||      ||  || ||   | || |     ||||  |||||||||||||| || || || |||||||||| ||||| ||| || || ||||| || || ||||||||||||
--atgattatgccttttgtcgaactatgctgttgaattttacatcctagcaaacagttcccaattcattatagatttttgaaaatgttatcctgtctaccagGTATAAATTTGATGATGAGCGTGTAACTAAAGAAGATACTAAGAAGGCCCTTGAAGAGCAATACGGGGGTGAGGAAGAG

upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 11
ttttgattttctattattt-taattatggtgtctcatcattttcactagtgtcgtttctgtattttttattctaactttcaattggagttctttgctttagGTTCAAATTTGATGATGAACGGGTGACAAAAGAAGATATTAAGAGGGCACTAGAGGAGCAGTATGGTGGTGAGGAAGAG
    ||   ||| |||     |      || | |    |  |  || | | |         |   |||||     | ||    || |     |   || ||||  ||||||||||||||||| || |||||||||||||  || |  || || || ||||||||||| ||||| ||||||
-aaagacactcttttagggacagaggcagtatatatctaggtaaacaattctgaacatgccacaatttatgtattcgtttggctgcatgctgtcatttcagGTATAAATTTGATGATGAACGAGTAACAAAAGAAGATACCAAAAAAGCCCTTGAAGAGCAGTATGGGGGTGAAGAAGAG

upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 1
------ttttgattttctattattttaattatggtgtctcatcattttcactagtgtcgtttctgtattttttattctaactttcaattggagttctttgctttagGTTCAAATTTGATGATGAACGGGTGACAAAAGAAGATATTAAGAGGGCACTAGAGGAGCAGTATGGTGGTGAGGAAGAG
      || |||     |  |  |  | |||   | |||    | ||| |  |  ||  |     ||   | |  | |   |||    |||  |  |||||   |||| ||||||||||||||| ||||| ||||||||||| | ||| | |||||| || ||||||||||| ||||||||||||
ctttgcttatgagcacattatcatccagttactatatctttgaagtttgaa-aacgttatacaaataccatct-ctatggtttttttctggt-tggtttgc---agGTACAAATTTGATGATGAGCGGGTTACAAAAGAAGACACTAAAAAGGCACTTGAAGAGCAGTATGGGGGTGAGGAAGAG

upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 11
ttttgattttctattatt--ttaattatggtgtctcatcattttcactagtgt-cgtttctgtattttttattctaactttcaattggagttctttgctttagGTTCAAATTTGATGATGAACGGGTGACAAAAGAAGATATTAAGAGGGCACTAGAGGAGCAGTATGGTGGTGAGGAAGAG
  | || |  || |  ||  ||    ||      |  ||||   |  || | |   |||    || |||||    |||| | ||||    |  |    || |||| |||||| |||||||| ||||| ||||||||||| | ||| | |||||| || ||||||||||| ||||||||||||
-atggaatcactttctttgcttgtgcataacacattgtcatcc-cgttactatatctttgaacatattttacaa-aactctgaatttttctggtggttttcagGTACAAATTCGATGATGAGCGGGTTACAAAAGAAGACACTAAAAAGGCACTTGAAGAGCAGTATGGGGGTGAGGAAGAG

upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G551402_T02 (Zea mays), 3'ss of exon 5
--ttttgattttctattatttta-attatggtgtctcatcattttcactagtgtcgtttctgtattttttattctaactttcaattggagttctttgctttagGTTCAAATTTGATGATGAACGGGTGACAAAAGAAGATATTAAGAGGGCACTAGAGGAGCAGTATGGTGGTGAGGAAGAG
       | |   | |  |||||  | |  || |   ||  |      |       |   |||||  | | |   || |||||  |   |||       | ||||  ||||||||||||||||| || ||||||||||||  ||||| ||| || || || || ||||| ||||| ||||||
agaaaaaaatgcttgtctttttatgtgaaagtattctatactgcatgatctgcatatccttgtatactgtctctgaattttcacctcatgttgcgc---tcagGTATAAATTTGATGATGAACGTGTAACAAAAGAAGATGCTAAGAAGGCTCTTGAAGAACAATATGGGGGTGATGAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtgtcgtttctgtattttttattctaactttcaattggagttctttgctttagGTTCAAATTTGATGATGAACGGGTGACAAAAGAAGATATTAAGAGGGCACTAGAGGAGCAGTATGGTGGTGAGGAAGAG
                       ttctaac  putative branch site (score: 1)
                                          ttctttgcttt  putative PPT
              tattttttattctaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgattttctattattttaattatggtgtctcatcattttcactagtgtcgtttctgtattttttattctaactttcaattggagttctttgctttagGTTCAAATTTGATGATGAACGGGTGACAAAAGAAGATATTAAGAGGGCACTAGAGGAGCAGTATGGTGGTGAGGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - -ctcatca