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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaaaccttgaaagtgcctgttatcttcattttattcacttttgcatggaaatctgctattccctcaggattactaattttttcaggtagtggtctgcagGGAAAACTGTAATAACCAGTGATCAAGCACTTAAATTGGAATTTATTCCTGATTGGATAGCCATTGTTGGCAGTGGCTACATTGGTCTTGAGTTTAGTGA

Basic information

species Vitis vinifera
transcript Vv14s0060g01410.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g01410.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 4
--gaaaaccttgaaagtgcctgttatcttca---ttttattcacttttgcatggaa-atctgctattccctcaggattactaattttttcaggtagtggtctgcagGGAAAACTGTAATAACCAGTGATCAAGCACTTAAATTGGAATTTATTCCTGATTGGATAGCCATTGTTGGCAGTGGCTACATTGGTCTTGAGTTTAGTGA
  ||  | |   |  | |  ||    |   |   | ||    ||  || | ||  | | ||  | |||   ||| |         |  |  |  | |  | |||||||||||||||  | ||||||||||| ||||| ||| | || | | | || || |||||||| || ||||| ||||| |||||||| ||||| || |||||
aagattagcacaattgggtttgcagacccaaatgtgttgcctaccatttcttgttatacctattgttcttacagaa------gcctgctgggcaacttttgtgcagGGAAAACTGTTTTTACCAGTGATCATGCACTAAAACTTGAGTCTGTCCCGGACTGGATAGCAATCGTTGGAAGTGGATACATTGGGCTTGAATTCAGTGA

upper sequence: Vv14s0060g01410.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
-gaaaaccttgaaagtgcctgttatcttcattttattcacttttgcatggaaatctgctattccctcaggattactaattttt-tcaggtagtggtctgcagGGAAAACTGTAATAACCAGTGATCAAGCACTTAAATTGGAATTTATTCCTGATTGGATAGCCATTGTTGGCAGTGGCTACATTGGTCTTGAGTTTAGTGA
 |    | ||     |   ||  || |  |||   || || |||     | | | | ||  |         | || || || |    | |  |  | |||||||||||||||| | || |||||||| ||||| ||| | || |   |||| || |||||||| |||||||| ||||| |||||||| |||||||| |||||
tgggtgcattttttat-tgtgacatgtgtatta-gttgacattttttgtgtactttccttgttgtatgttctcacaaaattctactggatgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA

upper sequence: Vv14s0060g01410.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 4
gaaaaccttgaaagtgcctgttatct-tcattttattcacttttgcatggaaatctgctattccctcaggattactaattttt--tcaggtagtg-gtctgcagGGAAAACTGTAATAACCAGTGATCAAGCACTTAAATTGGAATTTATTCCTGATTGGATAGCCATTGTTGGCAGTGGCTACATTGGTCTTGAGTTTAGTGA
       |   ||||    ||  |   |   || |    |||||  |    |  ||| |      | |  || | ||  | ||  |||    | | || | |||| || || ||  | ||||| ||||| || || ||  |||| |  || || || ||||| ||||||||||| ||||| ||||||||||||||||| || ||
------gtaagaagtcatggtcgttggtggattaaaatgcttttaaagtttatgctggtcgattgtaaaaatgattatctcttgatcaaactgcgtgtatccagGAAAGACGGTGTTCACCAGCGATCATGCGCTGAAGCTGGAGTGGATCCCAGACTGGATTGCCATTGTTGGAAGTGGTTACATTGGTCTTGAGTTCAGCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggaaatctgctattccctcaggattactaattttttcaggtagtggtctgcagGGAAAACTGTAATAACCAGTGATCAAGCACTTAAATTGGAATTTATTCCTGATTGGATAGCCATTGTTGGCAGTGGCTACATTGGTCTTGAGTTTAGTGA
                          tactaat  putative branch site (score: 1)
                        attactaattttttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaaaccttgaaagtgcctgttatcttcattttattcacttttgcatggaaatctgctattccctcaggattactaattttttcaggtagtggtctgcagGGAAAACTGTAATAACCAGTGATCAAGCACTTAAATTGGAATTTATTCCTGATTGGATAGCCATTGTTGGCAGTGGCTACATTGGTCTTGAGTTTAGTGA

gaaaacc
- - - - - - - tgcctgt
- - - - - - - - - - - - - - - - tattcac
- - - - - - - - - - - - - - - - - - - - - -gcatgga