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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctggggagtacttgcaactgctttattcatttgattaatcattctcagttattttagctattcacatacgacttatttttctagTTAGTGGAAGCATTTCATGCAACCTTGGAAGAAGTGGTGGAAGCAGACTTACTAGTG

Basic information

species Vitis vinifera
transcript Vv00s0734g00020.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0734g00020.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os03g51790.1 (Oryza sativa), 3'ss of exon 9
gtagctggggagta--cttgcaactg--ctttattcatttg-attaatcattctcagttattttagc-----tattcacatacga--cttatttttctagTTAGTGGAAGCATTTCATGCAACCTTGGAAGAAGTGGTGGAAGCAGACTTACTAGTG
|   ||  ||  ||  | | ||   |  | ||| | ||       |  | || |||  || | | |      || | | |||  |  |||  || |  || ||||||||||||||||||| || ||||||||||| || ||||||||  |  |||||
gccactttggtctaggcctccaggggaaccttaatgatgcatgaaagcctttttcaactactgtggtgacagtaataatatagtaacctttcttgtgcagCTAGTGGAAGCATTTCATGCTACTTTGGAAGAAGTTGTTGAAGCAGATATGTTAGTG

upper sequence: Vv00s0734g00020.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G101460_T01 (Zea mays), 3'ss of exon 9
----------gtagctggggagtacttgcaactgctttat-tcatttgat--taatcattctcagttattttagctattcacatacgacttatttttctagTTAGTGGAAGCATTTCATGCAACCTTGGAAGAAGTGGTGGAAGCAGACTTACTAGTG-------------------------------------------
           |   | || |    |  |   |  | |   |  |||||   |    ||     |||||| |     |    ||     || |||  | || | ||||||||||||||||| ||| | |||||||| || ||||||||| |  |||||                                           
ttaatttgtactgatttggcaaccttgacctttcttctgcattgtttgacactttctatgtcaggttattgttaacctctttattttgttt-tttccccagCTTGTGGAAGCATTTCATGCGACCCTAGAAGAAGTTGTTGAAGCAGACATGTTAGTGGTAGGTTTTCTTTTCTTCTTGAAGTCTGGAGTTGAGCATGACT

upper sequence: Vv00s0734g00020.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G101460_T02 (Zea mays), 3'ss of exon 10
----------gtagctggggagtacttgcaactgctttat-tcatttgat--taatcattctcagttattttagctattcacatacgacttatttttctagTTAGTGGAAGCATTTCATGCAACCTTGGAAGAAGTGGTGGAAGCAGACTTACTAGTG
           |   | || |    |  |   |  | |   |  |||||   |    ||     |||||| |     |    ||     || |||  | || | ||||||||||||||||| ||| | |||||||| || ||||||||| |  |||||
ttaatttgtactgatttggcaaccttgacctttcttctgcattgtttgacactttctatgtcaggttattgttaacctctttattttgttt-tttccccagCTTGTGGAAGCATTTCATGCGACCCTAGAAGAAGTTGTTGAAGCAGACATGTTAGTG

upper sequence: Vv00s0734g00020.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA02G44930.1 (Glycine max), 3'ss of exon 9
-----------------------------------gtagctggggagtacttgcaactgctttattcatttgat-taatcattctcagttattttagctat-tcacatacgacttatttttctagTTAGTGGAAGCATTTCATGCAACCTTGGAAGAAGTGGTGGAAGCAGACTTACTAGTG
                                    |  |||   | || ||  | |    |||||| |    | |  || ||  || | |      |||  |      |  || |||||| ||| | |||||||||||||| || ||| ||||||||||||||||||||||| | || |||
gtaatggtaaaacatgagcaaattgccatgtcagtatgactgtttattatttttatcaatattattcttcaactgtcttctttgacaataacccagcctacctttttctcttctaatttttgtagCTGGTGGAAGCATTTCAAGCTACCCTGGAAGAAGTGGTGGAAGCAGACCTGCTTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgattaatcattctcagttattttagctattcacatacgacttatttttctagTTAGTGGAAGCATTTCATGCAACCTTGGAAGAAGTGGTGGAAGCAGACTTACTAGTG
   gattaat  putative branch site (score: 3)
                                          cttatttttct  putative PPT
                   ttattttagctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagctggggagtacttgcaactgctttattcatttgattaatcattctcagttattttagctattcacatacgacttatttttctagTTAGTGGAAGCATTTCATGCAACCTTGGAAGAAGTGGTGGAAGCAGACTTACTAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG