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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtagattccgttagtgaacatttggtttttttttccttaactttttactttttatttttttatttttcctttttttaatctcactattgaattgttccagGCAATTGACCATATAATTAATTCAGCTGCAAAGTCAAACTATATGTCTGCTGGTCAGATATCTGTGCCAATTGTTTTCAGAGGGCCAAATGGGGCTGCTG

Basic information

species Vitis vinifera
transcript Vv17s0000g00690.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os09g33500.1 (Oryza sativa), 3'ss of exon 6
gtagattccgttagtgaacatttg-gtttttttttccttaactttttactttt-tatttttttatttttcctttttttaatctcactattgaattgttccagGCAATTGACCATATAATTAATTCAGCTGCAAAGTCAAACTATATGTCTGCTGGTCAGATATCTGTGCCAATTGTTTTCAGAGGGCCAAATGGGGCTGCTG
    |   | ||||||   | ||  |  || |||     ||     || ||   | ||| | |  | |   ||  ||| |  |   |||   |    | ||||||||||| ||||| || ||||||||||| ||||||||||| ||||| || |||||||||||||| || |||||||||||||| || ||||| |||||||
--gtacctcattagtgtttacttctgcattatttgtaccaatgacatatttcagtttttgtatgctgtgatttcgttttaattatttatattacacattcagGCAATTGATCATATCATCAATTCAGCTGCCAAGTCAAACTACATGTCAGCGGGTCAGATATCTGTCCCTATTGTTTTCAGAGGACCTAATGGAGCTGCTG

upper sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 4
gtagattccgttagtgaacatttggtttttttttcc---ttaactttttactttttatttttttatttttccttt--ttttaatctcactattgaattgttccagGCAATTGACCATATAATTAATTCAGCTGCAAAGTCAAACTATATGTCTGCTGGTCAGATATCTGTGCCAATTGTTTTCAGAGGGCCAAATGGGGCTGCTG
     |  | |   || | || ||| | |||| | |   |  | |||    | | |||  | | |   ||    |  |||  ||  ||| |||    | ||| |||||||||| || || || ||||||||||| ||||| ||||| ||||| ||||||||||||   || || |||||||| ||||||||||| || |||||||
----ttcacttccatgcatatctggatcttttatacaaatatattttcccatctatatgatgtaaagattaaaatagtttctataacaccatttgcatattc-agGCAATTGATCACATCATAAATTCAGCTGCCAAGTCGAACTACATGTCAGCTGGTCAGATAAACGTTCCTATTGTTTTTAGAGGGCCAAACGGTGCTGCTG

upper sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G043198_T03 (Zea mays), 3'ss of exon 6
gtagattccgttagtgaacatttggtttttttttccttaactttttactttttatttttttatttttcctttttttaatctcactattgaattgttccagGCAATTGACCATATAATTAATTCAGCTGCAAAGTCAAACTATATGTCTGCTGGTCAGATATCTGTGCCAATTGTTTTCAGAGGGCCAAATGGGGCTGCTG
    ||   ||| || |   | |   |||       | ||   | |    |   | |  |          | | |||||  ||| |||   |   | ||||||||||| || ||||||||||||||||| ||||| ||||| ||||||||||| ||||||||||| || ||||| || || || |||||||| |||||||
aacaataatgtttgttattctctatctttgagaatatgaatactgtcgaatccgtatgctggcaaacaaatctcttaattgcaccattttttatgttcagGCAATTGATCACATAATTAATTCAGCTGCCAAGTCGAACTACATGTCTGCTGGGCAGATATCTGTTCCTATTGTCTTTAGGGGTCCAAATGGTGCTGCTG

upper sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G097226_T02 (Zea mays), 3'ss of exon 6
-gtagattccgttagtgaacatttggtttttttttccttaact---ttttactttttatttttttatttttcc-tttttttaatctcactattgaattgttccagGCAATTGACCATATAATTAATTCAGCTGCAAAGTCAAACTATATGTCTGCTGGTCAGATATCTGTGCCAATTGTTTTCAGAGGGCCAAATGGGGCTGCTG
 |||| ||| || | |||   ||     ||  | || |  ||    ||  || ||  || ||||| |         |   ||||||   || || ||   | ||||| ||||| ||||| || ||||||||||| |||||||| |||||||| ||||||||||||||||| || |||||||| ||||| ||||| || |||||||
agtagtttctgt-actgatttttccccattaatgtcatccaccaaattcaacattccatatttttgtgaaaaaacctgagtaatcta--tactgtatc--ttcagGCTATTGATCATATCATCAATTCAGCTGCCAAGTCAAATTATATGTCAGCTGGTCAGATATCTGTTCCTATTGTTTTTAGAGGACCAAACGGAGCTGCTG

upper sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 6
----gtagattccgttagtgaacatttggtttttttttccttaactttttactttttatttttttatttttcctttttttaatctcactattgaattgttccagGCAATTGACCATATAATTAATTCAGCTGCAAAGTCAAACTATATGTCTGCTGGTCAGATATCTGTGCCAATTGTTTTCAGAGGGCCAAATGGGGCTGCTG
    ||   |    || |    |||||| ||  | |     | | |  |      |||||   |      |   || |||| | | |   ||    |||| |||||||| || ||||| ||||| || || ||||| |||||||| ||||||||||| || |||||||| || ||||| || ||||| || ||||| |||||||
aatggtgtttagttttgggattcatttgtttgatatacagctgaatcatcttaacttattagctagcagattaattatttagttttaacctt----tgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTACCTATTGTCTTTAGAGGACCCAATGGTGCTGCTG

upper sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA02G46380.2 (Glycine max), 3'ss of exon 6
-gtagattccgttagtgaacatttggtttttttttccttaactttttactttttatttttttatttttcctttttttaatctcactattgaattgttccagGCAATTGACCATATAATTAATTCAGCTGCAAAGTCAAACTATATGTCTGCTGGTCAGATATCTGTGCCAATTGTTTTCAGAGGGCCAAATGGGGCTGCTG
  | |  |    |  ||  | ||   ||| ||  |     |||   |  | || |||| ||   |      ||  ||| ||    |      ||||| |||||||| || ||||| ||||| || || ||||| |||||||| ||||||||||| || ||||||||||| ||||| || ||||| || ||||| || ||||
aatggtgtttagttttgggc-ttcattttattgatataccactgcatcatcttgatttattagctagcagattaattattcagttttaacctttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTGCCTATTGTCTTTAGAGGACCCAATGGTGCCGCTG

upper sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA14G02380.2 (Glycine max), 3'ss of exon 6
--gtagattccgttagtgaacatttggtttttttttccttaactttttactttttatttttttatttttcctttttttaatctcactattga--attgttccagGCAATTGACCATATAATTAATTCAGCTGCAAAGTCAAACTATATGTCTGCTGGTCAGATATCTGTGCCAATTGTTTTCAGAGGGCCAAATGGGGCTGCTG
   | |  |   ||  ||  | ||   || |||  |    | ||   |  | || |||| ||   |      ||  |||  |||| | || |   ||||| |||||||| || ||||| ||||| || || ||||| |||||||| ||||||||||| || ||||| || || ||||| || ||||| || ||||| |||||||
taatggtgtttattt-tgggc-ttcatttgtttgatatgcagctacatcatcttcatttattggctagcggattaatta--ctcagttttaacctttgttgcagGCAATAGATCATATTATTAACTCTGCCGCAAAATCAAACTACATGTCTGCTGGGCAAATATCGGTACCTATTGTCTTTAGAGGACCCAATGGTGCTGCTG

upper sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 7
gtagattccgttagtgaacatttggtttttttttccttaactttttactttttatttttttatttttcctttttttaatctcactattgaat-----tgttccagGCAATTGACCATATAATTAATTCAGCTGCAAAGTCAAACTATATGTCTGCTGGTCAGATATCTGTGCCAATTGTTTTCAGAGGGCCAAATGGGGCTGCTG
     | | ||||  | ||| ||  | || |||     |      | |  |  | || |   | |||||   | |  |||  | |||  | |     | || ||||||||||| ||||| || ||||| |||||||||||||| || ||||||||||| ||||||  ||| || || || || ||||| || ||||| |||||||
-----tccagttatcgtacactttatcttctttcggacattaaagtgcactaaagttctaattatttcccaatgtgtatcctaatatctagtaatcttctttcagGCAATTGATCATATCATCAATTCCGCTGCAAAGTCAAATTACATGTCTGCTGGACAGATAAATGTACCCATCGTCTTTAGAGGACCCAATGGTGCTGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactttttatttttttatttttcctttttttaatctcactattgaattgttccagGCAATTGACCATATAATTAATTCAGCTGCAAAGTCAAACTATATGTCTGCTGGTCAGATATCTGTGCCAATTGTTTTCAGAGGGCCAAATGGGGCTGCTG
                                atctcac  putative branch site (score: 3)
                                              ttgttcc  putative PPT
     tttatttttttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagattccgttagtgaacatttggtttttttttccttaactttttactttttatttttttatttttcctttttttaatctcactattgaattgttccagGCAATTGACCATATAATTAATTCAGCTGCAAAGTCAAACTATATGTCTGCTGGTCAGATATCTGTGCCAATTGTTTTCAGAGGGCCAAATGGGGCTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT