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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaatgagaggtgaatacttcttttcgactcctgtggacatgaaactttgtgattttagacttccaatttgaccattttattctggttctacttttcagGTATGTACATAGTTACCAAAGCTATCTGTGGAACCATGCAGCTAGTATGAGAGTGCAAAACTATG

Basic information

species Vitis vinifera
transcript Vv14s0030g01850.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0030g01850.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os01g56620.1 (Oryza sativa), 3'ss of exon 11
-------------------agaaatgagaggtgaatacttc----ttttcgactcctgtggacatgaaactttgtgat---tttagact-tccaatttgac-catt---ttattctggttctacttttcagGTATGTACATAGTTACCAAAGCTATCTGTGGAACCATGCAGCTAGTATGAGAGTGCAAAACTATG
                    |||||      |  | | | |      |   | |  |||     |     |||  ||    ||||| || | |||||  ||  |||   || ||||| || | || ||||||||||| ||||||||||| || ||  | ||||||||||| || ||||||||||| ||||| ||||
gtatgttatgttcaatatctgaaattttgtctagagattccaacacctgaaattaatgtaattttccttatttacgacaaatttaggctatacaattctacatattaagttgttctgattattctattcagGTATGTGCATAGTTACCAGAGTTACTTATGGAACCATGCTGCAAGTATGAGAGTTCAAAAGTATG

upper sequence: Vv14s0030g01850.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G096553_T02 (Zea mays), 3'ss of exon 11
agaaatgagaggtgaatacttcttt--tcgactcctgtggacatgaaactttgtgattttagacttccaatttgaccattttattctggttctacttttcagGTATGTACATAGTTACCAAAGCTATCTGTGGAACCATGCAGCTAGTATGAGAGTGCAAAACTATG
     |   | || | || |  |    | || |  ||| ||       |  |||  ||||    |      |  | | ||| ||| ||  | |  | |  ||||| ||||||||||||||||| ||||||||||| ||||| || |||||||||||| |||| ||||
-atgctctcatgttagtattcttacagttgaattttgttgaatgatggccatgttttttttctatgttttctgaatcttttcatt-tgaatattttatgtagGTACGTACATAGTTACCAAAGTTATCTGTGGAATCATGCTGCCAGTATGAGAGTGGAAAAGTATG

upper sequence: Vv14s0030g01850.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G096553_T03 (Zea mays), 3'ss of exon 11
agaaatgagaggtgaatacttcttt--tcgactcctgtggacatgaaactttgtgattttagacttccaatttgaccattttattctggttctacttttcagGTATGTACATAGTTACCAAAGCTATCTGTGGAACCATGCAGCTAGTATGAGAGTGCAAAACTATG
     |   | || | || |  |    | || |  ||| ||       |  |||  ||||    |      |  | | ||| ||| ||  | |  | |  ||||| ||||||||||||||||| ||||||||||| ||||| || |||||||||||| ||||     
-atgctctcatgttagtattcttacagttgaattttgttgaatgatggccatgttttttttctatgttttctgaatcttttcatt-tgaatattttatgtagGTACGTACATAGTTACCAAAGTTATCTGTGGAATCATGCTGCCAGTATGAGAGTGGAAAA-----

upper sequence: Vv14s0030g01850.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA03G40600.1 (Glycine max), 3'ss of exon 12
-agaaatgagaggtgaatacttcttttcgactcctgtggacatgaaac-tttgtgattttagacttccaatttgaccattttattctggttctacttttcagGTATGTACATAGTTACCAAAGCTATCTGTGGAACCATGCAGCTAGTATGAGAGTGCAAAACTATG
          |    ||||    | |   |      |  | || |    ||||     ||| | |   |  || |  || |  |||   | ||  |||| |||||||| |||||||||||||||||| ||||||||||||| || |||| ||| |||||||| ||||
tctgctcagaacacaaataaagttgtaatatattattcaagatcatttatttgaaggattatattggta--ttcattatatagttccactgcttttttttagGTATGTTCATAGTTACCAAAGCTATTTGTGGAACCATGCTGCAAGTAAGAGGGTGCAAAAATATG

upper sequence: Vv14s0030g01850.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA19G43270.1 (Glycine max), 3'ss of exon 12
agaaatgagaggtgaatacttcttttcgactcctgtggacatgaaactttgtgattttagacttccaatt--tgaccattttattctggttctactttt--cagGTATGTACATAGTTACCAAAGCTATCTGTGGAACCATGCAGCTAGTATGAGAGTGCAAAACTATG
   | |  |    ||  ||   |    |  |  | |     | ||  |   | |||| |    |   |||  |    ||||||| ||    ||||||||   |||||||| |||||||||||||||||| | ||||||||||| || |||| ||| |||||||| ||||
---agtctggtcagagcacaaataaaag-ttgttatattattcaagatcatttatttgaaggattatattggtatttattttatacttcaactactttttttagGTATGTTCATAGTTACCAAAGCTATTTATGGAACCATGCTGCAAGTAAGAGGGTGCAAAAATATG

upper sequence: Vv14s0030g01850.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT3G04820.1 (Arabidopsis thaliana), 3'ss of exon 12
------------------------------agaaatgagaggtgaatacttctttt-cgactcctgtggacatg--aaactttgtgattttag---acttccaattt----gaccattttat-tctggttct-acttttcagGTATGTACATAGTTACCAAAGCTATCTGTGGAACCATGCAGCTAGTATGAGAGTGCAAAACTATG
                                |  |    |   | |  | ||||| |||||  |   ||||||  || |     |      |   |  || | |||    |   | | ||| |||| | || |   | |||||||||||||||||| ||||||||  | |||||| ||||||| ||| || | ||  |||| ||||
gtaagcgctcgattctttaatatatctttagtaccttccggaacagtgttccttttgcgactggttatgacatgccaagccacagggcacaggcgcagatcaagttttttagcttactgtatatctgatccttatcatgcagGTATGTACATAGTTATCAAAGCTACTTATGGAACAATGCAGCAAGTCTGCGCGTCAAAAATTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actttgtgattttagacttccaatttgaccattttattctggttctacttttcagGTATGTACATAGTTACCAAAGCTATCTGTGGAACCATGCAGCTAGTATGAGAGTGCAAAACTATG
                      atttgac  putative branch site (score: 4)
                                          ttctacttttc  putative PPT
                              attttattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaaatgagaggtgaatacttcttttcgactcctgtggacatgaaactttgtgattttagacttccaatttgaccattttattctggttctacttttcagGTATGTACATAGTTACCAAAGCTATCTGTGGAACCATGCAGCTAGTATGAGAGTGCAAAACTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- -aatgaga
- - - - - - - - - - - - - - -ctcctgt
- - - - - - - - - - - - - - - - - - ggacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttccaa