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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctggtttgtattcaatgggtattctatgcttgttcttttgagttggcgttgtggatgattaatttgtctgagcagGTTTTGAAGTCTGATGTTGAAGCTGCTTTGAAAGTTCTAAATTTTGCTATATATCATAAAGAATTGACTGAGATGGAGGAGCGTGAGGAAGAAAGGGAGA

Basic information

species Vitis vinifera
transcript Vv10s0003g03080.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g03080.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os05g39850.1 (Oryza sativa), 3'ss of exon 12
gtacc-tggt-ttgta-ttcaatgggtattctatgcttgttcttttga---gttggcgttgtgg---------atga---ttaatttgtctga----gcagGTTTTGAAGTCTGATGTTGAAGCTGCTTTGAAAGTTCTAAATTTTGCTATATATCATAAAGAATTGACTGAGATGGAGGAGCGTGAGGAAGAAAGGGAGA
 |||  | || || || |||   |   | | |   ||  || ||||||    | |    ||  |         ||||   |  |||| |||      ||||||| | ||  |||| |||||||||||  || ||||||| |||||||| ||||| || ||||| || ||||||||||| ||||||||  |   |  |  | 
-tactgtagtattataattctgggaacagttttatctcattgttttgaaggatagaaaatgcagggcaatctaatgaagttgcatttatcttgcattgcagGTTCTAAAAACTGACGTTGAAGCTGCACTGCAAGTTCTGAATTTTGCAATATACCACAAAGAGTTAACTGAGATGGAAGAGCGTGAACAGAGAGAGATGG

upper sequence: Vv10s0003g03080.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G162445_T01 (Zea mays), 3'ss of exon 12
------------------gtacctggtttgtattc---aatgggtattcta--tgcttgttcttttgagttggcgttgtgg-atgattaatttgtctgagcagGTTTTGAAGTCTGATGTTGAAGCTGCTTTGAAAGTTCTAAATTTTGCTATATATCATAAAGAATTGACTGAGATGGAGGAGCGTGAGGAAGAAAGGGAGA
                    |    |||| | ||     | || ||    |  || |||| |||     |   | |  ||| |  | |   |||| ||  |||||  |||| ||||||||||| ||||| ||| |||||||||||||||| ||||| || || ||||||||||||||||| ||||| ||  |   |   | | 
aagcaatttctccattttacaaacagtttatgtttttggaaggataactgagttgtttgtccttgacgatct-catcatggcagcaatgtcttgtttg--cagGTACTGAAATCTGATGTTGAGGCTGCATTGCAAGTTCTAAATTTTGCAATATACCACAAGGAATTGACTGAGATGGAAGAGCGAGAACAGAGAGAAGCGG

upper sequence: Vv10s0003g03080.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G100639_T01 (Zea mays), 3'ss of exon 12
----------------------------------------------------------------------------------------gtacctggtttgtattcaat--gggtattctatgct-tgttcttttgagttggcgttgtggatg-attaatttgtctgagcagGTTTTGAAGTCTGATGTTGAAGCTGCTTTGAAAGTTCTAAATTTTGCTATATATCATAAAGAATTGACTGAGATGGAGGAGCGTGAGGAAGAAAGGGAGA
                                                                                          |     ||| | ||   |  || ||  ||  ||  | |    |||||  |   |  |    |  | ||| | |    ||||||| |||| || |||||||| ||||| ||| |||||||||||||||| ||||| || || ||||||||||||||||| ||| | ||  |   |     | 
gtattttgtttattctaccagcaacctagccacatcaataattttctggatgaaagttcaccaagaaatgaagcaatttctctgttttacaaacactttattttttgtaaggataaactgagccgtttgtccttgagaagatctcatcatggcgtcaatgtcttgttgcagGTTCTGAAATCCGATGTTGAGGCTGCATTGCAAGTTCTAAATTTTGCAATATACCACAAGGAATTGACTGAGATGGAAGAGAGAGAACAGAGAGAAATGG

upper sequence: Vv10s0003g03080.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA05G25980.1 (Glycine max), 3'ss of exon 12
-----------------gtacctggtttgtattcaatgg-gtattctatgcttgttcttttgagttggcgttgtggatgattaa---tttgtctgagcagGTTTTGAAGTCTGATGTTGAAGCTGCTTTGAAAGTTCTAAATTTTGCTATATATCATAAAGAATTGACTGAGATGGAGGAGCGTGAGGAAGAAAGGGAGA
                  || |||||     | |||  | || |  | |  ||||| | || ||| | | || |   |||   |    ||||||   |||||||  |||||||||||||||||||||||||| |||||||||||||| |||||||| |||||| | || || ||||||||||||||| |||| |||||||
tattctgcttataagttttaactggtagtactacaacagcgtgtgttttcattgttgtgttcagtagactttcttattgagccagcacttgtcttgtcagGTTTCAAAGTCTGATGTTGAAGCTGCTTTGAAGGTTCTAAATTTTGCAATATATCACAAAGAACTAACAGAAATGGAGGAGCGTGAGCAAGAGAGGGAGA

upper sequence: Vv10s0003g03080.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA08G08920.1 (Glycine max), 3'ss of exon 12
------------gtacctggt--ttgta-ttcaatgg---gtattctatgcttgttcttttgagttggcgttgtggatgattaa---tttgtctgagcagGTTTTGAAGTCTGATGTTGAAGCTGCTTTGAAAGTTCTAAATTTTGCTATATATCATAAAGAATTGACTGAGATGGAGGAGCGTGAGGAAGAAAGGGAGA
            |||  |  |  | ||| |||||  |   || |  | |   |||| | ||  || | | ||     |||   |    ||||||   |||||||  ||||||||||||||||| |||||||| |||||||||||||| |||||||| |||||| |||| || ||||||||||||||| |||| |||||||
ttctgcttataagtatttactggtggtacttcaacagcctgtgtgttttcactgttgtgttctgtagactttccaattgagccagtacttgtcttgtcagGTTTCTAAGTCTGATGTTGAAGCAGCTTTGAAGGTTCTAAATTTTGCAATATATCACAAAGAACTGACAGAAATGGAGGAGCGTGAGCAAGAGAGGGAGA

upper sequence: Vv10s0003g03080.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT5G46280.1 (Arabidopsis thaliana), 3'ss of exon 12
---------------gtacctggtttgtattcaatgggtattctatgcttgttcttttgagttggcgttgtggatgattaatttgtctgagcagGTTTTGAAGTCTGATGTTGAAGCTGCTTTGAAAGTTCTAAATTTTGCTATATATCATAAAGAATTGACTGAGATGGAGGAGCGTGAGGAAGAAAGGGAGA
                 | ||  | | |   ||   |||  |  ||   |||||| || || |    |      |||| | ||| | |    |||||   ||  ||||||  || ||||| |||||  || | || ||||| ||||||||| ||||||| ||||||||||| || |||||| |||||       
gtaacaatctaactcaaatcttctgtttccccacctggtcgtgaata--tgttctattcagattctttctaaagtgataactttattttgaaagGTTACTAAAGCTGATGCAGAGGCTGCCTTGAAGCTTATGAACTTTGCAATATATCATCAAGAATTAACTGAGATGGATGATCGTGAGCAAGAAGAACGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctatgcttgttcttttgagttggcgttgtggatgattaatttgtctgagcagGTTTTGAAGTCTGATGTTGAAGCTGCTTTGAAAGTTCTAAATTTTGCTATATATCATAAAGAATTGACTGAGATGGAGGAGCGTGAGGAAGAAAGGGAGA
                                    gattaat  putative branch site (score: 3)
                                          tttgtct  CT-rich tract
                                  atgattaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacctggtttgtattcaatgggtattctatgcttgttcttttgagttggcgttgtggatgattaatttgtctgagcagGTTTTGAAGTCTGATGTTGAAGCTGCTTTGAAAGTTCTAAATTTTGCTATATATCATAAAGAATTGACTGAGATGGAGGAGCGTGAGGAAGAAAGGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA