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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattgacaccctcacctccattttctcttttctttgtttcttatttttactaacacttgggttccccatgaacagcaagCTGAAACACAGATAAAGAGAAGAATGGGAATTGGAAGCCACATATCGGAGAGACGGCTGATTGATGATATGACCAGGATGGGAATGAATGAATCTATTGT

Basic information

species Vitis vinifera
transcript Vv11s0149g00130.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 17
---------gtgattgacaccctcacctccattttctcttttctttgtttcttatttttactaacacttgggttccccatgaacagcaagCTGAAACACAGATAAAGAGAAGAATGGGAATTGGAAGCCACATATCGGAGAGACGGCTGATTGATGATATGACCAGGATGGGAATGAATGAATCTATTGT
            ||  | |     ||  |||  || ||   | | | ||||| | ||||  |  |  ||  |||||     |||||||||||||  |||| ||||||||||| ||||||||||||||||||||||| ||| |||| ||||| |||||  | |  |||||||| ||||||||||| |    
gttaatcttcccatccaaaagtgaactgccaacttgtcaactttgt-tttctgaattttgttgcccattttgttcc-----aacagCAAGCTGAGGCACAAATAAAGAGAAGGATGGGAATTGGAAGCCACATATCCGAGCGACGCCTGATCGATGAACTAAATAGGATGGGGATGAATGAATCCA----

upper sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GRMZM2G450055_T01 (Zea mays), 3'ss of exon 17
----gtgattg-acaccctcacctccattttctcttttctttgtttcttatttttactaac--acttgggttccccatgaacagcaagCTGAAACACAGATAAAGAGAAGAATGGGAATTGGAAGCCACATATCGGAGAGACGGCTGATTGATGATATGACCAGGATGGGAATGAATGAATCTATTGT
    |   ||| |  |||  |   | |  |||  |   | |||    ||   ||| || |    | |   ||        ||||||||| ||| ||||||||||| |||||||||| ||||||||||||||||| ||| |||||||||||||||   | | ||||||||||||||| ||||| |    
gttagcctttgcatccccagagtacaaaattcagtggcccttgaaatttgcgttttctgaatgccctccattttatcccgacagCAAGCGGAAGCACAGATAAAGCGAAGAATGGGCATTGGAAGCCACATATCTGAGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCA----

upper sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 17
-------------gtgattgacaccctcacctccattttct--cttttctttgtttcttatttttactaacacttgggttccccatgaacagcaagCTGAAACACAGATAAAGAGAAGAATGGGAATTGGAAGCCACATATCGGAGAGACGGCTGATTGATGATATGACCAGGATGGGAATGAATGAATCTATTGT
                   |  |  |  |  ||   | |    | || | || |     |    |   | || ||   || |   ||| |||||||| ||  |||| ||||||||||||||||| || || ||||||||||| ||| ||||||||||||||||| | | | ||||||| ||||||||||| |    
gttagtatttgcatcccagggtatacaaaattcagctattgaaccttgcattttcctgaacggctttcatcatttttttttcatctga-cagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCCGAGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCA----

upper sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA17G11220.1 (Glycine max), 3'ss of exon 16
gtgattgacaccctcacctccattttctcttttctttgttt--cttatttttactaacacttgggttcc-ccatgaacagcaagCTGAAACACAGATAAAGAGAAGAATGGGAATTGGAAGCCACATATCGGAGAGACGGCTGATTGATGATATGACCAGGATGGGAATGAATGAATCTATTGT
    ||       | |    |||   |  | || ||  | |  |||| | |    |    ||   || |    ||| |||||||||||||||||||||||||||||||| |||||||||| |||||||||||| ||| |||||||||||||  | | ||| ||||| |||||||||||||    
---gtttgtcttgtgatagacatagaccgtcttgttcatctagcttaatatcctaatggattactttacattgtgagcagCAAGCTGAAACACAGATAAAGAGAAGAATTGGAATTGGAAACCACATATCGGAAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTA----

upper sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA13G22420.1 (Glycine max), 3'ss of exon 16
---------gtgattgacaccctcacctccattttctcttttctttgtttcttatttttactaac-acttgggttccccatgaacagcaagCTGAAACACAGATAAAGAGAAGAATGGGAATTGGAAGCCACATATCGGAGAGACGGCTGATTGATGATATGACCAGGATGGGAATGAATGAATCTATTGT
         |||||  |||     |||  | | || | |     | | ||  |||  | ||  |  ||||   | |    ||| |||||||||||||| ||||||||||||||||| || ||||||| ||||||||| || ||| |||||||||||||  | | ||| ||||| |||||||||||||    
gtttgtcttgtgataaacatag--accatcttgttttttccgtctagcttagtatcctaacggattactt---tacattgtgagcagCAAGCTGAAACTCAGATAAAGAGAAGAATTGGGATTGGAAACCACATATCAGAAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTA----

upper sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: AT2G07690.1 (Arabidopsis thaliana), 3'ss of exon 16
----gtgattgacaccctcacctccattttctcttttctttgtttcttatttttactaacacttgggttccccatgaacagcaagCTGAAACACAGATAAAGAGAAGAATGGGAATTGGAAGCCACATATCGGAGAGACGGCTGATTGATGATATGACCAGGATGGGAATGAATGAATCTATTGT
    ||   |               ||  ||   | |||   | |  ||  |  | |     ||||  |    |  |||||||||| |||||||||||||||||||||||||| || |||   |   |||| |||||| | ||||| || ||| || | || ||||||||||| || || |    
gttagttgcttgtggggaagaaagaatcatcgtatctctagatgtaataactaaatttggtattgg--tgtgaaaaaacagCAAGCGGAAACACAGATAAAGAGAAGAATGGGGATCGGAGCTCGATTATCAGAGAGAAGACTGATAGAGGATCTGGCTAGAATGGGAATGAACGATTCAA----


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttttctttgtttcttatttttactaacacttgggttccccatgaacagcaagCTGAAACACAGATAAAGAGAAGAATGGGAATTGGAAGCCACATATCGGAGAGACGGCTGATTGATGATATGACCAGGATGGGAATGAATGAATCTATTGT
                       tactaac  putative branch site (score: 0)
        tttgtttcttattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattgacaccctcacctccattttctcttttctttgtttcttatttttactaacacttgggttccccatgaacagcaagCTGAAACACAGATAAAGAGAAGAATGGGAATTGGAAGCCACATATCGGAGAGACGGCTGATTGATGATATGACCAGGATGGGAATGAATGAATCTATTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG