Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaggtctcactcctattttgtttcccctccatctcaactgcattgtattgatttcaatactttatgttctccttgtccatgaattggattgaaattgcagGCAAGCAAAGGATGCCCTGAAGATACTCAAGAAGCGCCTGGGGAGTAAAAATCCTAAGATACAACTTCTTGCTCTGTTT

Basic information

species Vitis vinifera
transcript Vv18s0001g01180.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g01180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA04G42250.1 (Glycine max), 3'ss of exon 2
--aaggtctcactcctattttgtttcccctccatctcaactgcattgtattgatttcaatactttatgttctccttgtccatgaattggattgaaattgcagGCAAGCAAAGGATGCCCTGAAGATACTCAAGAAGCGCCTGGGGAGTAAAAATCCTAAGATACAACTTCTTGCTCTGTTT
  | |   |   | | |||     |    |  || ||   ||  |  |  | | ||  ||  ||  || | | ||     || | |   ||| || |||||||||||||||||||||  |||||||||||||||||||  |||  ||||||||||| || ||||| ||||| ||||| |||
gtatgtaattgattcaattcatccttatgttgatttctcatgggtattccttaattatattgttcctgatattctgtgttataact--aattcaatttgcagGCAAGCAAAGGATGCTTTGAAGATACTCAAGAAGCGTTTGGCCAGTAAAAATCCAAAAATACAGCTTCTGGCTCTTTTT

upper sequence: Vv18s0001g01180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA06G12570.1 (Glycine max), 3'ss of exon 2
----aaggtctcactcctattttgtttcccctccatctcaactgcattgtattgatttcaatactttatgttctccttgtccatgaattggattgaaattgcagGCAAGCAAAGGATGCCCTGAAGATACTCAAGAAGCGCCTGGGGAGTAAAAATCCTAAGATACAACTTCTTGCTCTGTTT
    | | | |   | | |||     |    |  || ||   || ||  |  | | || | |  ||  || ||| ||  |  || | |   ||| || || ||||||||| ||||||||  |||||||||||||||||||  |||| ||||||||||| || ||||| ||||| ||||| |||
aagtatgttattgattcaattgatccttatgttgatttctcatggatattccttaattaagttgttcctgatcttctgtt--ataact--aattaaattttcagGCAAGCCAAGGATGCTTTGAAGATACTCAAGAAGCGTTTGGGCAGTAAAAATCCAAAAATACAGCTTCTGGCTCTTTTT

upper sequence: Vv18s0001g01180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G09390.1 (Glycine max), 3'ss of exon 1
aaggtctcactcctattttgtttcc-cctccatctcaactgcattgtattgatttcaatactttatgttctccttgtcca----tgaattggattgaaattgcagGCAAGCAAAGGATGCCCTGAAGATACTCAAGAAGCGCCTGGGGAGTAAAAATCCTAAGATACAACTTCTTGCTCTGTTT
    ||  | |   |  ||| |||  ||   || |  | |   |   || |  |||  |  |  || |||  | | | ||    |||| || ||| || |||||||||||||||||||||  | |||||||| ||||||||  || | |||||||||||  | ||||||||| | ||||| |||
---ctcaaagtataaaattgcttcaacccttattttgaatttttctcatgggattcctt-ttacattttcctcatattcaatgttgaactg-atttaatttgcagGCAAGCAAAGGATGCAATAAAGATACTTAAGAAGCGTTTGAGCAGTAAAAATCCCCAAATACAACTTTTGGCTCTTTTT

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|161720688|gb|FC069937.1|FC069937
EST:     GACTGGGCAATAAACATCGAGCTATGTGATATCATTAACATGGATCCTGG                         GCAAGCAAAGGATGCCCTGAAGATACTCAAGAAGCGCCTGGGGAGTAAAAA
genomic: GACTGGGCAATAAACATCGAGCTATGTGATATCATTAACATGGATCCTGGgtatcatact ... gaaattgcagGCAAGCAAAGGATGCCCTGAAGATACTCAAGAAGCGCCTGGGGAGTAAAAA
EST: gi|77587150|gb|DV222704.1|DV222704
EST:     GACTGGGCAATAAACATCGAGCTATGTGATATCATTAACATGGATCCTGG                         GCAAGCAAAGGATGCCCTGAAGATACTCAAGAAGCGCCTGGGGAGTAAAAA
genomic: GACTGGGCAATAAACATCGAGCTATGTGATATCATTAACATGGATCCTGGgtatcatact ... gaaattgcagGCAAGCAAAGGATGCCCTGAAGATACTCAAGAAGCGCCTGGGGAGTAAAAA
EST: gi|110724482|gb|EE100348.1|EE100348
EST:     GACTGGGCAATAAACATCGAGCTATGTGATATCATTAACATGGATCCTGG                         GCAAGCAAAGGATGCCCTGAAGATACTCAAGAAGCGCCTGGGGAGTAAAAA
genomic: GACTGGGCAATAAACATCGAGCTATGTGATATCATTAACATGGATCCTGGgtatcatact ... gaaattgcagGCAAGCAAAGGATGCCCTGAAGATACTCAAGAAGCGCCTGGGGAGTAAAAA
EST: gi|161716239|gb|FC066502.1|FC066502
EST:     GACTGGGCAATAAACATCGAGCTATGTGATATCATTAACATGGATCCTGG                         GCAAGCAAAGGATGCCCTGAAGATACTCAAGAAGCGCCTGGGGAGTAAAAA
genomic: GACTGGGCAATAAACATCGAGCTATGTGATATCATTAACATGGATCCTGGgtatcatact ... gaaattgcagGCAAGCAAAGGATGCCCTGAAGATACTCAAGAAGCGCCTGGGGAGTAAAAA
EST: gi|161718465|gb|FC067304.1|FC067304
EST:     GACTGGGCAATAAACATCGAGCTATGTGATATCATTAACATGGATCCTGG                         GCAAGCAAAGGATGCCCTGAAGATACTCAAGAAGCGCCTGGGGAGTAAAAA
genomic: GACTGGGCAATAAACATCGAGCTATGTGATATCATTAACATGGATCCTGGgtatcatact ... gaaattgcagGCAAGCAAAGGATGCCCTGAAGATACTCAAGAAGCGCCTGGGGAGTAAAAA
EST: gi|161708941|gb|FC060484.1|FC060484
EST:     GACTGGGCAATAAACATCGAGCTATGTGATATCATTAACATGGATCCTGG                         GCAAGCAAAGGATGCCCTGAAGATACTCAAGAAGCGCCTGGGGAGTAAAAA
genomic: GACTGGGCAATAAACATCGAGCTATGTGATATCATTAACATGGATCCTGGgtatcatact ... gaaattgcagGCAAGCAAAGGATGCCCTGAAGATACTCAAGAAGCGCCTGGGGAGTAAAAA
EST: gi|161710321|gb|FC059835.1|FC059835
EST:     GACTGGGCAATAAACATCGAGCTATGTGATATCATTAACATGGATCCTGG                         GCAAGCAAAGGATGCCCTGAAGATACTCAAGAAGCGCCTGGGGAGTAAAAA
genomic: GACTGGGCAATAAACATCGAGCTATGTGATATCATTAACATGGATCCTGGgtatcatact ... gaaattgcagGCAAGCAAAGGATGCCCTGAAGATACTCAAGAAGCGCCTGGGGAGTAAAAA
EST: gi|110721049|gb|EE097599.1|EE097599
EST:     GACTGGGCAATAAACATCGAGCTATGTGATATCATTAACATGGATCCTGG                         GCAAGCAAAGGATGCCCTGAAGATACTCAAGAAGCGCCTGGGGAGTAAAAA
genomic: GACTGGGCAATAAACATCGAGCTATGTGATATCATTAACATGGATCCTGGgtatcatact ... gaaattgcagGCAAGCAAAGGATGCCCTGAAGATACTCAAGAAGCGCCTGGGGAGTAAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgatttcaatactttatgttctccttgtccatgaattggattgaaattgcagGCAAGCAAAGGATGCCCTGAAGATACTCAAGAAGCGCCTGGGGAGTAAAAATCCTAAGATACAACTTCTTGCTCTGTTT
 tattgat  putative branch site (score: 3)
     atttcaatactttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaggtctcactcctattttgtttcccctccatctcaactgcattgtattgatttcaatactttatgttctccttgtccatgaattggattgaaattgcagGCAAGCAAAGGATGCCCTGAAGATACTCAAGAAGCGCCTGGGGAGTAAAAATCCTAAGATACAACTTCTTGCTCTGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - -ctcactc
- - - - - - - - - - - - ccctcca
- - - - - - - - - - - - - - - - - caactgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatgaa