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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattggtttcatggcatcaagatggaaagtttcttgccaagttttgtcaaatattttatcatagcagatgttaaatatcattctcctgattgtgttgcagGGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCACTTAAGGATAACTCTAACCCACAAATAGCTTTGCTTCCCTTACATCCAG

Basic information

species Vitis vinifera
transcript Vv01s0026g00920.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g00920.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G17350.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------------------------------------------cattggtttcatggcatcaagatgg--aaagtttcttgccaagttttgtcaaatattttatcatagcagatgttaaatatcattctcctgattgtgttgcagGGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCACTTAAGGATAACTCTAACCCACAAATAGCTTTGCTTCCCTTACATCCAG
                                                                                      | |  | | || |   || | | |     | |  |  |       ||    || ||||||  ||   |||  || | | |||  |  ||  | ||| |||||| |||||||| ||||||||||| |||||||| ||||||||||||||| | ||||||||| | || || ||||| ||||| || |||||| | |||||| 
ggtattaaagtgattcggtttttataatttttatcatttttcttttaacatcattgatgtaatcatctaaatgccagttgaacaggaattttgtaattgttccatggttgttgggggtggtgactggtgactgagctatgttttattttaattgattataga-agcataata-tgtctttgt-gcaGGGTGAAGAAATAATAGTGGTAATTCCCTGGGAAGAATGGTGGGAATTGGCTCTTAAGGATGATTCCAATCCACAGATAGCCTTACTTCCCCTGCATCCA-

upper sequence: Vv01s0026g00920.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA01G04400.1 (Glycine max), 3'ss of exon 3
cattggtttcatggcatcaagatggaaagtttcttgccaagttttgtcaaatattttatcatagcagatgttaaatatcattctcctgat-tgtgtt---gcagGGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCACTTAAGGATAACTCTAACCCACAAATAGCTTTGCTTCCCTTACATCCAG
  | | |  || || ||     ||   |   ||        |||| |  | ||| ||  ||||  | | | | | | | ||  |  || | ||| ||   |||||| |||||||| ||||||||||| |||||| |||||||||||  |||  | ||||| ||||| || |||||||| ||||| ||||||||| | |||||||
tgtagttgccaagggat---agtgactaacctccattatgtttttattgattatatttacataaaacagggtta-tgttatgttgatggtatgtctttgtgcagGGTGAAGAAATAATAGTGGTAATTCCCTGGCATGAATGGTGGACATTAGCTCTTAAAGATAATTCCAACCCACAGATAGCCTTGCTTCCCCTGCATCCAG

upper sequence: Vv01s0026g00920.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G03160.1 (Glycine max), 3'ss of exon 3
cattggtttcatggcatcaagatggaaagtttcttgccaagttttgtcaaatattttatcatagcagatgttaaatatcattctcctgat-tgtgtt---gcagGGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCACTTAAGGATAACTCTAACCCACAAATAGCTTTGCTTCCCTTACATCCAG
   | ||| |   | ||   |||  |     ||        |||| |  | ||| ||| ||||  | | | | | | | ||  |  || | ||| ||   |||||| |||||||| ||||||||||| |||||| |||||||||||  |||  | || || ||||| || |||||||| ||||| ||||||||| | |||||||
ttgtagttgccgaggatagtgattaa---cctccattatgtttttattgattatattaacataaaacagggtta-tgttatattgatggtatgtctttctgcagGGTGAAGAAATAATAGTGGTAATTCCCTGGCATGAATGGTGGACATTAGCTCTCAAAGATAATTCCAACCCACAGATAGCCTTGCTTCCCCTGCATCCAG

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|27579647|gb|CB002342.1|CB002342
EST:     GGGTTGGTGAGTCGGGGCACGAGAACGAAAAG                         GGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCA
genomic: GGGTTGGTGAGTCGGGGCACGAGAACGAAAAGgtatgctagc ... tgtgttgcagGGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCA
EST: gi|18458423|gb|BM436701.1|BM436701
EST:     ATGAAGAGGGTAATCTTTGGGTTGGTGAGTCGGGGCACGAGAACGAAAAG                         GGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCA
genomic: ATGAAGAGGGTAATCTTTGGGTTGGTGAGTCGGGGCACGAGAACGAAAAGgtatgctagc ... tgtgttgcagGGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCA
EST: gi|71859638|gb|DT008693.1|DT008693
EST:     ATGAAGAGGGTAATCTTTGGGTTGGTGAGTCGGGGCACGAGAACGAAAAG                         GGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCA
genomic: ATGAAGAGGGTAATCTTTGGGTTGGTGAGTCGGGGCACGAGAACGAAAAGgtatgctagc ... tgtgttgcagGGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCA
EST: gi|30322099|gb|CD005361.1|CD005361
EST:     ATGAAGAGGGTAATCTTTGGGTTGGTGAGTCGGGGCACGAGAACGAAAAG                         GGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCA
genomic: ATGAAGAGGGTAATCTTTGGGTTGGTGAGTCGGGGCACGAGAACGAAAAGgtatgctagc ... tgtgttgcagGGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCA
EST: gi|27578697|gb|CB001392.1|CB001392
EST:     GGGTTGGTGAGTCGGGGCACGAGAACGAAAAG                         GGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCA
genomic: GGGTTGGTGAGTCGGGGCACGAGAACGAAAAGgtatgctagc ... tgtgttgcagGGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCA
EST: gi|27581381|gb|CB004076.1|CB004076
EST:     GGGTTGGTGAGTCGGGGCACGAGAACGAAAAG                         GGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCA
genomic: GGGTTGGTGAGTCGGGGCACGAGAACGAAAAGgtatgctagc ... tgtgttgcagGGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCA
EST: gi|30322426|gb|CD005688.1|CD005688
EST:     ATGAAGAGGGTAATCTTTGGGTTGGTGAGTCGGGGCACGAGAACGAAAAG                         GGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCA
genomic: ATGAAGAGGGTAATCTTTGGGTTGGTGAGTCGGGGCACGAGAACGAAAAGgtatgctagc ... tgtgttgcagGGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCA
EST: gi|34545798|gb|CF514030.1|CF514030
EST:     ATGAAGAGGGTAATCTTTGGGTTGGTGAGTCGGGGCACGAGAACGAAAAG                         GGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCA
genomic: ATGAAGAGGGTAATCTTTGGGTTGGTGAGTCGGGGCACGAGAACGAAAAGgtatgctagc ... tgtgttgcagGGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCA
EST: gi|30323405|gb|CD006667.1|CD006667
EST:     GGGTTGGTGAGTCGGGGCACGAGAACGAAAAG                         GGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCA
genomic: GGGTTGGTGAGTCGGGGCACGAGAACGAAAAGgtatgctagc ... tgtgttgcagGGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCA
EST: gi|28970697|gb|CB349730.1|CB349730
EST:     ATGAAGAGGGTAATCTTTGGGTTGGTGAGTCGGGGCACGAGAACGAAAAG                         GGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCA
genomic: ATGAAGAGGGTAATCTTTGGGTTGGTGAGTCGGGGCACGAGAACGAAAAGgtatgctagc ... tgtgttgcagGGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcaaatattttatcatagcagatgttaaatatcattctcctgattgtgttgcagGGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCACTTAAGGATAACTCTAACCCACAAATAGCTTTGCTTCCCTTACATCCAG
                                      tcctgat  putative branch site (score: 3)
                      atgttaaatatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattggtttcatggcatcaagatggaaagtttcttgccaagttttgtcaaatattttatcatagcagatgttaaatatcattctcctgattgtgttgcagGGAGAAGAAATTATAGTGGTAATGCCCTGGGATGAATGGTGGGAATTGTCACTTAAGGATAACTCTAACCCACAAATAGCTTTGCTTCCCTTACATCCAG

- - - - tcatggc
- - - - - - - - - - gatggaaa
- - - - - - - - - - - - - - - - cttgcca
- - - - - - - - - - - - - - - - - - - - - - - -caaatat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catagca