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'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtattatttttaaaatacatatgcttagttattcgtctatttaaatttctactgacacatttcatctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTGGAAAACCAGCTGCTATAGTGTTTGGAATGGGCTACGTGACAAACTCTGC

Basic information

species Vitis vinifera
transcript Vv14s0068g01300.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 4
-------------gtatgtgtattattt-ttaaaataca---tatgcttagtta--------ttcgtctatttaaatttctactgacacatttcatctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTGGAAAACCAGCTGCTATAGTGTTTGGAATGGGCTACGTGACAAACTCTGC
             || ||| | | |    |||||||      | || ||  |||        |  ||||  | |  ||||     |      |  || |  ||| ||||   || | ||   |||||||||  ||| ||| ||||| |||||||| || |||||||||||||| ||||| |||||||| ||||||||||||||
gtaggtactattagtttgtatttcagccattaaaatgtgaattttgtttgtttacatttgcatgtgtcttatcatgtttccttgaatgtggcttttccaatagGAACAACTGTGCTTCACCTTGAATTGGAGGAGTGTGTTGCAAACTTTGTTGGGAAGCCAGCTGCTATAGTTTTTGGTATGGGCTATGTGACAAACTCTGC

upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G26210.1 (Glycine max), 3'ss of exon 4
-------------gtatgtgtattattt-ttaaaataca------tatgcttagtt----attcgtctatttaaatttctactgacacatttcatctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTGGAAAACCAGCTGCTATAGTGTTTGGAATGGGCTACGTGACAAACTCTGC
             || ||| |   | |  |||||||         | || |||  |    ||  ||||  | |  ||||     |      |  || |  ||| ||||      | ||   |||| ||||  ||| ||| ||||| |||||||| || |||||||||||||| ||||| |||||||| ||||| ||||||||
gtaggtattattagtttgtattccagtcgttaaaatgtggttttttttgtttacatttgcatgtgtcttatcatgtttccttgaatgtggcttttccaatagGGACAACTGCACTTCACCTTGAACTGGAGGAGTGTGTTGCAAAATTTGTTGGGAAGCCAGCTGCTATAGTTTTTGGTATGGGCTATGTGACGAACTCTGC
















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|352778118|gb|FQ467171.1|FQ467171
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|349823630|gb|FQ415040.1|FQ415040
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|349832894|gb|FQ423016.1|FQ423016
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|351033557|gb|FQ447716.1|FQ447716
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|351041981|gb|FQ456191.1|FQ456191
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|351054108|gb|FQ450190.1|FQ450190
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|352773004|gb|FQ470619.1|FQ470619
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|351046320|gb|FQ448625.1|FQ448625
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCANATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|351054020|gb|FQ441786.1|FQ441786
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|349808540|gb|FQ405684.1|FQ405684
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTTGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|349807664|gb|FQ402055.1|FQ402055
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|349820492|gb|FQ408442.1|FQ408442
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTTGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|349822627|gb|FQ412891.1|FQ412891
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|351015401|gb|FQ447230.1|FQ447230
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|349819861|gb|FQ404535.1|FQ404535
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|349819166|gb|FQ412060.1|FQ412060
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTTGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|349820920|gb|FQ408628.1|FQ408628
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|351056259|gb|FQ453721.1|FQ453721
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|352782149|gb|FQ470051.1|FQ470051
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|351037559|gb|FQ462542.1|FQ462542
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|349813001|gb|FQ411241.1|FQ411241
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|351021667|gb|FQ437052.1|FQ437052
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|349822644|gb|FQ412908.1|FQ412908
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATG-CTGCAAATTTTGTT
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTC-GCAAATTTTGTT
EST: gi|352789617|gb|FQ476215.1|FQ476215
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|351032559|gb|FQ458924.1|FQ458924
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|352772806|gb|FQ473844.1|FQ473844
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|349808891|gb|FQ406741.1|FQ406741
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|351032958|gb|FQ461847.1|FQ461847
EST:     ATCACTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|349823382|gb|FQ402581.1|FQ402581
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|349826514|gb|FQ418605.1|FQ418605
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|349810608|gb|FQ402851.1|FQ402851
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
EST: gi|349817896|gb|FQ407885.1|FQ407885
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTTGCAAATTTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTG
EST: gi|351057058|gb|FQ448575.1|FQ448575
EST:     ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTG                         GCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG
genomic: ATCATTGAAGAAATTTTCACCAAGCACCTGTAGTAGCCGGGCTGATGGTGgtatgtgtat ... catctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatgcttagttattcgtctatttaaatttctactgacacatttcatctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTGGAAAACCAGCTGCTATAGTGTTTGGAATGGGCTACGTGACAAACTCTGC
                                tactgac  putative branch site (score: 1)
                                          tttcatct  putative PPT
                  tctatttaaatttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgtattatttttaaaatacatatgcttagttattcgtctatttaaatttctactgacacatttcatctatcagGCACAATAATGATGCATAATGAATTGGAAAAGTATGTCGCAAATTTTGTTGGAAAACCAGCTGCTATAGTGTTTGGAATGGGCTACGTGACAAACTCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT