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

...acgcatatgttattagatcattactatgcttcttaatcatggtgtgctaaaattcttactttgaactgtttattctgaatgagtatcattttcctttcagTGGTATGAGAAATTCATAGATGTTGATGAGGTCATACCAGTGAGTGCCAAGTATGGTCAAGGAGTAGATGATGTCAAGGATTGGATATTGTCAAAACTTC

Basic information

species Vitis vinifera
transcript Vv04s0023g02120.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g02120.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G158024_T01 (Zea mays), 3'ss of exon 4
acgcatatgttattagatcattactat---gcttcttaatcatggtgtgctaaaattcttactttga-actgtttattctgaatgagtatcattttcctttcagTGGTATGAGAAATTCATAGATGTTGATGAGGTCATACCAGTGAGTGCCAAGTATGGTCAAGGAGTAGATGATGTCAAGGATTGGATATTGTCAAAACTTC
  ||  |  |||| | ||  |    |    | | | |  |  |  ||||||    |    |    ||   | || |||   |      |  | | |  |  ||||||||  | ||||| |   |||||||||| || |||||| | ||||| || | |||||| ||||| |||||| ||||||| |||||||||||||| || |
gtgcgaaccttataaaattgtcgaaaggtggttccctgtttcttttgtgctttcctctgcataaagacggtattgatttctag-----acgactcttttaacagTGGTACCAAAAATTTACTAATGTTGATGATGTTATACCAATAAGTGCTAAATTTGGTCATGGAGTGGATGATATCAAGGAGTGGATATTGTCAAAGCTCC

upper sequence: Vv04s0023g02120.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G06100.1 (Glycine max), 3'ss of exon 4
------acgcatatgttattagat-cattactatgcttc--ttaatcatggtgtgctaaaattcttactttgaactgtttattctgaatgagtatcattttcctttcagTGGTATGAGAAATTCATAGATGTTGATGAGGTCATACCAGTGAGTGCCAAGTATGGTCAAGGAGTAGATGATGTCAAGGATTGGATATTGTCAAAACTTC
      ||  |    ||| ||  |  ||||  |||  |   |||||      ||  |   ||  ||  |      | ||   ||  ||| | | |||  |||||| ||||||||||||||||| |  |||||||||||||| |||||||| |||||||| |||||||| || || || ||||| ||||| |||||| ||||||| ||||
gttggaacagagtaattagtatttatattagcatgtattagttaattcactggttttggcatgatttttcctgtgttttatgtcccaattatt-tcaaattccttgcagTGGTATGAGAAATTAACTGATGTTGATGAGGTTATACCAGTAAGTGCCAAATATGGTCAGGGGGTTGAAGATGTAAAGGACTGGATACTGTCAAAGCTTC

upper sequence: Vv04s0023g02120.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G24870.1 (Glycine max), 3'ss of exon 4
------acgcatatgttattagat-catta--ctatgcttcttaatcatggtgtgctaaaattcttactttgaactgtttattctgaatgagtatcattttcctttcagTGGTATGAGAAATTCATAGATGTTGATGAGGTCATACCAGTGAGTGCCAAGTATGGTCAAGGAGTAGATGATGTCAAGGATTGGATATTGTCAAAACTTC
      ||  |    ||| ||  |  ||||  || |     |||||   |  ||  |   ||   |  ||  |    ||||| |   |    | |||  |||||||||||||||||||||||| |  || ||||||||||| ||||| || |||||||| |||||||| || || || ||||||||||| |||||| ||||||| ||||
gttggaacaaaataattagtatttatattagcctgtataagttaattcagtggttttggcatgact-tttgcagtattttatgccctaattatttcaacttcctttcagTGGTATGAGAAATTTACTGAAGTTGATGAGGTTATACCTGTTAGTGCCAAATATGGTCAGGGGGTTGAAGATGTCAAGGACTGGATACTGTCAAAGCTTC

upper sequence: Vv04s0023g02120.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G66470.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------------------------------------------------------------------acgcata-tgttattagat-cattactatgcttctta-atcatggtgtgctaaaattcttactttgaactgtttatt-ctgaatgagtatcatt-ttcctttcagTGGTATGAGAAATTCATAGATGTTGATGAGGTCATACCAGTGAGTGCCAAGTATGGTCAAGGAGTAGATGATGTCAAGGATTGGATATTGTCAAAACTTC
                                                                            ||    | || |   |||| | | |||||     | | |||| | | ||    | |  |    |||   ||||  || || |||   |        ||||| ||||||||||| ||||| |  ||||||||||| || ||||| || ||||| |||||||| || ||| |||| |||||||| || |||||||| || |||||||
gtgagtatgctgtcgttgctatccttgaaccttggtaatactgtcctgttattaaaatcccaccattctagaatgaacttgcagtggtggaagatgcttcactataaacttgagatcaagatttg---gagtcatggtattgctatgttctttgcttaatagatgctgcaactccttgcagTGGTATGAAAAATTTACGGATGTTGATGAAGTTATACCTGTAAGTGCAAAGTATGGACATGGAATAGAGGATGTCAAAGAGTGGATATTATCCAAACTTC

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|34546865|gb|CF515097.1|CF515097
EST:     TGAATAAGAAAGATCTTATCAAACCTGGTGAAATTGCAAAGAAACTCGAG                         TGGTATGAGAAATTCATAGATGTTGACGAGGTCATACCAGTGAGTGCTAAG
genomic: TGAATAAGAAAGATCTGATCAAACCTGGTGAAATTGCAAAGAAACTCGAGgtcagaacct ... ttcctttcagTGGTATGAGAAATTCATAGATGTTGATGAGGTCATACCAGTGAGTGCCAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctaaaattcttactttgaactgtttattctgaatgagtatcattttcctttcagTGGTATGAGAAATTCATAGATGTTGATGAGGTCATACCAGTGAGTGCCAAGTATGGTCAAGGAGTAGATGATGTCAAGGATTGGATATTGTCAAAACTTC
       ttcttac  putative branch site (score: 2)
                                      tatcattttcctttc  putative PPT
                                      tatcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acgcatatgttattagatcattactatgcttcttaatcatggtgtgctaaaattcttactttgaactgtttattctgaatgagtatcattttcctttcagTGGTATGAGAAATTCATAGATGTTGATGAGGTCATACCAGTGAGTGCCAAGTATGGTCAAGGAGTAGATGATGTCAAGGATTGGATATTGTCAAAACTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- gcatatg
- - - - - - - - - - - -ctatgct
- - - - - - - - - - - - - - - - - - - -tggtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgaatg