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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctgttcatcaaatcttatacaacatgatattccccttgttgaaagattatgtttcttttgtatcagtttgaaaagtatttaatatgattgttgaacagGGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTAAAGGAAGAGACAGGAGTTGCTTCAGCAGAGGTTCTTGCAGAG

Basic information

species Vitis vinifera
transcript Vv08s0056g00030.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0056g00030.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G33600.1 (Glycine max), 3'ss of exon 2
--tgctgttcatcaaatcttatacaacat--gatattccccttgttgaaagattatgtttcttttgtatcagtttgaaaagtat-ttaatatgattgttgaacagGGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTAAAGGAAGAGACAGGAGTTGCTTCAGCAGAGGTTCTTGCAGAG
  || ||    |    | |||   | | |    | ||    |||||||||||  ||| |  |  |||||   | | | ||  || |||||   ||  ||    |||||||||||||||| ||||| ||||| |||||||| ||||| ||||||||||  |||||||||||||||  ||| ||||| ||  |||| |||
tctgatgagtttgtgcttttacttatctttcagttttttgtttgttgaaagag-atgatg-tactgtatgtttgtaataatcatgttaatgacatcttt---tagGGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCCATCAGGGAATTAAGAGAAGAGACAGGAGTTAATTCTGCAGAAGTGATTGCTGAG

upper sequence: Vv08s0056g00030.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G33990.1 (Glycine max), 3'ss of exon 2
-----tgctgttcatcaaatcttatacaacatgatattccccttgttgaaagattatgtttcttttgtatcagtttgaaaagtatttaatatgattgttgaacagGGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTAAAGGAAGAGACAGGAGTTGCTTCAGCAGAGGTTCTTGCAGAG
     |||  ||  | |  | | || ||   |  | ||   ||     | |||| ||||    |  || |       ||   | || ||| ||    |     |||||||||||||||| ||||| ||||| |||||||| || || ||||| |||   |||||||||||||||  ||||| ||| ||  | || |||
gagtttgcactt--ttacttttcattcagtgttttgttttgctga--aagagatgatgtactgtaagtttgtaacataatcatgttaaatgtggc-atcttttagGGTGGTATTGATGAAGGTGAGGATCCAAGAAATGCAGCTATCAGGGAGTTACGAGAAGAGACAGGAGTTAATTCAGTAGAAGTGATCGCTGAG
















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|110703134|gb|EE079712.1|EE079712
EST:     TATTTGCTGCTTCAAGGCTTGATATACCTGATGCATGGCAAATGCCGCAG                         GGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTA
genomic: TATTTGCTGCTTCAAGGCTTGATATACCTGATGCATGGCAAATGCCGCAGgtgatttgga ... tgttgaacagGGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTA
EST: gi|351033064|gb|FQ446417.1|FQ446417
EST:     TATTTGCTGCTTCAAGGCTTGATATACCTGATGCATGGCAAATGCCGCAG                         GGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTA
genomic: TATTTGCTGCTTCAAGGCTTGATATACCTGATGCATGGCAAATGCCGCAGgtgatttgga ... tgttgaacagGGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTA
EST: gi|110702464|gb|EE081204.1|EE081204
EST:     TATTTGCTGCTTCAAGGCTTGATATACCTGATGCATGGCAAATGCCGCAG                         GGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTA
genomic: TATTTGCTGCTTCAAGGCTTGATATACCTGATGCATGGCAAATGCCGCAGgtgatttgga ... tgttgaacagGGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTA
EST: gi|351026488|gb|FQ428500.1|FQ428500
EST:     TATTTGCTGCTTCAAGGCTTGATATACCTGATGCATGGCAAATGCCGCAG                         GGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTA
genomic: TATTTGCTGCTTCAAGGCTTGATATACCTGATGCATGGCAAATGCCGCAGgtgatttgga ... tgttgaacagGGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTA
EST: gi|77584900|gb|DV221533.1|DV221533
EST:     TATTTGCTGCTTCAAGGCTTGATATACCTGATGCATGGCAAATGCCGCAG                         GGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTA
genomic: TATTTGCTGCTTCAAGGCTTGATATACCTGATGCATGGCAAATGCCGCAGgtgatttgga ... tgttgaacagGGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTA
EST: gi|27582290|gb|CB004985.1|CB004985
EST:     TATTTGCTGCTTCAAGGCTTGATATACCTGATGCATGGCAAATGCCGCAG                         GGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTA
genomic: TATTTGCTGCTTCAAGGCTTGATATACCTGATGCATGGCAAATGCCGCAGgtgatttgga ... tgttgaacagGGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTA
EST: gi|71870980|gb|DT020035.1|DT020035
EST:     TATTTGCTGCTTCAAGGCTTGATATACCTGATGCATGGCAAATGCCGCAG                         GGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTA
genomic: TATTTGCTGCTTCAAGGCTTGATATACCTGATGCATGGCAAATGCCGCAGgtgatttgga ... tgttgaacagGGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTA
EST: gi|110382971|gb|EC947304.1|EC947304
EST:     TATTTGCTGCTTCAAGGCTTGATATACCTGATGCATGGCAAATGCCGCAG                         GGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTA
genomic: TATTTGCTGCTTCAAGGCTTGATATACCTGATGCATGGCAAATGCCGCAGgtgatttgga ... tgttgaacagGGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTA
EST: gi|18458074|gb|BM436352.1|BM436352
EST:     TATTTGCTGCTTCAAGGCTTGATATACCTGATGCATGGCAAATGCCGCAG                         GGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTA
genomic: TATTTGCTGCTTCAAGGCTTGATATACCTGATGCATGGCAAATGCCGCAGgtgatttgga ... tgttgaacagGGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTA
EST: gi|71867829|gb|DT016884.1|DT016884
EST:     TATTTGCTGCTTCAAGGCTTGATATACCTGATGCATGGCAAATGCCGCAG                         GGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTA
genomic: TATTTGCTGCTTCAAGGCTTGATATACCTGATGCATGGCAAATGCCGCAGgtgatttgga ... tgttgaacagGGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattatgtttcttttgtatcagtttgaaaagtatttaatatgattgttgaacagGGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTAAAGGAAGAGACAGGAGTTGCTTCAGCAGAGGTTCTTGCAGAG
                                 atttaat  putative branch site (score: 4)
                       tttgaaaagtatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctgttcatcaaatcttatacaacatgatattccccttgttgaaagattatgtttcttttgtatcagtttgaaaagtatttaatatgattgttgaacagGGTGGTATTGATGAGGGTGAAGATCCGAGAAATGCTGCCATGAGGGAATTAAAGGAAGAGACAGGAGTTGCTTCAGCAGAGGTTCTTGCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
tgctgtt
- - - - atcaaat
- - - - - - - - - - -caacatg
- - - - - - - - - - - - - - - - tcccctt
- - - - - - - - - - - - - - - - - - - - -tgaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagta