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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCATGAGAATCTACTCTATCTCAAGAGCCGgtaatttttatggttttagttggaacagcatctaatgtttttgcattgctaatcaattagatcataccagttaccatttttctcccatttttttggacttttactcacag

Basic information

species Vitis vinifera
transcript Vv12s0034g01440.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0034g01440.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA05G30330.1 (Glycine max), 5'ss of exon 3
GGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCATGAGAATCTACTCTATCTCAAGAGCCGgtaatttttatggttttagttggaacagcatctaatgtttttgcattgctaatcaattagatcatacca-gttaccatttttctcccatttttttggacttttactcacag
|| || ||||||||| ||||||| || ||||||||||| |||||||||||||||||  | |||||||| ||| |  |||||||   ||    | |     | |  |  ||     || |  ||||| ||| ||  |  || ||||   || ||      |||     | |  | |  | |        
GGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAGgtaattccaatcacatcaac---atcttcccctgtaaattgtttattgcaaataaaaaacttcgtaccccattgcccagaggctcttcgctatgcgaaggtat--------

upper sequence: Vv12s0034g01440.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA08G13470.1 (Glycine max), 5'ss of exon 3
GGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTG-GAGGCCATCCATGAGAATCTACTCTATCTCAAGAGCCGgtaatttttatggttttagttggaacagcatctaatgtttttgcattgctaatcaattagatcataccagttaccatttttctcccatttttttggacttttactcacag
|| |||||||||||| ||||||| || || ||||||||  |||||||||||||||||| | |||||||| ||| || |||||||   ||    | | |   | |  |  |||    |  |  ||| | | |   ||  |  | | |  ||   || |||      |  |||| |  ||| |       
GGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGTAAGAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGCAGgtaattccaatcacatcaat---atctccccctataaatagtttatttcaatttttttttaaaaaaacttttcatatgtttaatttttggtttttgggtttcag------

upper sequence: Vv12s0034g01440.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA07G08660.1 (Glycine max), 5'ss of exon 1
------------GGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCATGAGAATCTACTCTATCTCAAGAGCCGgtaatttttatggttttagttggaacagcatctaatgtttttgcattgctaatcaattagatcataccagttac-catttttctcccatttttttggacttttactcacag
            || || ||||||||| ||||||| || ||||||| |||  ||||||||||||||||| | |||||||| ||| |  |||||||   ||    | |     | |  |  ||     || |  | |||  || | ||     | ||   | |     ||   |    |||||| ||   |||| |||   
ATGGATACCTATGGAGTCGAGCTTGAGCTGAGAAAGCTAGAAGGAGAAGTAAAGGCCATCCATGAGAATTTGCTCTATCTTAAGGGAAGgtaattccaatcacatcaac---atcttcccctgtaaattgtttaatgcatataattttttaaaaacttttcatatgcttaatttttgttttttgggttatttattcag--

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|77587717|gb|DV223037.1|DV223037
EST:     GAAGGAGCAGTGGAGGCCATCCATGAGAATCTACTCTATCTCAAGAGCCG                         AGAAGCAGAAATGAGGATGGTGAGCG
genomic: GAAGGAGCAGTGGAGGCCATCCATGAGAATCTACTCTATCTCAAGAGCCGgtaattttta ... ttactcacagAGAAGCAGAAATGAGGATGGTGAGCG
EST: gi|351016734|gb|FQ424161.1|FQ424161
EST:     GAAGGAGCAGTGGAGGCCATCCATGAAAATCTACTCTATCTCAAGAGCCG                         AGAAGCAGAAATGAGGATGGTGAGCGAAAAAACAAAATGCA-GAGTGGCAT
genomic: GAAGGAGCAGTGGAGGCCATCCATGAGAATCTACTCTATCTCAAGAGCCGgtaattttta ... ttactcacagAGAAGCAGAAATGAGGATGGTGAGCGAAAAAACAAA-TGCAAGAGTGGCAT
EST: gi|349826899|gb|FQ418990.1|FQ418990
EST:     GAAGGAGCAGTGGAGGCCATCCATGAGAATCTACTCTATCTCAAGAGCCG                         AGAAGCAGAAATGAGGATGGTGAGCGAAAAAACAAATGCAAGAGTGGCATG
genomic: GAAGGAGCAGTGGAGGCCATCCATGAGAATCTACTCTATCTCAAGAGCCGgtaattttta ... ttactcacagAGAAGCAGAAATGAGGATGGTGAGCGAAAAAACAAATGCAAGAGTGGCATG
EST: gi|351028478|gb|FQ444759.1|FQ444759
EST:     GAAGGAGCAGTGGAGGCCATCCATGAGAATCTACTCTATCTCAAGAGCCG                         AGAAGCAGAAATGAGGATGGTGAGCGAAAAAACAAATGCAAGAGTGGCATG
genomic: GAAGGAGCAGTGGAGGCCATCCATGAGAATCTACTCTATCTCAAGAGCCGgtaattttta ... ttactcacagAGAAGCAGAAATGAGGATGGTGAGCGAAAAAACAAATGCAAGAGTGGCATG
EST: gi|110390944|gb|EC955893.1|EC955893
EST:     GAAGGAGCAGTGGAGGCCATCCATGAGAATCTACTCTATCTCAAGAGCCG                         AGAAGCAGAAATGAGGATGGTGAGCGAAAAAACAAATGCAAGAGTGGCATG
genomic: GAAGGAGCAGTGGAGGCCATCCATGAGAATCTACTCTATCTCAAGAGCCGgtaattttta ... ttactcacagAGAAGCAGAAATGAGGATGGTGAGCGAAAAAACAAATGCAAGAGTGGCATG
EST: gi|351034240|gb|FQ448037.1|FQ448037
EST:     GAAGGAGCAGTGGAGGCCATCCATGAGAATCTACTCTATCTCAAGAGCCG                         AGAAGCAGAAATGAGGATGGTGAGCGAAAAAACAAATGCAAGAGTGGCATG
genomic: GAAGGAGCAGTGGAGGCCATCCATGAGAATCTACTCTATCTCAAGAGCCGgtaattttta ... ttactcacagAGAAGCAGAAATGAGGATGGTGAGCGAAAAAACAAATGCAAGAGTGGCATG
EST: gi|351014680|gb|FQ437880.1|FQ437880
EST:     GAAGGAGCAGTGGAGGCCATCCATGAGAATCTACTCTATCTCAAGAGCCG                         AGAAGCAGAAATGAGGATGGTGAGCGAAAAAACAAATGCAAGAGTGGCATG
genomic: GAAGGAGCAGTGGAGGCCATCCATGAGAATCTACTCTATCTCAAGAGCCGgtaattttta ... ttactcacagAGAAGCAGAAATGAGGATGGTGAGCGAAAAAACAAATGCAAGAGTGGCATG
EST: gi|351029626|gb|FQ427466.1|FQ427466
EST:     GAAGGAGCAGTGGAGGCCATCCATGAGAATCTACTCTATCTCAAGAGCCG                         AGAAGCAGAAATGAGGATGGTGAGCGAAAAAACAAATGCAAGAGTGGCATG
genomic: GAAGGAGCAGTGGAGGCCATCCATGAGAATCTACTCTATCTCAAGAGCCGgtaattttta ... ttactcacagAGAAGCAGAAATGAGGATGGTGAGCGAAAAAACAAATGCAAGAGTGGCATG
EST: gi|351017782|gb|FQ436135.1|FQ436135
EST:     GAAGGAGCAGTGGAGGCCATCCATGAGAATCTACTCTATCTCAAGAGCCG                         AGAAGCAGAAATGAGGATGGTGAGCGAAAAAACAAATGCAAGAGTGG
genomic: GAAGGAGCAGTGGAGGCCATCCATGAGAATCTACTCTATCTCAAGAGCCGgtaattttta ... ttactcacagAGAAGCAGAAATGAGGATGGTGAGCGAAAAAACAAATGCAAGAGTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGTTGAGCTTGAGTTGAGAAAACTTGAAGGAGCAGTGGAGGCCATCCATGAGAATCTACTCTATCTCAAGAGCCGgtaatttttatggttttagttggaacagcatctaatgtttttgcattgctaatcaattagatcataccagttaccatttttctcccatttttttggacttttactcacag

- - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - -  TGGAGG