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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGTCTTACCTTTTTTGCTCCAAGTGAAGAGAGACTCGAGTCTGGACTGTACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAGgttagttgcttaatcccatctccaggaccccacaggtggttgtgttatagttcgtagtgtcttttaagaaggcaattttgtgagaatcatatctgcagat...

Basic information

species Vitis vinifera
transcript Vv18s0001g00190.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g00190.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os06g51029.1 (Oryza sativa), 5'ss of exon 3
GTGGTCTTACCTTTTTTGCTCCAAGTGAAGAGAGACTCGAGTCTGGACTGTACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAGgttagttgcttaatcccatctccaggacccc--acaggtggttgtgttatagttcgtagtgtcttttaagaaggcaattttgtgagaatcatatctgcagat
|||| || || || ||||||||||| || ||||| || ||||||||| ||||||| || || ||||| ||||| || ||||| || || || ||||||||||  |||  ||| |   || | ||   |  |  ||| ||| |  |||| | || |  |||    || ||    |  |  ||    |  |   |         
GTGGACTCACATTCTTTGCTCCAAGCGAGGAGAGGCTTGAGTCTGGATTGTACAGCAGGAGCTACCTAGAGAACCAAATGGCCGTAGCTCTTGGTGGAAGgtgggtt--ttagtgaaatgttcatatctgcgtacatgtgctattgttgttgtgcaaagt---cttgaactgtgtgagcttacatggtttgcag--------

upper sequence: Vv18s0001g00190.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA04G02100.1 (Glycine max), 5'ss of exon 3
GTGGTCTTACCTTTTTTGCTCCAAGTGAAGAGAGACTCGAGTCTGGACTGTACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAGgttagt------tgcttaatcccatctccaggaccccacaggtggttgtgttatagttcgtagtgtcttttaagaaggcaattttgtgagaatcatatctgcagat
||||||| || ||||||||||| || |||||||| |||||||||||| ||||||||||||||||||| || ||||||||||||||||| ||||||||||||| |||      |||  |||  | | |    || |    |  | |   | ||  |  || |    ||||| |  ||  | | ||  ||  |||  |  ||   |  
GTGGTCTCACATTTTTTGCTCCCAGCGAAGAGAGGCTCGAGTCTGGATTGTACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCCTGGGTGGAAGgtcagtgcaacgtgcacaattac-tttgtttgatcttggattttgacat-ttgcaagtcattcattctttaacaaactccacttgttgtcaat--tggctaatg--

upper sequence: Vv18s0001g00190.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA06G02200.1 (Glycine max), 5'ss of exon 3
GTGGTCTTACCTTTTTTGCTCCAAGTGAAGAGAGACTCGAGTCTGGACTGTACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAGgttagttgcttaatcccatctccaggaccccacaggtggttgtgttatagttcgtagtgtcttttaagaaggcaattttgtgagaatcatatctgcagat-------
||||||| || ||||||||||| ||||||||||| || ||||||||| ||||||||||||||||||| || |||||||||||||||||  |||||||||||| ||| |   ||  | |  | ||      |     | |||   || ||| |  |    | |  ||   |  || | || |   ||   ||   ||  |        
GTGGTCTCACATTTTTTGCTCCCAGTGAAGAGAGGCTTGAGTCTGGATTGTACAGTAGAAGTTACCTTGAAAATCAGATGGCTGTTGCCTTGGGTGGAAGgtcagtgg---aacacaacatgcacagttacc----ttgtttgattttagattttgacatttgctagtcattcattcttatatcaacactactggcctactcttgag

upper sequence: Vv18s0001g00190.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT1G50250.1 (Arabidopsis thaliana), 5'ss of exon 3
GTGGTCTTACCTTTTTTGCTCCAAGTGAAGAGAGACTCGAGTCTGGACTGTACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAGgttagttgcttaatcccatctccaggaccccacaggtggttgtgttatagttcgtagtgtcttttaagaaggcaattttgtgagaatcatatctgcagat-------------------
|||| || || |||||||||||||| ||||| ||||| ||||||||| |||||||||| || ||||| |||||||| |||||||||||||| || ||||||||||||  | |||  | ||  |    |  ||||   |   || ||  | |    || |      |||     |||| ||| | || ||| |||     |                   
GTGGGCTCACTTTTTTTGCTCCAAGCGAAGAAAGACTTGAGTCTGGATTGTACAGTAGGAGCTACCTTGAGAATCAAATGGCTGTTGCACTTGGCGGAAGgttagttagt-aatggcctccacgcctcgtcacaaaagccagtctttgaatatacagag------aagggtttaattatgtta-aaccatctctatctctgttgtgttggctatgtcag

upper sequence: Vv18s0001g00190.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT5G42270.1 (Arabidopsis thaliana), 5'ss of exon 3
GTGGTCTTACCTTTTTTGCTCCAAGTGAAGAGAGACTCGAGTCTGGACTGTACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAGgttagttgcttaatcccatctccaggaccccacaggtggttgtgttatagttcgtagtgtcttttaagaaggcaattttgtgagaatcatatctgcagat-
|||| || |||||||| ||||| || |||||||| || ||||| ||| |||| || ||||| ||||| ||||| || |||||||||||||| ||||||||||   || |  ||        |    ||   || |||  |||  ||| |    ||||| |         |  |||| ||    |  |   | ||   |   
GTGGGCTCACCTTTTTCGCTCCTAGCGAAGAGAGGCTAGAGTCCGGATTGTATAGCAGAAGCTACCTTGAGAACCAAATGGCTGTTGCACTTGGTGGAAGgtagtttac--aa--------ctgaaactgtactggtt-ttgatttacaaga-gtagtcttcgagtgttaaacaatgtttattgtgtttcacctatggtag

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|110391145|gb|EC956102.1|EC956102
EST:     TACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAG                         GGTTGCAGAAGAGGTAATATTTGGAGAGGATAATGTAACAACAGGGGCATC
genomic: TACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAGgttagttgct ... actaatgcagGGTTGCAGAAGAGGTAATATTTGGAGAGGATAATGTAACAACAGGGGCATC
EST: gi|110717414|gb|EE093251.1|EE093251
EST:     TACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAG                         GGTTGCAGAAGAGGTAATATTTGGAGAGGATAATGTAACAACAGGGGCATC
genomic: TACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAGgttagttgct ... actaatgcagGGTTGCAGAAGAGGTAATATTTGGAGAGGATAATGTAACAACAGGGGCATC
EST: gi|26262505|gb|CA813568.1|CA813568
EST:     TACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTGGCACTGGGTGGAAG                         GGTTGCAGAAGAGGTAATATTTGGAGAGGATAATGTAACAACGGGGGCATC
genomic: TACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAGgttagttgct ... actaatgcagGGTTGCAGAAGAGGTAATATTTGGAGAGGATAATGTAACAACAGGGGCATC
EST: gi|26262506|gb|CA813569.1|CA813569
EST:     TACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAG                         GGTTGCAGAAGAGGTAATATTTGGAGAGGATAATGTAACAACGGGGGCATC
genomic: TACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAGgttagttgct ... actaatgcagGGTTGCAGAAGAGGTAATATTTGGAGAGGATAATGTAACAACAGGGGCATC
EST: gi|352790761|gb|FQ478309.1|FQ478309
EST:     TACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAG                         GGTTGCAGAAGAGGTAATATTTGGAGAGGATAATGTAACAACAGGGGCATC
genomic: TACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAGgttagttgct ... actaatgcagGGTTGCAGAAGAGGTAATATTTGGAGAGGATAATGTAACAACAGGGGCATC
EST: gi|352794299|gb|FQ481530.1|FQ481530
EST:     TACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAG                         GGTTGCAGAAGAGGTAATATTTGGAGAGGATAATGTAACAACAGGGGCATC
genomic: TACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAGgttagttgct ... actaatgcagGGTTGCAGAAGAGGTAATATTTGGAGAGGATAATGTAACAACAGGGGCATC
EST: gi|37183867|gb|CF603221.1|CF603221
EST:     TACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAG                         GGTTGCAGAAGAGGTAATATTTGGAGAGGATAATGTAACAACAGGGGCATC
genomic: TACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAGgttagttgct ... actaatgcagGGTTGCAGAAGAGGTAATATTTGGAGAGGATAATGTAACAACAGGGGCATC
EST: gi|30320659|gb|CD003921.1|CD003921
EST:     TACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAG                         GGTTGCAGAAGAGGTAATATTTGGAGAGGATAATGTAACAACAGGGGCATC
genomic: TACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAGgttagttgct ... actaatgcagGGTTGCAGAAGAGGTAATATTTGGAGAGGATAATGTAACAACAGGGGCATC
EST: gi|352798544|gb|FQ480569.1|FQ480569
EST:     TACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAG                         GGTTGCAGAAGAGGTAATATTTGGAGAGGATAATGTAACAACAGGGGCATC
genomic: TACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAGgttagttgct ... actaatgcagGGTTGCAGAAGAGGTAATATTTGGAGAGGATAATGTAACAACAGGGGCATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGTCTTACCTTTTTTGCTCCAAGTGAAGAGAGACTCGAGTCTGGACTGTACAGTAGAAGTTACCTGGAGAATCAGATGGCTGTTGCACTGGGTGGAAGgttagttgcttaatcccatctccaggaccccacaggtggttgtgttatagttcgtagtgtcttttaagaaggcaattttgtgagaatcatatctgcagat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - accccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaggcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgagaa