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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTGTTGATGGTGATTTTGACAGCAATGATCCAGGAAAAGAATGTGTTATCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATGgtaagtgcattatcttgtttatttttgggatggctgtaataaaatgaggaagcgagaagggctaaaatagcccaatggttagctgcccagtattccttga...

Basic information

species Vitis vinifera
transcript Vv08s0040g01940.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g01940.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os10g13670.1 (Oryza sativa), 5'ss of exon 2
CTCTGTTGATGGTGATTTTGACAGCAATGATCCAGGAAAAGAATGTGTTATCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATGgtaagt------gcattatctt--gtttatttttgggatggctgtaataaaatgaggaagcgagaagggcta-aaatagcccaatggttagctgcccagta--ttccttga-------------------------------------------------------------
||||||||| |||||    ||  | |||||||| || ||||| |||||||||||| | ||||| ||  |||| ||||||||||| || ||| ||||||||||||||       ||   ||||  |||||| ||||   |   | | |    |||  |||   |   |  ||| || |   |   |  |    | |  ||||  | ||| ||                                                             
CTCTGTTGAAGGTGACACCGAAGGGAATGATCCTGGCAAAGAGTGTGTTATCTGCCTATCGGAGCCAAGGGATACAACTGTCCTCCCATGTAGACATATGgtaagtcttgaaacaggctcttgagtttatgtttgtcctttattttactttatgctgaaattat--gtcctacaactcttctgttcatgttttacatagtagatgcctagatcgtcatcgtcgtgaaattttcggaatgacaaacccttttgacattttccttatggtgcag

upper sequence: Vv08s0040g01940.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G036697_T01 (Zea mays), 5'ss of exon 2
CTCTGTTGATGGTGATTTTGACAGCAATGATCCAGGAAAAGAATGTGTTATCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATGgtaagtgcattatcttgtttatttttgggatggctgtaata-aaatgaggaagcgagaagggctaaaatagcccaa---tggt-tagctgcccagtattccttga
|||  | || ||||||  |||    ||||||||||| |||||||||||||| ||| | || |||||  |||| || |||||||| || ||| | ||||||||||||    |   |  | ||||   ||  ||  | |  |     ||  ||| | | | |  |||   | |   ||   |||| ||  |   || ||||      
CTCCATGGAAGGTGATGCTGATGCAAATGATCCAGGGAAAGAATGTGTTATTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATGgtaagtctgctgg-taatctattcaaggattgcattttgtgtgtgtgtagaaacta-acgatctattcttgaagaaacttggtataagttttcattatttaa---

upper sequence: Vv08s0040g01940.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM5G860152_T02 (Zea mays), 5'ss of exon 2
CTCTGTTGATGGTGATTTTGACAGCAATGATCCAGGAAAAGAATGTGTTATCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATGgtaagtgcattatcttgtttatttttgggatg---gctgtaataaaatgaggaagcgagaagggctaaaatagcccaatggttagctgcccagtattccttga
||| || || ||||||  |||    ||||||||||| |||||||||||||| ||| | || |||||  |||| || |||||||| || ||| | ||||||||||||    |  |   | ||||   ||  ||     | |  |  |   |  ||     ||    | || || |    |   ||  |   || ||||     |
CTCCGTGGAAGGTGATGCTGATGCAAATGATCCAGGGAAAGAATGTGTTATTTGCCTCTCAGAACCAAGGGATACTACTGTCCTCCCATGTAGGCATATGgtaagtatgctggca-atctattcaaggattgcatttttttttgtagaaactaatgctcaatttttgaagtaacttggta--taagttttcattatttgacta

upper sequence: Vv08s0040g01940.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA10G05930.1 (Glycine max), 5'ss of exon 2
CTCTGTTGATGGTGATTTTGACAGCAATGATCCAGGAAAAGAATGTGTTATCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATGgt----aagtgcattatcttgtttatttttgggatggctgtaataaaatgaggaagcgagaagggctaaaatagcccaatggttagc-tgcccagtattccttga
 || || ||  ||||| | ||  | ||||| || |||||||| |||||||| |||||||| || ||||||||||||||||||||||| ||||| || |||||    || | |    |    ||| || ||    |   |    | || ||    |  ||     |||   || |   | |  |||        ||||||  |   
TTCAGTGGAGAGTGATGTGGATGGGAATGACCCGGGAAAAGAGTGTGTTATATGCTTGTCAGAGCCTCGGGACACAACTGTCCTTCCATGTCGCCACATGgtatttaattactggtttcctttttttcttacattaatttcttttaattggttgactgaatgatgctctgatggt--agtcattaatactatgagtattagt---

upper sequence: Vv08s0040g01940.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA13G20270.1 (Glycine max), 5'ss of exon 2
CTCTGTTGATGGTGATTTTGACAGCAATGATCCAGGAAAAGAATGTGTTATCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATGgtaagtgcattatcttgtttatttttgggatggctgtaataaaatgaggaagcgagaagggctaaaatagcccaatggttagc-tgcccagtattccttga-
 || || ||  ||||| | ||  | ||||| ||||||||||| |||||||| |||||||| || ||||||||||||||||||||||| || || || ||||||  | |  | ||   ||| | ||         | |  | || ||    |  ||     ||    || |   | |  |||   |   ||| |    || | 
TTCAGTGGAGAGTGATGTGGATGGGAATGACCCAGGAAAAGAGTGTGTTATATGCTTGTCAGAGCCTCGGGACACAACTGTCCTTCCATGCCGCCACATGgtatttaccatttcccttttttcttaaattaatttctttttaattggttgacagaatgatgccctgatggt--agtcattaatgtattcagaaagtgtttaa

upper sequence: Vv08s0040g01940.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA03G33770.1 (Glycine max), 5'ss of exon 3
---CTCTGTTGATGGTGATTTTGACAGCAATGATCCAGGAAAAGAATGTGTTATCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATGgtaagtgcattatcttgtttatttttgggatggct-gtaataaaatgaggaagcgagaagggc-taaaatagcccaatggttagctgcccagtattccttga
    | || |  | |  |||        ||||| | |||||||   |||||||| |||||||| || || || || |||| |||||||||||| || |||||||||  |     | |||   | |||    |||   | || || |  |||   |  ||    |   | |       ||    |    |  ||| | ||  |  |
GATATATGGTATTAGAAATTCAACGGAGAATGACCAAGGAAAA---TGTGTTATTTGCTTGTCAGAGCCCCGAGATACAATTGTCCTTCCCTGCCGGCATATGgtatatttgc-agcttccctttttgaatgatattttgtgattagttgatagaatgatgctgatgtgatggtaggcatcaatatcataaccaat-tttatcaa

upper sequence: Vv08s0040g01940.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT3G09770.1 (Arabidopsis thaliana), 5'ss of exon 2
CTCTGTTGATGGTGATTTTGACAGCAATGATCCAGGAAAAGAATGTGTTATCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATGgtaagtgcattatcttgtttatttttgggatggctgtaataaaatgaggaagcgagaagggctaaaatagcccaatggttagctgcccagtattccttga
   || ||||   | |  |||    |||||||| || |||||||||||||| || ||||| ||||| || ||||| ||||| ||||| ||||||||||||||||||| |  | ||  |   ||  |   ||   ||| || |       |       | |   ||||| |      | || |  |  |||          
GGATGATGATTCAGCTGATGATGCTAATGATCCTGGTAAAGAATGTGTTATATGTTTGTCTGAACCACGAGACACCACTGTTCTTCCATGTCGACATATGgtaagtgaa--agctgatgatttactactatta-tgtgatgatggacatatatatagatgttaaaaattgtttgg-gtttggtggtgcag----------

upper sequence: Vv08s0040g01940.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: PP1S131_9V6.2 (Physcomitrella patens), 5'ss of exon 3
CTCTGTTGATGGTGATTTTGACAGCAATGATCCAGGAAAAGAATGTGTTATCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATGgtaagtgcattatcttgtttatttttgggatggctgtaataaaatgaggaagcgagaagggctaaaatagcccaatggttagctgcccagtattccttga--
    |  | |||| |||||||  ||| |||| | ||||||||||| ||| ||||  |||| ||||||||||| ||||||||||| || |||||||| ||||| ||  ||   |  |  || |  |||  || |||  |   |   |  | |  |  ||| ||| |   ||       || | | |   | ||   |   |  
TGGAGGGGGTGGTAATTTTGATGGCACTGATTCTGGAAAAGAATGCGTTGTCTGTATGTCCGAACCTCGGGATACAACTGTCCTGCCTTGTCGACACATGgtgagaccac--ttgtccttgtcgttgaaattgcttgatctagccggtgtatgggaaagcgctgatgcagtaggtatgtcatcagttaaatacaacaaaatc

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|161705868|gb|FC054794.1|FC054794
EST:     TCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATG                         TGTATGTGCAGTGGGTGTGCTAAAGTTTTGAGGTTCCAAACAGACCGGTGC
genomic: TCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATGgtaagtgcat ... tttgttgcagTGTATGTGCAGTGGGTGTGCTAAAGTTTTGAGGTTCCAAACGGACCGGTGC
EST: gi|110408370|gb|EC974005.1|EC974005
EST:     GTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATG                         TGTATGTGCAGTGGGTGTGCTAAAGTTTTGAGGTTCCAAACAGACCGGTGC
genomic: GTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATGgtaagtgcat ... tttgttgcagTGTATGTGCAGTGGGTGTGCTAAAGTTTTGAGGTTCCAAACGGACCGGTGC
EST: gi|28960915|gb|CB340465.1|CB340465
EST:     TCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATG                         TGTATGTGCAGTGGGTGTGCTAAAGTTTTGAGGTTCCAAACAGACCGGTGC
genomic: TCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATGgtaagtgcat ... tttgttgcagTGTATGTGCAGTGGGTGTGCTAAAGTTTTGAGGTTCCAAACGGACCGGTGC
EST: gi|83276153|gb|DV940161.1|DV940161
EST:     TCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATG                         TGTATGTGCAGTGGGTGTGCTAAAGTTTTGAGGTTCCAAACAGACCGGTGC
genomic: TCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATGgtaagtgcat ... tttgttgcagTGTATGTGCAGTGGGTGTGCTAAAGTTTTGAGGTTCCAAACGGACCGGTGC
EST: gi|110703387|gb|EE080188.1|EE080188
EST:     TCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATG                         TGTATGTGCAGTGGGTGTGCTAAAGTTTTGAGGTTCCAAACAGACCGGTGC
genomic: TCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATGgtaagtgcat ... tttgttgcagTGTATGTGCAGTGGGTGTGCTAAAGTTTTGAGGTTCCAAACGGACCGGTGC
EST: gi|110693541|gb|EE069862.1|EE069862
EST:     TCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATG                         TGTATGTGCAGTGGGTGTGCTAAAGTTTTGAGGTTCCAAACAGACCGGTGC
genomic: TCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATGgtaagtgcat ... tttgttgcagTGTATGTGCAGTGGGTGTGCTAAAGTTTTGAGGTTCCAAACGGACCGGTGC
EST: gi|22010602|gb|BQ795636.1|BQ795636
EST:     TCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCGGTCGACATATG                         TGTATGTGCAGTGGGTGTGCTAAAGTTTTGAGGTTCCAAACGGACCGGTGC
genomic: TCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATGgtaagtgcat ... tttgttgcagTGTATGTGCAGTGGGTGTGCTAAAGTTTTGAGGTTCCAAACGGACCGGTGC
EST: gi|28960060|gb|CB340031.1|CB340031
EST:     TTTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATG                         TGTATGTGCAGTGGGTGTGCTAAAGTTTTGAGGTTCCAAACAGACCGGTGC
genomic: TCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATGgtaagtgcat ... tttgttgcagTGTATGTGCAGTGGGTGTGCTAAAGTTTTGAGGTTCCAAACGGACCGGTGC
EST: gi|71884843|gb|DT033898.1|DT033898
EST:     TCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATG                         TGTATGTGCAGTGGGTGTGCTAAAGTTTTGAGGTTCCAAACAGACCGGTGC
genomic: TCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATGgtaagtgcat ... tttgttgcagTGTATGTGCAGTGGGTGTGCTAAAGTTTTGAGGTTCCAAACGGACCGGTGC
EST: gi|30129099|gb|CB914438.1|CB914438
EST:     TCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATG                         TGTATGTGCAGTGGGTGTGCTA
genomic: TCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATGgtaagtgcat ... tttgttgcagTGTATGTGCAGTGGGTGTGCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCTGTTGATGGTGATTTTGACAGCAATGATCCAGGAAAAGAATGTGTTATCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATGgtaagtgcattatcttgtttatttttgggatggctgtaataaaatgaggaagcgagaagggctaaaatagcccaatggttagctgcccagtattccttga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcgagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaatag