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'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactccagatgttaacttgatgtgtattaagtggcatatggttttgctttattattctttctgcatctacaatgcccttgttattgtaacatatatttgttgcattttcagGTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAATCAAGTGCTATTAAAGTGATTGATTTTGGAAGCACAACATATGAGCGAC

Basic information

species Vitis vinifera
transcript Vv17s0000g09500.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
------------gtactccagatgttaacttgatgtgtattaagtggcatatggttttgctttattattctttctgcatctacaatgccct--tgttattgtaacatatatttgttgcattttcagGTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAATCAAGTGCTATTAAAGTGATTGATTTTGGAAGCACAACATATGAGCGAC
             | || |  || | | |||   |  | || |  | | | |  ||   |  | |   |  || ||  || |||||    |  | |  || |||    | |    | |  |   |||||||||||||||| || ||||| ||||| || || |||    | || || || ||||||||||| |||||||||||||| |||||||||||||| |  |
gtatactttgttcttctacctatttgaccttttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaat-ctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 6
gtactccagatgttaacttgatgtgtattaagtggcatatggttttgctttattattctttctgcatctacaatgcccttgttattgt--aacatatatttgttgcatttt-cagGTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAATCAAGTGCTATTAAAGTGATTGATTTTGGAAGCACAACATATGAGCGAC------
           |  ||  | | |   |  |||||||   ||   ||||| |  ||||   || |   |   ||||   |   |    |  |     ||||  ||  ||||  |||  | || || | ||||| |      | || |  || |||||||| || || ||||||||||| ||||| ||||||||||| ||||| |||||||| |||       
-----------ggaaaagtaa-gaacaccaagtggc---tgaaattgctatgctattaggtcagatacagaaatgtgatcactgacatccattgcttattgtttatatttaacagAGTACAACCAGATCACCAA------GCTCCTTTTTCAAGAGAGTGCCCAAGTCAAGTGCTATAAAAGTTATTGATTTTGGCAGCACTACATATGAACGAGAAGATC

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA05G02740.1 (Glycine max), 3'ss of exon 6
gtactccagatgttaacttgatgtgtattaagtggcatatggttttgctttattattctttctgcatctacaatgcccttgttattgtaacatatatttgttgcattttcagGTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAATCAAGTGCTATTAAAGTGATTGATTTTGGAAGCACAACATATGAGCGAC------
      |  |  |  | |  ||    || ||   |  |||||   | |  | || |   ||  ||||     ||       | ||||  ||||  ||||  |   ||| |||  ||||||  | ||| |     ||| ||| || || |||||||| || |||||||||||||| || || ||||||||||| ||||| || |||||||||       
----gtcgtacctgga-tgaataaaaatgaaactgagtatggaagtacccttttctatctttagcatt---gattgatcaatcattg--acatccattt--tatttttacagAGTTCATCTAGATCATC-----ATG-TTCCTATTTCAAGAGAGTTCCCAAATCAAGTGCTATAAAGGTTATTGATTTTGGCAGCACCACTTATGAGCGAGAAGATC

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA17G13440.1 (Glycine max), 3'ss of exon 6
gtactccagatgtta-acttgatgtgtattaagtggcatatggttttgctttattattcttt--ctgcatctacaatgcccttgttattgtaacatatatttgttgcattttcagGTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAATCAAGTGCTATTAAAGTGATTGATTTTGGAAGCACAACATATGAGCGAC------
           |||  || ||  |  ||  || ||  |    || | |   ||   || | |  ||  | |  | ||       | ||||  ||||  ||||  |   ||| |||  ||||||  | ||||| |      |||| || || |||||||| || |||||||||||||| || || ||||||||||| ||||| || |||||||||       
-----------gttggacctggaggataaaaaatgaaaccaagtatggaactacccttttctagctttagcatcgattgatcaatcattg--acattcattt--tatttttacagAGTTCATCTAGATCACCAA------GTTCCTATTTCAAGAGAGTTCCCAAATCAAGTGCTATAAAGGTTATTGATTTTGGCAGCACCACTTATGAGCGAGAAGATC

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 6
gtactccagatgttaacttgatgtgtattaagtggcatatggttttgctttattattctttctgcatctacaatgcccttgttattgtaacatatatttgttgcatttt-cagGTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAATCAAGTGCTATTAAAGTGATTGATTTTGGAAGCACAACATATGAGCGAC------
              ||  | | |   |  |||||||  |   |  |    |||||       | ||   |  |   |  ||  ||   |      |||  ||  ||||  |||  | || || | ||||| |      |||| |  || |||||||| || || ||||||||||| ||||| ||||||||||| ||||| |||||||| |||       
-----------aggaaagtaa-gaacaccaagtggctgaaattgctatgctattaggtcagatacagaaatgagatcactgacatc-cattgctgattgtttatatttaacagAGTACAACCAGATCACCAA------GTTCCTTTTTCAAGAGAGTGCCCAAGTCAAGTGCTATAAAAGTTATTGATTTTGGCAGCACTACATATGAACGAGAAGATC

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT4G24740.1 (Arabidopsis thaliana), 3'ss of exon 7
gtactccagatgttaacttgatgtgtattaagtggcatatggttttgctttattattctttctgcatctacaatgcccttgttattgtaacatatatttgttgcatt-ttcagGTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAATCAAGTGCTATTAAAGTGATTGATTTTGGAAGCACAACATATGAGCGAC------
                     | | | |  | ||  |    || |  | ||| | |           | || ||     || |   | ||  |   | |||| | |  | ||||     ||||| | ||  | |||||     | || ||| ||||| || ||||||||||| || || |||||||||||||| |||||||| |||||||| |      
--------------------gtatatctcgaatgcaactgtgtgtgaccttaatgtg--------gccaactatttaagtgctgaaggaatttggttgtgtttcctgatgcagGG---GTCCCGATTACAAAGGGATG---TATGCTATAAAAGAGTGCCTAAATCAAGTGCAATAAAGGTGATTGATTTTGGTAGCACAACTTATGAGCGCCAGGACC

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|30322713|gb|CD005975.1|CD005975
EST:     AGAATATACTTCTAGTGTCTCCAGAATATGTTAAAGTTCCAGACTACAAG                         GTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAA
genomic: AGAATATACTTCTAGTGTCTCCAGAATATGTTAAAGTTCCAGACTACAAGgtactccaga ... gcattttcagGTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAA
EST: gi|110373955|gb|EC938383.1|EC938383
EST:     AGAATATACTTCTAGTGTCTCCAGAATATGTTAAAGTTCCAGACTACAAG                         GTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAA
genomic: AGAATATACTTCTAGTGTCTCCAGAATATGTTAAAGTTCCAGACTACAAGgtactccaga ... gcattttcagGTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAA
EST: gi|110362754|gb|EC926306.1|EC926306
EST:     AGAATATACTTCTAGTGTCTCCAGAATATGTTAAAGTTCCAGACTACAAG                         GTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAA
genomic: AGAATATACTTCTAGTGTCTCCAGAATATGTTAAAGTTCCAGACTACAAGgtactccaga ... gcattttcagGTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAA
EST: gi|32272087|gb|CD721246.1|CD721246
EST:     AGAATATACTTCTAGTGTCTCCAGAATATGTTAAAGTTCCAGACTACAAG                         GTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAA
genomic: AGAATATACTTCTAGTGTCTCCAGAATATGTTAAAGTTCCAGACTACAAGgtactccaga ... gcattttcagGTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAA
EST: gi|32268109|gb|CD717268.1|CD717268
EST:     AGAATATACTTCTAGTGTCTCCAGAATATGTTAAAGTTCCAGACTACAAG                         GTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAA
genomic: AGAATATACTTCTAGTGTCTCCAGAATATGTTAAAGTTCCAGACTACAAGgtactccaga ... gcattttcagGTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAA
EST: gi|30255726|gb|CB971858.1|CB971858
EST:     AGAATATACTTCTAGTGTCTCCAGAATATGTTAAAGTTCCAGACTACAAG                         GTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAA
genomic: AGAATATACTTCTAGTGTCTCCAGAATATGTTAAAGTTCCAGACTACAAGgtactccaga ... gcattttcagGTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAA
EST: gi|30324825|gb|CD008087.1|CD008087
EST:     AGAATATACTTCTAGTGTCTCCAGAATATGTTAAAGTTCCAGACTACAAG                         GTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAA
genomic: AGAATATACTTCTAGTGTCTCCAGAATATGTTAAAGTTCCAGACTACAAGgtactccaga ... gcattttcagGTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAA
EST: gi|32268970|gb|CD718129.1|CD718129
EST:     AGAATATACTTCTAGTGTCTCCAGAATATGTTAAAGTTCCAGACTACAAG                         GTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAA
genomic: AGAATATACTTCTAGTGTCTCCAGAATATGTTAAAGTTCCAGACTACAAGgtactccaga ... gcattttcagGTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAA
EST: gi|32248754|gb|CD714573.1|CD714573
EST:     AGAATATACTTCTAGTGTCTCCAGAATATGTTAAAGTTCCAGACTACAAG                         GTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAA
genomic: AGAATATACTTCTAGTGTCTCCAGAATATGTTAAAGTTCCAGACTACAAGgtactccaga ... gcattttcagGTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAA
EST: gi|71856051|gb|DT005106.1|DT005106
EST:     AGAATATACTTCTAGTGTCTCCAGAATATGTTAAAGTTCCAGACTACAAG                         GTTTCATCCCGTTCA
genomic: AGAATATACTTCTAGTGTCTCCAGAATATGTTAAAGTTCCAGACTACAAGgtactccaga ... gcattttcagGTTTCATCCCGTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttctgcatctacaatgcccttgttattgtaacatatatttgttgcattttcagGTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAATCAAGTGCTATTAAAGTGATTGATTTTGGAAGCACAACATATGAGCGAC
                           ttgtaac  putative branch site (score: 2)
                                              cattttc  putative PPT
                     ttgttattgtaacata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactccagatgttaacttgatgtgtattaagtggcatatggttttgctttattattctttctgcatctacaatgcccttgttattgtaacatatatttgttgcattttcagGTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAATCAAGTGCTATTAAAGTGATTGATTTTGGAAGCACAACATATGAGCGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG