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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attggttccaattgtaaaagttgtgactgtccatgagaattgttactatttgccatttatccatatgacaacattaattatctgcttgtaatgcatccagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCAAAAGAGAAATCCCCATGTATCATTTTCATTGATGAAATTGATGCCATTG

Basic information

species Vitis vinifera
transcript Vv05s0020g01180.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g01180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 5
---attggttccaattgtaaaagttgtgactgtccatgagaattgttactatttgccatttatccatatgacaacattaattatctgcttgtaatgcatccagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCAAAAGAGAAATCCCCATGTATCATTTTCATTGATGAAATTGATGCCATTG
        || |  | ||  |   |  | || |         || ||  |  || |   ||     ||     | ||||||  |||    | | ||  ||||||||||||| || ||||||||||| ||||| || ||||| || ||||||||||| ||||||||||| || |||||||| |||||||||||||| || ||||
gaagaatattgctttggtccagtgttggtctattttcttcctttattggttctt-ctgcttgctgctagatacatattaat-gtctatgcgaattg-gtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTG

upper sequence: Vv05s0020g01180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os04g21660.1 (Oryza sativa), 3'ss of exon 5
---attggttccaattgtaaaagttgtgactgtccatgagaattgttactatttgccatttatccatatgacaacattaattatctgcttgta-atgcatccagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCAAAAGAGAAATCCCCATGTATCATTTTCATTGATGAAATTGATGCCATTG
    |||    |   || |||  || | | || | |   || |||    | |||    | | | |   ||| |  | || |  | |  ||||  |  | | |||| | | || || || || |||| ||||||||| ||||| || |||||||| ||||||||| ||||||| || ||||||||||||||||||||||| ||||
atctttgagctcctctgaaaagtttcttagtg-ctacatgatttgcctttttttt---tatgtacgattgagattaatactggtttctttgtggactcgtgcagAAGCTTATTGGTGAGGGAGCAAGACTTGTTCGTGATGCCTTTCAGCTTGCTAAAGAGAAAGCCCCATGCATTATTTTCATTGATGAAATTGATGCAATTG

upper sequence: Vv05s0020g01180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 5
attggttccaattgtaaaagttgtgactgtccatgagaattgttactatttgc-catttatccatatgacaacattaattatctgcttgtaa-tgcatccagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCAAAAGAGAAATCCCCATGTATCATTTTCATTGATGAAATTGATGCCATTG
     |   ||  |       |      ||| ||     |  |   || ||||  ||   |   ||   ||||| |||| || |  || |        ||||||||| || || ||||| ||||| || ||||| ||||| || |||||||| || |||||| | || || ||||||||||||||||| |||||||||||||
--acatatgaacagccttgccttcagaagtctatttatttactatttacttgcatatggttttctagcgcaacaataatcatatttttttgggcttgcccagATGTTTATCGGTGATGGAGCAAAGCTGGTTCGGGATGCTTTTCAGCTTGCTAAGGAGAAAGCTCCCTGCATCATTTTCATTGATGAGATTGATGCCATTG

upper sequence: Vv05s0020g01180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 5
attggttccaattgtaaaagttgtgactgtccatgagaattgttactatttgccatttatccatatgacaacattaattatctgcttgt-aatgcatccagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCAAAAGAGAAATCCCCATGTATCATTTTCATTGATGAAATTGATGCCATTG
 ||   |  |||  |   || |   | | ||  |   | |  | | ||| |    ||  |  |  | | |  |  | | |  |  |||| |||   | ||||||||||| || ||||| || || |||||| ||||||| || |||||||| || |||||| |||| || ||||| || ||||||||||||||||||||||
ttttcctgaaatactgcgaggt-caattttcagttctattattgattatcttttcttagtttaatttagacgaacattaacatctttgtgaattgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCTAAGGAGAAAGCCCCGTGCATCATCTTTATTGATGAAATTGATGCCATTG

upper sequence: Vv05s0020g01180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 5
----attggttccaattgtaaaagttgtgactgtccatgagaattgttactatttgccatttatccatatgacaacattaattatctgcttgtaatgcatccagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCAAAAGAGAAATCCCCATGTATCATTTTCATTGATGAAATTGATGCCATTG
    ||||  |     || ||||  |||     ||       ||  | |  |      || | | ||  | |  | | |||  || | ||||       | |||||||| || || ||||| ||||| ||||| || ||||||||||||||||| ||||||||| | || ||||| || || |||||||| || ||||||||||
agacattgcattaccatggaaaatatgttttattctgatgttatcttgagcacactttatattttcaagt-atgatagtaacgatgttcttgctg---gttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATTG

upper sequence: Vv05s0020g01180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G173849_T01 (Zea mays), 3'ss of exon 1
attggttccaattgtaaaagttgtgactgtccatgagaattgttactatttgccattta-tccatatgacaacat----taattatctgcttgtaatgcatccagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCAAAAGAGAAATCCCCATGTATCATTTTCATTGATGAAATTGATGCCATTG
       | || || | |  |||  | |  |   || |||   |  ||||       || |  ||||    |  |    || | |     || |      | |||||||| || || ||||| ||||| ||||| || ||||||||||||||||| ||||||||| | || ||||| || || |||||||| || |||||||| |
----cgacaaaatggagatattgc-attaccatggaaaatctgttttattctgagcatactttatattttgaagtagggtagtaacgatgttcttgctggttcagATGTTTATTGGTGATGGAGCAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATCG

upper sequence: Vv05s0020g01180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------------------------------------------------------attggttccaattgtaaaagttgtgactgtccatgagaattgttactatttgccatttatccatatgacaaca-ttaattatctgc------ttgtaatgcatc----cagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCAAAAGAGAAATCCCCATGTATCATTTTCATTGATGAAATTGATGCCATTG
                                                                    ||    ||  |   |     |     | |||||| |    || | | ||   |||||||||   | |   |  || |||  || |      |  | || | |     |||||||| || || |||||||||||||||||  | || || |||||||| ||||| || ||| | || |||||||| |||||||||||| | ||||| ||||
gtgatttcttggttttacttgtttatctatggactctcgtcagttctggtttaggatgttgttttgccttaacgcctttgtcatttacttaatttttccatgggtggagtca-tcttgttcatttatcctggtcaaggctcttcattgactacaagatatcctgatacgtaatcacagATGTTTATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTCCAGCTAGCAAAGGAAAAAGCTCCCTGTATCATCTTCATTGATGAAGTAGATGCAATTG

upper sequence: Vv05s0020g01180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ37626 (Selaginella moellendorffii), 3'ss of exon 5
attggttccaattgtaaaagttgtgactgtccatgagaattgttactatttgccatttatccatatgacaacattaattatctgcttgtaatgcatc-cagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCAAAAGAGAAATCCCCATGTATCATTTTCATTGATGAAATTGATGCCATTG
                                       || |   ||    |  |||| |  |  |      ||||      |||| |  | | || ||||||||||| || ||||| ||||| || ||  ||||||| || ||||| |||||||||||  | || || ||||||||||| |||||| | || || ||||
--------------------------------------gttctgtgtaggaactctttacctgtcgggt--tcttaaactcaagcttctggttcgtcgcagATGTTCATCGGAGATGGAGCAAAGCTCGTAAGAGATGCCTTTCAGCTGGCAAAAGAGAAGGCGCCCTGCATCATTTTCATCGATGAAGTCGACGCTATTG

upper sequence: Vv05s0020g01180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ15061 (Selaginella moellendorffii), 3'ss of exon 5
attggttccaattgtaaaagttgtgactgtccatgagaattgttactatttgccatttatccatatgacaacattaattatctgcttgtaatgcatc-cagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCAAAAGAGAAATCCCCATGTATCATTTTCATTGATGAAATTGATGCCATTG
                                       || |   ||    |  |||| |  |  |      ||||      |||| |  | | |  ||||||||||| || ||||| ||||| || ||  ||||||| || ||||| |||||||||||  | || || ||||||||||| |||||| | || || ||||
--------------------------------------gttctgtgtaggaactctttacctgtcgggt--tgttaaactcaagcttcttgttcgttgcagATGTTCATCGGAGATGGAGCAAAGCTCGTAAGAGATGCCTTTCAGCTGGCAAAAGAGAAGGCGCCCTGCATCATTTTCATCGATGAAGTCGACGCTATTG

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|349808282|gb|FQ403469.1|FQ403469
EST:     CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAG                         ATGTTCATAGGGGATGGTGCAAAACTTGT
genomic: CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAGgtcagtgtcc ... atgcatccagATGTTCATAGGGGATGGTGCAAAACTTGT
EST: gi|349828325|gb|FQ416278.1|FQ416278
EST:     CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAG                         ATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCA
genomic: CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAGgtcagtgtcc ... atgcatccagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCA
EST: gi|110717892|gb|EE094156.1|EE094156
EST:     CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAG                         ATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCA
genomic: CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAGgtcagtgtcc ... atgcatccagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCA
EST: gi|110360884|gb|EC924326.1|EC924326
EST:     CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAG                         ATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCA
genomic: CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAGgtcagtgtcc ... atgcatccagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCA
EST: gi|351026518|gb|FQ428530.1|FQ428530
EST:     CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAG                         ATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCA
genomic: CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAGgtcagtgtcc ... atgcatccagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCA
EST: gi|351019753|gb|FQ439570.1|FQ439570
EST:     CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAG                         ATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCA
genomic: CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAGgtcagtgtcc ... atgcatccagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCA
EST: gi|349814278|gb|FQ398704.1|FQ398704
EST:     CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAG                         ATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCA
genomic: CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAGgtcagtgtcc ... atgcatccagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCA
EST: gi|351012252|gb|FQ426974.1|FQ426974
EST:     CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAG                         ATGTTCATCCGGGGATGG
genomic: CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAGgtcagtgtcc ... atgcatccagATGTTCATA-GGGGATGG
EST: gi|351019480|gb|FQ429615.1|FQ429615
EST:     CACAGACAAACGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAG                         ATGTTCATAGGGAATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCA
genomic: CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAGgtcagtgtcc ... atgcatccagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCA
EST: gi|349807880|gb|FQ402271.1|FQ402271
EST:     CACGGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACCTGTCCAG                         ATGTTCATAGGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGC
genomic: CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAGgtcagtgtcc ... atgcatccagATGTTCATAGGGG-ATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGC
EST: gi|351033839|gb|FQ447877.1|FQ447877
EST:     CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAG                         ATGTTCATAGGGGA
genomic: CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAGgtcagtgtcc ... atgcatccagATGTTCATAGGGGA
EST: gi|349811159|gb|FQ406103.1|FQ406103
EST:     CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAG                         ATGTTCATAGGGG
genomic: CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAGgtcagtgtcc ... atgcatccagATGTTCATAGGGG
EST: gi|349820629|gb|FQ408458.1|FQ408458
EST:     CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAG                         ATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCA
genomic: CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAGgtcagtgtcc ... atgcatccagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCA
EST: gi|351023695|gb|FQ448246.1|FQ448246
EST:     CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAG                         ATATTCATAGGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGC
genomic: CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAGgtcagtgtcc ... atgcatccagATGTTCATAGGGG-ATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGC
EST: gi|351012427|gb|FQ427028.1|FQ427028
EST:     CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAG                         ATGTTCATAGGGGATGGTGCAAAACTTGTTCAAGATGCATTCCAGCTTGCA
genomic: CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAGgtcagtgtcc ... atgcatccagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCA
EST: gi|110699646|gb|EE076827.1|EE076827
EST:     CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAG                         ATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCA
genomic: CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAGgtcagtgtcc ... atgcatccagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCA
EST: gi|351037562|gb|FQ462545.1|FQ462545
EST:     CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAG                         ATATTCATAAGGGATG
genomic: CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAGgtcagtgtcc ... atgcatccagATGTTCATAGGGGATG
EST: gi|349816463|gb|FQ403838.1|FQ403838
EST:     CACGGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACCTGTCCAG                         ATGTTCATAGGGGATGGTGCAAAACTTGT
genomic: CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAGgtcagtgtcc ... atgcatccagATGTTCATAGGGGATGGTGCAAAACTTGT
EST: gi|351027526|gb|FQ446689.1|FQ446689
EST:     CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAG                         ATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCA
genomic: CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAGgtcagtgtcc ... atgcatccagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCA
EST: gi|349816484|gb|FQ403859.1|FQ403859
EST:     CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTTCACAACTTGTCCAG                         ATGTTCATAGGGGATGGTGCAAAA
genomic: CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAGgtcagtgtcc ... atgcatccagATGTTCATAGGGGATGGTGCAAAA
EST: gi|352798843|gb|FQ478478.1|FQ478478
EST:     CACAGACAAATGCCACTTTTCTGAAACTAGCTGGTCCACAACTTGTCCAG                         AAATTCATAAGGGATGGTGCAAAACTTGTTCGAG
genomic: CACAGACAAATGCCACTTTTCTGAAGCTAGCTGGTCCACAACTTGTCCAGgtcagtgtcc ... atgcatccagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatttgccatttatccatatgacaacattaattatctgcttgtaatgcatccagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCAAAAGAGAAATCCCCATGTATCATTTTCATTGATGAAATTGATGCCATTG
                          cattaat  putative branch site (score: 3)
                      acaacattaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attggttccaattgtaaaagttgtgactgtccatgagaattgttactatttgccatttatccatatgacaacattaattatctgcttgtaatgcatccagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCAAAAGAGAAATCCCCATGTATCATTTTCATTGATGAAATTGATGCCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- tggttcc
- - - - - - -gtaaaag
- - - - - - - - - - - - - ctgtcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gacaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttgt