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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttcaacatctgtcataacatggcttgtttggtagtatttttttcattttttttgtctctgatcttgctctttttctcccaccgtagAACCTTCTTCGTCGTGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTATATAAAGGATGCTATTGAAGCAGTCTTGTTGATGA

Basic information

species Vitis vinifera
transcript Vv03s0017g00680.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 5
gttagtt--tcaacatctgtcataacatggcttgtttggtagtatttttttcattttttttgtctctgatcttgctctttttctcccaccgtagAACCTTCTTCGTCGTGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTATATAAAGGATGCTATTGAAGCAGTCTTGTTGATGA
||  ||    ||    || ||  |  ||    |   |     | |  || |  |  ||||| ||        |          |      | |||| || || ||||| ||||| || || ||||| ||||||||||| ||||||||||| |||||||| || |||||||| |||||||| ||    |||||||
gtatgtcaaccagtccctttctgagaataatatacct--ccatttcgttatggtcgtttttctcataagatgtatgtcgccaatgaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAGAGAACTTTTGTTTACATTAAGGATGCCATTGAAGCTGTTCACTTGATGA

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 5
gttagtttcaacatctgtcat--aacatggcttgtttggtagtatttttttcat-tttttttgtctctgatcttgctctttttc--tcccaccgtagAACCTTCTTCGTCGTGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTATATAAAGGATGCTATTGAAGCAGTCTTGTTGATGA
|| ||| |     | | |     |  ||   |   ||  |  | | |    ||| ||   |  |||| ||   ||| |  |  |  |      | |||| || || ||  | |||||  | |||||||| ||||| || || || |||||||||||||| || || ||||||||||| ||||| ||  || ||||||
gtaagtgttcttgtttcttggtgaggatcattatcttaattatttatgcaccatgttcagtcttctcagaagatgcacggtaccaatggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGA

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G167872_T02 (Zea mays), 3'ss of exon 3
gttagtttcaacatctgtcataacatggcttgtttg-gtagtatttttttcatttt---ttttgtctctgatcttgctctttttctcccaccgtagAACCTTCTTCGTCGTGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTATATAAAGGATGCTATTGAAGCAGTCTTGTTGATGA
    || |   ||  |||  |   ||   || | || |||   ||   || |||||      |  |  |  |||       |   |      | |||| || || || || |||||  | |||||||| ||||| ||||| || |||||||||||||| || || |||||||| || ||||| ||  || ||||||
----gtatgtgcacttgtttttttatttattttctgagtatggttggcttaattttgcaccatagcattcttctgagaagatgcatggttttgcagAATCTGCTCCGCCGAGAGCCTTTGAAGCTTGTCGATGGGGGCCAGTCTCAGAGAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGA

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA12G30490.2 (Glycine max), 3'ss of exon 5
gttagtttcaacatctgtcataacatggctt--gtttggtagtatttttttc-attttttttgtctctgatcttgctctttttctcc-------caccgtagAACCTTCTTCGTCGTGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTATATAAAGGATGCTATTGAAGCAGTCTTGTTGATGA
|| |||||  |  |   |    || | | ||  | |||    ||| ||  || || ||||| |    ||||  |     ||||||||         | |||||| || || ||| | ||||| |||||||||||||||||||||||||||||||| || ||||| ||||| ||||||||||||||||| ||||| |||||||
gtgagtttacattttgatttagactttgtttaagcttgtatatatgttactcgatatttttggataatgattctaaatattttctccattccttttctgtagAATCTCCTCCGTGGAGAGCCCCTCAAGCTTGTGGATGGTGGCCAATCCCAGAGGACTTTTGTGTATATTAAGGATGCTATTGAAGCTGTCTTATTGATGA

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA12G08930.1 (Glycine max), 3'ss of exon 5
gttagtttca-acatctgtcataacatggcttgtttggtagtatttttttcattttt-----tttgtctctgatcttgctctttttctcccaccgtagAACCTTCTTCGTCGTGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTATATAAAGGATGCTATTGAAGCAGTCTTGTTGATGA
|| |||| |  || | ||  ||      | || || | |  | ||      | ||||     |||||     || || || |||| ||    | | |||| |||||  |  | ||||| |||||||||||||| |||||||| |||||||||||||||||||| || || |||||||||||||| |||||| ||||||
gtcagttacttacttttgctatgttgaagttt-ttagatgattttagccagagttttgaaaatttgttcaaaatttt-ctgttttcctttgtctgcagAATCTTCTCAGAGGAGAGCCCCTCAAGCTTGTGGACGGTGGCCAGTCCCAGAGAACCTTTGTTTACATTAAAGATGCTATTGAAGCTGTCTTGCTGATGA

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G05440.1 (Glycine max), 3'ss of exon 3
gttagtttcaacatctgtcataacatggctt--gtttggtagtatttttttc-----attttttt------tgtctctgatcttgctctttttctcccacc-gtagAACCTTCTTCGTCGTGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTATATAAAGGATGCTATTGAAGCAGTCTTGTTGATGA
|| |||||  |  |   |    || | | ||  | |||    |||| || |      || |||||      ||  ||| |   |  ||||  | ||    | |||||| || || ||  | ||||| |||||||||||||||||||| ||||||||||| || ||||| ||||| ||||||||||||||||| ||||| |||||||
gtgagtttacattttgatttagactttgtttaagcttgtatatattgttgttagtcaatatttttaaataatgattctaaatattttcttcatttcttttctgtagAATCTCCTCCGCGGAGAGCCCCTCAAGCTTGTGGATGGTGGTCAATCCCAGAGGACTTTTGTGTATATTAAGGATGCTATTGAAGCCGTCTTATTGATGA

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 5
gttagtttca-acatctgtcataacatggctt----gtttggtagtatttttttcattttttt-----tgtctctgatcttgctctttttctcccaccgtagAACCTTCTTCGTCGTGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTATATAAAGGATGCTATTGAAGCAGTCTTGTTGATGA
|| |||| |  || | ||  ||  | |    |    ||||| |  ||||||   |    ||||     | | |   |  || || |||| ||    | | |||| ||||| ||  | ||||| |||||||||||||| |||||||| ||||||||||||||  |||| || || |||||||||||||| |||||||||||||
gtcagttacttacttttgctattgctttttgttgaagtttgttgatattttagccggagttttgaaaatttgttcaaattttctgttttcctttgtctgcagAATCTTCTCCGAGGAGAGCCCCTCAAGCTTGTGGACGGTGGCCAGTCCCAGAGAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGA

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 5
gttagt-ttcaacatctgtcataacatggcttgtttggtagtat-ttttttcattttttttgtctctgatcttgctctttttctcccaccgtagAACCTTCTTCGTCGTGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTATATAAAGGATGCTATTGAAGCAGTCTTGTTGATGA
|| ||| |||||   |    |||  |     || | |   || | | | | ||   |||| ||   | ||    |||| | | ||   |   |||| ||||| ||||||||||| ||||||||||| ||||||||  |||| |||||||| || || || || || |||||||||||||| ||| | |||||||
gtaagtgttcaaatccaagtatataacccaatgctagtctgtgtatatatgcaagcttttagt---taatgcatctctatctatctttc---agAATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGA

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 5
gttagttt-caacatctgtc--ataacatggcttgtttggtagtatttttttcattttttttgtctctgatcttgctctttttctcccaccgtagAACCTTCTTCGTCGTGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTATATAAAGGATGCTATTGAAGCAGTCTTGTTGATGA
|| ||| | ||   |  |||  || || ||  || ||     |  |     | |  |||||||| |    | ||| |   | | | |      |||| ||||| || || ||||| ||||||||||||||||||||  |||| |||||||||||  | || || || |||||||| ||||| ||| | |||||||
gtaagtatacaggcttagtccaatgacctgagttcttctcatggctgcagcttaacttttttgtttaactttttggtgggtattttc------agAATCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTGGAGAATCACAGAGAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGA

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|110359156|gb|EC920189.1|EC920189
EST:     TGATGGTCC-AGGTGAAGGTGTTCCAAGGGTTCTGGCATGCTTCAGCAAT                         ACCCTTCTTCGTCGTGAGCCACT
genomic: TGATGGTCCTAG-TGAAGGTGTTCCAAGGGTTCTGGCATGCTTCAGCAATgttagtttca ... cccaccgtagAACCTTCTTCGTCGTGAGCCACT
EST: gi|110696696|gb|EE073040.1|EE073040
EST:     TTGATGGTCCTAGTGAAGGTGTTCCAAGGGTTCTGGCATGCTTCAGCAAT                         AACCTTCTTCGTCGTGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAG
genomic: TTGATGGTCCTAGTGAAGGTGTTCCAAGGGTTCTGGCATGCTTCAGCAATgttagtttca ... cccaccgtagAACCTTCTTCGTCGTGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAG
EST: gi|30320980|gb|CD004242.1|CD004242
EST:     TTGATGGTCCTAGTGAAGGTGTTCCCAGGGTTCTGGCATGCTTCCGCAAT                         AACCCTTCTTCGTC
genomic: TTGATGGTCCTAGTGAAGGTGTTCCAAGGGTTCTGGCATGCTTCAGCAATgttagtttca ... cccaccgtagAACC-TTCTTCGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtatttttttcattttttttgtctctgatcttgctctttttctcccaccgtagAACCTTCTTCGTCGTGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTATATAAAGGATGCTATTGAAGCAGTCTTGTTGATGA
                        ctctgat  putative branch site (score: 4)
       tttttcattttttttg  CT-rich tract
     tttttttcattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtttcaacatctgtcataacatggcttgtttggtagtatttttttcattttttttgtctctgatcttgctctttttctcccaccgtagAACCTTCTTCGTCGTGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTATATAAAGGATGCTATTGAAGCAGTCTTGTTGATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC