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'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattcttccatagttccattttcatgtgaagcagttgtttttctcccctttccagttgggtttcatttaataatgtttaatgcatgtgctgtttccgcagGAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTGCTGCTAATGTTTCAGTTGCAGAAAAAATCCTAAAGCATTTTCCGCTTTG

Basic information

species Vitis vinifera
transcript Vv07s0031g02190.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g02190.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: LOC_Os03g03710.1 (Oryza sativa), 3'ss of exon 16
tattcttccatagttccattttcatgtgaagcagttgtttttctcccctttcca-gttgggtttcatttaataatgtttaatgcatgtgctgtttccgcagGAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTGCTGCTAATGTTTCAGTTGCAGAAAAAATCCTAAAGCATTTTCCGCTTTG
                       ||||||    || |   |  |     |   |  |     || || |||  |  ||  |   ||       |||  ||||||| || ||||||||||| ||||| |||||| |||| ||||||||| | ||||| ||| | || || || || || ||  | ||||| || ||  | ||
---------------------gtatgtgat-tggtagacctcataggtgtcatatatccaaatttatgtaaataaatt--acttattcaaaagttcatcagGAATATATCAAATTCGTGAGGCAAATCAAATGATTGAAGAGTTTATGTTGGCTGCAAATATCTCTGTCGCTGAGAAGATTTTGAAGCACTTCCCCTTGTG

upper sequence: Vv07s0031g02190.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA06G14870.2 (Glycine max), 3'ss of exon 16
--------tattcttccatagttccattttcatgtgaagcagttgtttttctcccctttccagttgggtttcatttaataatgtttaatgcatgtgctgtttccgcagGAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTGCTGCTAATGTTTCAGTTGCAGAAAAAATCCTAAAGCATTTTCCGCTTTG
        ||| | | ||| |    |     |    || ||||| |||| |  |||||||  |||   ||| |   ||| || | || |   ||   | | |  |||||||||||||| || || || || || |||||||| ||||||||||||||||||||||||||||| |||||| || |||| || ||   ||||||  |   
cttttagctatcccttcatggaaggagagggagaaaaaacagtt-ttttcccgccctttctggtt---tttaa---aattatttctagtatttg-attttatttgcagGAATGTACCAGATCCGGGAGGCCAATCAAATGGTGGAGGAGTTTATGCTTGCTGCTAATGTTTCCGTTGCACAACAAATTCTTAATAGTTTTCCATTGGT

upper sequence: Vv07s0031g02190.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA04G39980.1 (Glycine max), 3'ss of exon 16
--------tattcttccatagttccattttcatgtgaagcagttgtttttctcccctttccagttgggtttcatttaataatgtttaatgcatgtgctgtt-tccgcagGAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTGCTGCTAATGTTTCAGTTGCAGAAAAAATCCTAAAGCATTTTCCGCTTTG
        ||||| | | | |    |     |    || ||||| ||   |  |||||||   ||         |||| | | ||||     | || |||| |  |||||||||||||| || || || || ||||||||||| ||||||||||||||||| ||||||||||| |||||| || |||| || ||   ||||||  | ||
cttttagctattccttcgtggaaggagagggagaaaaaacagtttttccccctccctttctgatt---------ttaaaattatttatactgtttgatgttatttgcagGAATGTACCAGATCCGGGAGGCCAACCAAATGGTGGAGGAGTTTATGCTTGCAGCTAATGTTTCCGTTGCACAACAAATTCTTAAAAGTTTTCCATTGTG

upper sequence: Vv07s0031g02190.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: AT2G17510.1 (Arabidopsis thaliana), 3'ss of exon 16
-------------------------------------------------------tattcttccatagttccattttcatgtgaagcagttgtttttctcccctttccagttgggtttcatttaataatgtttaatgcatgtg-----------ctgtttc-cgcagGAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTGCTGCTAATGTTTCAGTTGCAGAAAAAATCCTAAAGCATTTTCCGCTTTG
                                                       || ||||    |     |    ||||  |  ||      | | |||   |   || ||  ||  ||||| | || | |  | ||| ||           ||||||  |||||| ||||| || ||||  ||||||||||||||||||||||| || ||||||||||| |||||||| || || | | | ||||| || |  || ||   |||
gtatgttatctgagcaaaatttgtttcttcttgatgaatacgaacgatgttttcttagtctttttcacccaaacacccatgaaatacaaccacctctatccttctgaaagatgtattcaatttattcatctgtttttcatttgtcatcatgactctgttttgcgcagGTATGTATCAGATTCTCGAAGCAAACCAAATGGTTGAGGAATTCATGCTTGCTGCAAATGTTTCCGTCGCTGGACAGATCCTGAAACTATTCCCTTCTTG

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|349815930|gb|FQ403547.1|FQ403547
EST:     AGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTG                         GAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTG
genomic: AGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTGgtatggtatt ... gtttccgcagGAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTG
EST: gi|351013790|gb|FQ433942.1|FQ433942
EST:     AGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTG                         GAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTG
genomic: AGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTGgtatggtatt ... gtttccgcagGAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTG
EST: gi|351054754|gb|FQ462784.1|FQ462784
EST:     AGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTG                         GAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTG
genomic: AGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTGgtatggtatt ... gtttccgcagGAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTG
EST: gi|351048032|gb|FQ441204.1|FQ441204
EST:     AGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTG                         GAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTG
genomic: AGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTGgtatggtatt ... gtttccgcagGAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTG
EST: gi|351055546|gb|FQ442342.1|FQ442342
EST:     AGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTG                         GAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTG
genomic: AGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTGgtatggtatt ... gtttccgcagGAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTG
EST: gi|351025060|gb|FQ433477.1|FQ433477
EST:     AGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTG                         GAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTG
genomic: AGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTGgtatggtatt ... gtttccgcagGAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTG
EST: gi|351036566|gb|FQ457279.1|FQ457279
EST:     AGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTG                         GAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTG
genomic: AGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTGgtatggtatt ... gtttccgcagGAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTG
EST: gi|351033178|gb|FQ461950.1|FQ461950
EST:     AGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTG                         GAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTG
genomic: AGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTGgtatggtatt ... gtttccgcagGAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTG
EST: gi|351054627|gb|FQ456824.1|FQ456824
EST:     AGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTG                         GAATGTACCAAATTCGTGAAGCAAACCGAATGGTTGAGGAGTTTATGCTTG
genomic: AGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTGgtatggtatt ... gtttccgcagGAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTG
EST: gi|349830463|gb|FQ416761.1|FQ416761
EST:     AGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTG                         GAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTG
genomic: AGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTGgtatggtatt ... gtttccgcagGAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTG
EST: gi|349810328|gb|FQ401774.1|FQ401774
EST:     AGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTG                         GAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTG
genomic: AGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTGgtatggtatt ... gtttccgcagGAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctttccagttgggtttcatttaataatgtttaatgcatgtgctgtttccgcagGAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTGCTGCTAATGTTTCAGTTGCAGAAAAAATCCTAAAGCATTTTCCGCTTTG
                             gtttaat  putative branch site (score: 4)
                                           ctgtttcc  putative PPT
               tttcatttaataatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattcttccatagttccattttcatgtgaagcagttgtttttctcccctttccagttgggtttcatttaataatgtttaatgcatgtgctgtttccgcagGAATGTACCAAATTCGTGAAGCAAACCAAATGGTTGAGGAGTTTATGCTTGCTGCTAATGTTTCAGTTGCAGAAAAAATCCTAAAGCATTTTCCGCTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - cttccat
- - - - - - - -ccatttt
- - - - - - - - - - - catgtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtgc