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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCACGCCAGGGACCAACATCCATGGCTGCATTCCAGGTCTGCTTGCAGGTTTGGTTGGCAACGTCTCTTCTTGCTGATGGCTTAGCGGTCGCCGGGCAGgttagaagtgcagatctttatactctcatcttggacaaatttgttttttgaggctctctttctttgaacttaccagtcttcaaaatttttcag

Basic information

species Vitis vinifera
transcript Vv06s0004g02140.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g02140.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os10g13940.1 (Oryza sativa), 5'ss of exon 8
TGCACGCCAGGGACCAACATCCATGGCTGCATTCCAGGTCTGCTTGCAGGTTTGGTTGGCAACGTCTCTTCTTGCTGATGGCTTAGCGGTCGCCGGGCAGgttagaagtgcagatctttatactc---tcatcttggacaaatttg------ttttttgaggctctctttctttgaacttaccagtcttcaaaatttttcag
|||||| |  ||  ||    | ||||||||||| ||| | ||||||||| | ||| ||||  ||||||||||||||||||| || ||  | || || ||||| ||     ||| | | |  ||||    ||     |||||   ||      | | ||||  ||   |||   ||||     |   ||    || |   |  
TGCACGGCTAGGTTCAGTTCCAATGGCTGCATTTCAGATTTGCTTGCAGATCTGGCTGGCTTCGTCTCTTCTTGCTGATGGATTGGCTTTTGCAGGACAGgtaaggga-acagttgtctccactcactccaatgctgacaatactgaaggtttctattgaaccttcattttaatgaaaaattctacctcagtaactgcacc-

upper sequence: Vv06s0004g02140.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA15G03930.1 (Glycine max), 5'ss of exon 8
TGCACGCCAGGGACCAACATCCATGGCTGCATTCCAGGTCTGCTTGCAGGTTTGGTTGGCAACGTCTCTTCTTGCTGATGGCTTAGCGGTCGCCGGGCAGgttagaagtgcagatctttatactctcatcttggacaaatttgttttttgaggctctctttctttgaactt--accagtcttcaaaatttttcag--------
|||||| |||||||||||||| ||||||||||| || || ||  |||||||||||||||||  |||||||||||| |||||  | || || || ||||||||||||  |  |  |  |   |       ||||  | |  || ||   ||| | | || | |    |   |  |  |     |||   | | ||         
TGCACGGCAGGGACCAACATCTATGGCTGCATTTCAAGTATGTCTGCAGGTTTGGTTGGCAGTGTCTCTTCTTGCGGATGGTCTGGCTGTTGCTGGGCAGgttagatat-tactttgtccaatcaatgccttg--ctatgttattacatgatggtttcataccaaaacagtggataaaataccaatgatatccacttgaataa

upper sequence: Vv06s0004g02140.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA13G41460.1 (Glycine max), 5'ss of exon 8
TGCACGCCAGGGACCAACATCCATGGCTGCATTCCAGGTCTGCTTGCAGGTTTGGTTGGCAACGTCTCTTCTTGCTGATGGCTTAGCGGTCGCCGGGCAGgttagaagtgcagatctttatactctcatcttggacaaatttgttttttgaggctctctttctttg--aacttaccagtcttcaaaatttttcag--------
|||||| |||||||||||||| ||||| ||||| || || ||  |||||||||||||||||  |||||||||||| |||||  | || || || ||||||||||||  |  |  |  |   |       ||||  | |  ||  ||  ||| | | || | |      |||  |  |     |||     | ||         
TGCACGGCAGGGACCAACATCTATGGCCGCATTTCAAGTATGTCTGCAGGTTTGGTTGGCAGTGTCTCTTCTTGCGGATGGTCTGGCTGTTGCTGGGCAGgttagatat-tactttgtccaataaatgccttg--ctatgttacttcatgatggtttcataccaaaacaacggataaaatagcaatgacctccacttgaatag

upper sequence: Vv06s0004g02140.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA12G14270.1 (Glycine max), 5'ss of exon 5
TGCACGCCAGGGACCAACATCCATGGCTGCATTCCAGGTCTGCTTGCAGGTTTGGTTGGCAACGTCTCTTCTTGCTGATGGCTTAGCGGTCGCCGGGCAGgttagaagtgcagatctttatactctcatcttggacaaatttgttttttgaggctctcttt------ctttgaacttaccagtcttcaaaatttttcag----
|||||| |||||||||||||| ||||||||||| || || ||  || ||||| ||||||||  |||||||||||| |||||  | || || || ||||||||||||  |  |  |  |   |       ||||  | |  ||  |   ||| | | || |       |  || |   |  ||   | | |     |       
TGCACGGCAGGGACCAACATCTATGGCTGCATTTCAAGTATGTCTGTAGGTTCGGTTGGCAGTGTCTCTTCTTGCGGATGGTCTGGCTGTTGCTGGGCAGgttagatat-tactttgtccaatcaatgccttg--ctatgttactacatgatggtttcatagcaaaacagtggataaaatagcaatgatatccacttgaataa

upper sequence: Vv06s0004g02140.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA19G43330.1 (Glycine max), 5'ss of exon 6
------------------------------------------------TGCACGCCAGGGACCAACATCCATGGCTGCATTCCAGGTCTGCTTGCAGGTTTGGTTGGCAACGTCTCTTCTTGCTGATGGCTTAGCGGTCGCCGGGCAGgttagaagtgcagatctttatactctcatcttggacaaatttgttttttgaggctctctttctttgaacttaccagtcttcaaaatttttcag
                                                | |||| |||||||||||||| | ||||||||| || || ||  || ||||||||||||||  |||||||||||| |||||  | || || ||  |||||||||||  |  |  |  |   |      |||||                                                            
GTTTTCTATTATTAATAAGAGTCATCGTTGTGTGACAGCATCACTAGCTACACGGCAGGGACCAACATCTAGGGCTGCATTTCAAgtatgtctgtaggtttggttggcagtgtctcttcttgcggatggtctggctgttgctaggcaggttagatat-tactttgtccaatcaatgtcttgctatg-------------------------------------------------------

upper sequence: Vv06s0004g02140.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT1G51340.1 (Arabidopsis thaliana), 5'ss of exon 8
TGCACGCCAGGGACCAACATCCATGGCTGCATTCCAGGTCTGCTTGCAGGTTTGGTTGGCAACGTCTCTTCTTGCTGATGGCTTAGCGGTCGCCGGGCAGgttagaagtgcagatctttata-ctctcatcttggacaaatttgttttttgaggctctctttctttgaacttaccagtcttcaaaatttttcag
||||||  | ||| |||| |||||||| || ||||| || ||||||||||||||||| || || || |||||||| || || |  || || || || ||||||     |  ||||  | ||  |||| |  ||| |    |||    ||  | || |    | |      ||| ||    ||    |  || ||
TGCACGAGAAGGATCAACTTCCATGGCAGCTTTCCAAGTTTGCTTGCAGGTTTGGTTAGCTACTTCACTTCTTGCAGACGGGTACGCCGTAGCTGGCCAGgtt-----tttagataatgatgtctctaacattgcatccttttacgatt--aagcgcgtggtttaaagttttaacaaatgtcttt-tcctttag

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|110699707|gb|EE076951.1|EE076951
EST:     TTTGGTTGGCAACGTCTCTTCTTGCTGATGGCTTAGCGGTCGCCGGGCAG                         GCCATACTTGCTAGCGCATTTGCTAAACAGGACTACAGCAAGGCCACAGCT
genomic: TTTGGTTGGCAACGTCTCTTCTTGCTGATGGCTTAGCGGTCGCCGGGCAGgttagaagtg ... aatttttcagGCCATACTTGCTAGCGCATTTGCTAAACAGGACTACAGCAAGGCCACAGCT
EST: gi|294967324|gb|GW836678.1|GW836678
EST:     TTTGGTTGGCAACGTCTCTTCTTGCTGATGGCTTAGCGGTCGCCGGGCAG                         GCCATACTTGCTAGCGCATTTGCTAAACAGGACTACAGCAAGGCCACAGCT
genomic: TTTGGTTGGCAACGTCTCTTCTTGCTGATGGCTTAGCGGTCGCCGGGCAGgttagaagtg ... aatttttcagGCCATACTTGCTAGCGCATTTGCTAAACAGGACTACAGCAAGGCCACAGCT
EST: gi|30252403|gb|CB969954.1|CB969954
EST:     TTTGGTTGGCAACGTCTCTTCTTGCTGATGGCTTAGCGGTTGCCGGGCAG                         GCCATACTTGCTAGCGCATTTGCTAAACAGGACTACAGCAAGGCCACAGCT
genomic: TTTGGTTGGCAACGTCTCTTCTTGCTGATGGCTTAGCGGTCGCCGGGCAGgttagaagtg ... aatttttcagGCCATACTTGCTAGCGCATTTGCTAAACAGGACTACAGCAAGGCCACAGCT
EST: gi|110698510|gb|EE076088.1|EE076088
EST:     TTTGGTTGGCAACGTCTCTTCTTGCTGATGGCTTAGCGGTCGCCGGGCAG                         GCCATACTTGCTAGCGCATTTGCTAAACAGGACTACAGCAAGGCCACAGCT
genomic: TTTGGTTGGCAACGTCTCTTCTTGCTGATGGCTTAGCGGTCGCCGGGCAGgttagaagtg ... aatttttcagGCCATACTTGCTAGCGCATTTGCTAAACAGGACTACAGCAAGGCCACAGCT
EST: gi|33405457|gb|CF211084.1|CF211084
EST:     TTTGGTTGGCAACGTCTCTTCTTGCTGATGGCTTAGCGGTTGCCGGGCAG                         GCCATACTTGCTAGCGCATTTGCTAAACAGGACTACAGCAAGGCCACAGCT
genomic: TTTGGTTGGCAACGTCTCTTCTTGCTGATGGCTTAGCGGTCGCCGGGCAGgttagaagtg ... aatttttcagGCCATACTTGCTAGCGCATTTGCTAAACAGGACTACAGCAAGGCCACAGCT
EST: gi|294965646|gb|GW837245.1|GW837245
EST:     TTTGGTTGGCAACGTCTCTTCTTGCTGATGGCTTAGCGGTCGCCGGGCAG                         GCCATACTTGCTAGCGCATTTGCTAAACAGGACTACAGCAAGGCCACAGCT
genomic: TTTGGTTGGCAACGTCTCTTCTTGCTGATGGCTTAGCGGTCGCCGGGCAGgttagaagtg ... aatttttcagGCCATACTTGCTAGCGCATTTGCTAAACAGGACTACAGCAAGGCCACAGCT
EST: gi|30301245|gb|CB978039.1|CB978039
EST:     TTTGGTTGGCAACGTCTCTTCTTGCTGATGGCTTAGCGGTCGCCGGGCAG                         GCCATACTTGCTAGCGCATTTGCTAAACAGGACTACAGCAAGGCCACAGCT
genomic: TTTGGTTGGCAACGTCTCTTCTTGCTGATGGCTTAGCGGTCGCCGGGCAGgttagaagtg ... aatttttcagGCCATACTTGCTAGCGCATTTGCTAAACAGGACTACAGCAAGGCCACAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCACGCCAGGGACCAACATCCATGGCTGCATTCCAGGTCTGCTTGCAGGTTTGGTTGGCAACGTCTCTTCTTGCTGATGGCTTAGCGGTCGCCGGGCAGgttagaagtgcagatctttatactctcatcttggacaaatttgttttttgaggctctctttctttgaacttaccagtcttcaaaatttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT