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

...tatagaacagtttctgttcttgctattagccaaaagtgttagcttccatccatttttctagacttctaaagcattgtctacttattttacttgatggcagGCATTTGTGAATCTCGTTCTTACATTATGTGATGCTGGAGATTTGGTTGTTATGTTTGCACCATACTACTTCAATGCATACATGTCCTTCCAGATGACAG

Basic information

species Vitis vinifera
transcript Vv09s0002g05250.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g05250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g08270.1 (Oryza sativa), 3'ss of exon 5
tatagaacagtttctgttcttgctattagccaaaagtgttagcttccatccatttt-----tctagacttctaaagcattgtctacttattttacttgatggcagGCATTTGTGAATCTCGTTCTTACATTATGTGATGCTGGAGATTTGGTTGTTATGTTTGCACCATACTACTTCAATGCATACATGTCCTTCCAGATGACAG
        | |||    | |  ||  |   |  ||   ||   | ||| | |  ||       || |  || ||   | ||    ||| | | |  |  |||||||| ||||| ||| | || || ||  | ||||||||||| |||   ||||| |||||||||||||| ||||||||| | |||||||| |||||||||||||
-----cttacttttctgtatgactgcttcacctaaaccttgtttaccaactaggttagccaaataaaagtcaaataaagtgatgtcttctatcaaattttggcagGCCTTTGTAAATGTGGTCCTCACCCTTTGTGATGCTGGGGATGCAGTTGTCATGTTTGCACCATATTACTTCAATTCCTACATGTCATTCCAGATGACAG

upper sequence: Vv09s0002g05250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G029135_T01 (Zea mays), 3'ss of exon 4
tatagaacagtttct---gttcttgctattagccaaaagtgttagcttccatccatttttctagacttctaaagcattgtctacttattttacttgatggcagGCATTTGTGAATCTCGTTCTTACATTATGTGATGCTGGAGATTTGGTTGTTATGTTTGCACCATACTACTTCAATGCATACATGTCCTTCCAGATGACAG
| | ||  | ||  |   |  |   || ||        || ||| || |    | ||  ||| | ||| | |     | | | ||||  ||  ||  |  ||||| ||||||||  | || || ||  | |||||||| || ||||  ||||| |||||||||||||| || |||||||| |||||||| |||||||||||||
tgttgattacttctttgggggcacactcttcctttcctgtttta-ctcctgaaccttgatcttgtcttattatctggtcttttcttacattgattttt--cagGCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCCGGTGATTCTGTTGTCATGTTTGCACCATATTATTTCAATGCCTACATGTCATTCCAGATGACAG

upper sequence: Vv09s0002g05250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G107639_T01 (Zea mays), 3'ss of exon 4
------------------------------------------------------------------------------tatagaacagtt-tctgttcttgctattagccaaaagtgttagcttccatccatttttctagacttctaaagcattgtctacttattttacttgatggcagGCATTTGTGAATCTCGTTCTTACATTATGTGATGCTGGAGATTTGGTTGTTATGTTTGCACCATACTACTTCAATGCATACATGTCCTTCCAGATGACAG
                                                                              | |  |  | || | ||      |  |   |        ||  || | |  | ||  ||| | ||| |||     | | | || |  ||  ||  |  ||||| ||||||||  | || || ||  | ||||||||||| ||||  ||||| ||||||||||| || || |||||||| |||||||| |||||||||||||
gtaagttctgcctgcatttactacctattttgccttgtagtgttttccaaatgggccttatgtttcccaatttacttctgttaattacttctttgggggcacactcttctttcctgtttcactgctagaccttgatcttgtcttataatctggtcttttctaacattgatttttt-cagGCTTTTGTGAACTTGGTCCTCACTCTCTGTGATGCTGGTGATTCCGTTGTCATGTTTGCACCGTATTATTTCAATGCCTACATGTCATTCCAGATGACAG

upper sequence: Vv09s0002g05250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G01520.2 (Glycine max), 3'ss of exon 1
-tatagaacagtttctgttcttg--ctattag---ccaaaagtgttagcttccatccatttttctagacttctaaagcattgtctacttattttacttgatggcagGCATTTGTGAATCTCGTTCTTACATTATGTGATGCTGGAGATTTGGTTGTTATGTTTGCACCATACTACTTCAATGCATACATGTCCTTCCAGATGACAG
   | || |  ||||||   |||  || | |     ||| ||| |||  ||     ||| |  ||| || |||   | |   | |  |  |  |||   |   ||||||||||||||||| ||||||||  | |||||| | || ||||  || ||||||||||| || |||||||||||||| |||||||||||||||||||| |
actttgatctctttctgagtttgaactttcaagtttcaacagtatta--ttgtgctcatct--ctaaacatctgtggtaacttgttgtattcctac--aaatacagGCATTTGTGAATCTAGTTCTTACTCTCTGTGATCCGGGTGATTCTGTGGTTATGTTTGCTCCTTACTACTTCAATGCGTACATGTCCTTCCAGATGACTG

upper sequence: Vv09s0002g05250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G43830.1 (Glycine max), 3'ss of exon 4
--tatagaacagtttctg--ttcttgctattag---ccaaaagtgttagcttccatccatttttctagacttctaaagcattgtctacttattttacttgatggcagGCATTTGTGAATCTCGTTCTTACATTATGTGATGCTGGAGATTTGGTTGTTATGTTTGCACCATACTACTTCAATGCATACATGTCCTTCCAGATGACAG
    | || |  ||||||  ||   ||| | |     ||| ||| |||  ||     ||| |  ||| || |||   | |    ||  || |||      |   ||||||||||||||||| ||||||||  | |||||| | || ||||  || ||||||||||| || |||||||||||||| |||||||||||||||||||| |
tactttgatctctttctgagtttgagctttcaagtttcaacagtatta--ttgtgctcatct--ctaaacatctgtggtaa---cttgttttttcctacaaatacagGCATTTGTGAATCTAGTTCTTACTCTCTGTGATCCGGGTGATTCCGTGGTTATGTTTGCTCCTTACTACTTCAATGCCTACATGTCCTTCCAGATGACTG

upper sequence: Vv09s0002g05250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G80360.1 (Arabidopsis thaliana), 3'ss of exon 5
tatagaacagtttctgttcttgctattagccaaaagtgttagcttccatccatttttctagacttctaaagcattgtctacttattttacttgatggcagGCATTTGTGAATCTCGTTCTTACATTATGTGATGCTGGAGATTTGGTTGTTATGTTTGCACCATACTACTTCAATGCATACATGTCCTTCCAGATGACAG
        |    ||||  ||| |          | || |  ||||| ||  ||||  |  |||   | |   |  |    || ||  |  | |||  |||| |||||||| || ||| ||||||||||||||||||| |||| |||||| |||||||  ||||||||||||||  | |||||| |||| ||||||||||
------gtataacctgtctttgtttactcttttgattgct--cttccttctgttttcttctactctcatactctgtttctgtttttgcatctaatg-tagGCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTCATGTTTGAGCCATACTACTTCAACTCCTACATGGCCTTTCAGATGACAG

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|71861182|gb|DT010237.1|DT010237
EST:     AAAATAAGTTATATAAATCTTCAGTGATGGTTACTGCAGGAGCAAATCAG                         GCATTTGTGAATCTCGTTCTTACATTATG
genomic: AAAATAAGTTATATAAATCTTCAGTGATGGTTACTGCAGGAGCAAATCAGgtgattggga ... ttgatggcagGCATTTGTGAATCTCGTTCTTACATTATG
EST: gi|161714897|gb|FC064519.1|FC064519
EST:     AAAATAAGTTATATAATTCTTCAGTGATGGTTACTGCAGGAGCAAATCAG                         GCATTTGTGAATCTCGTTCTTACATTATGTGATGCTGGAGATTTGGTTGTT
genomic: AAAATAAGTTATATAAATCTTCAGTGATGGTTACTGCAGGAGCAAATCAGgtgattggga ... ttgatggcagGCATTTGTGAATCTCGTTCTTACATTATGTGATGCTGGAGATTTGGTTGTT
EST: gi|110724133|gb|EE099692.1|EE099692
EST:     AAAATAAGTTATATAATTCTTCAGTGATGGTTACTGCAGGAGCAAATCAG                         GCATTTGTGAATCTCGTTCTTACATTATGTGATGCTGGAGATTTGGTTGTT
genomic: AAAATAAGTTATATAAATCTTCAGTGATGGTTACTGCAGGAGCAAATCAGgtgattggga ... ttgatggcagGCATTTGTGAATCTCGTTCTTACATTATGTGATGCTGGAGATTTGGTTGTT
EST: gi|349816605|gb|FQ399594.1|FQ399594
EST:     AAAATAAGTTATATAATTCTTCAGTGATGGTTACTGCAGGAGCAAATCAG                         GCATTTGTGAATCTCGTTCTTACATTATGTGATGCTGGAGATTTGGTTGTT
genomic: AAAATAAGTTATATAAATCTTCAGTGATGGTTACTGCAGGAGCAAATCAGgtgattggga ... ttgatggcagGCATTTGTGAATCTCGTTCTTACATTATGTGATGCTGGAGATTTGGTTGTT
EST: gi|26257746|gb|CA808809.1|CA808809
EST:     AAAATAAGTTATATAATTCTTCAGTGATGGTTACTGCAGGAGCAAATCAG                         GCATTTGTGAATCTCGTTCTTACATTATGTGATGCTGGAGATTTGGTTGTT
genomic: AAAATAAGTTATATAAATCTTCAGTGATGGTTACTGCAGGAGCAAATCAGgtgattggga ... ttgatggcagGCATTTGTGAATCTCGTTCTTACATTATGTGATGCTGGAGATTTGGTTGTT
EST: gi|110394684|gb|EC959919.1|EC959919
EST:     AAAATAAGTTATATAATTCTTCAGTGATGGTTACTGCAGGAGCAAATCAG                         GCATTTGTGAATCTCGTTCTTACATTATGTGATGCTGGAGATTTGGTTGTT
genomic: AAAATAAGTTATATAAATCTTCAGTGATGGTTACTGCAGGAGCAAATCAGgtgattggga ... ttgatggcagGCATTTGTGAATCTCGTTCTTACATTATGTGATGCTGGAGATTTGGTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatccatttttctagacttctaaagcattgtctacttattttacttgatggcagGCATTTGTGAATCTCGTTCTTACATTATGTGATGCTGGAGATTTGGTTGTTATGTTTGCACCATACTACTTCAATGCATACATGTCCTTCCAGATGACAG
                                       ttttactt  CT-rich tract
                                 tacttattttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatagaacagtttctgttcttgctattagccaaaagtgttagcttccatccatttttctagacttctaaagcattgtctacttattttacttgatggcagGCATTTGTGAATCTCGTTCTTACATTATGTGATGCTGGAGATTTGGTTGTTATGTTTGCACCATACTACTTCAATGCATACATGTCCTTCCAGATGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- -agaacag
- - - - - - - - ttcttgc
- - - - - - - - - - - - - -agccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattgtc