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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCTCAAACTCATCAACGCCAAGAACACCATGGAAATCGGCGTTTACACCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAGgtaagaaaaaatcatcacccatcaagacaaaatcaaagaaaaaacactctgtttggtttcatagaaaaccaaggaaatgcagagaaaaattttgaccatt...

Basic information

species Vitis vinifera
transcript Vv07s0031g00350.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g00350.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os06g06980.3 (Oryza sativa), 5'ss of exon 2
GCTGCTCAAACTCATCAACGCCAAGAACACCATGGAAATCGGCGTTTACACCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAGgtaagaaaaaatca--tcacccatc------aagacaaaatcaaagaaaaaac---actctgtttggtttcatagaaaaccaaggaaatgcagagaaaaattttgaccatt
|||||| || ||||||  ||||||||| |||||||| |||||||| |||||||||||||||||||||||||||||||||||  | ||||||||||| | ||| || || |  ||  || ||||||      |   || |       | ||| |   | ||  ||    | |||       | |   |||||||                  
GCTGCTGAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCCCTCCTCGCCACCGCCCTCGCCATCCCCGACGACGGCACGgtcagcaacacgcaaatcccccatctcttccatcgcagatctggcaagaaatccccaatcgattgacgtccatccctctgctaactaatgcag------------------

upper sequence: Vv07s0031g00350.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G099363_T03 (Zea mays), 5'ss of exon 2
GCTGCTCAAACTCATCAACGCCAAGAACACCATGGAAATCGGCGTTTACACCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAGgtaagaaaaaatcatcacc----catcaagacaaaatcaaagaaaaaacactctgtttggtttcatagaaaaccaaggaaatgcagagaaaaattttgaccatt---------
|||  |||| ||||||  ||||||||| |||||||| |||||||| |||||||||||||| |||||||||||||| ||||| || || || ||||| | |||  |      |  || |     |       |    ||  |||     ||| |     |       |      |       ||          | |||  | |          
GCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCGCTCCTCGCCACCGCGCTCGCACTCCCGGAGGACGGCACGgtcggtgccctttctctctttctctctctctctctttcccagatctgccacccacccagaccaaggatctttacccctctctgtctctctctctgttgctcgtccccccgcag

upper sequence: Vv07s0031g00350.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G127948_T02 (Zea mays), 5'ss of exon 4
-------------------------------------------GCTGCTCAAACTCATCAACGCCAAGAACACCATGGAAATCGGCGTTTACACCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAGgtaagaaaaaatcatcacccatcaagacaaaatcaaagaaaaaacactctgtttggtttcatagaaaaccaaggaaatgcagagaaaaattttgaccatt
                                           |||  |||| ||||||  ||||||||| |||||||| |||||||| |||||||||||||||||||||||||| || ||||| || || || ||||| | |||  |      |   | ||| |          ||  |||     ||| |    |   |  |    |                                  
ACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTActccctcctcgccacggcgctcgccctcccggaggacggcacggtccgtcgttgttccctcccttt---------tctcagatctgccaccccacctccctgaaggcga----------------------------------

upper sequence: Vv07s0031g00350.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G127948_T04 (Zea mays), 5'ss of exon 5
GCTGCTCAAACTCATCAACGCCAAGAACACCATGGAAATCGGCGTTTACACCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAGgtaagaaaaaatcatcacccat----caag-----------acaaaatcaaagaaaaaacactctgtt-tggtttcataga-aaaccaaggaaatgcagagaaaaattttgaccatt---------------
|||  |||| ||||||  ||||||||| |||||||| |||||||| |||||||||||||||||||||||||| || ||||| || || || ||||| | |||  |      |   | ||| |    ||             ||       |||   || ||    |   |  |  ||  || ||||||||||  |           | ||     ||               
GCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCCCTCCTCGCCACGGCGCTCGCCCTCCCGGAGGACGGCACGgtccgtcgttgttccctcccttttctcagatctgccaccccacctccctgaaggcgaagcagctagcggtcctcccactgataaaccaaggatttctctctccctctctttgttgttcgtcccgccccgcag

upper sequence: Vv07s0031g00350.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: EFJ35623 (Selaginella moellendorffii), 5'ss of exon 3
GCTGCTCAAACTCATCAACGCCAAGAACACCATGGAAATCGGCGTTTACACCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAGgtaagaaaaaatcatcacccatcaagacaaaatcaaagaaaaaacactctgtttggtttcatagaaaaccaaggaaatgcagagaaaaattttgaccatt
|||  | ||  |||| ||||||||||||||||| ||||||||||| | ||| ||||| || || |||  ||| || || || || || || || |||||||| | ||  ||            |   ||  |  ||  |        |||     |                                            
GCTAGTAAAGATCATGAACGCCAAGAACACCATCGAAATCGGCGTCTTCACGGGCTATTCTCTTCTCAGCACAGCGCTGGCGCTGCCAGAGGATGGAAAGgtgaaaacgaagtcctggatcgaagttcacgactaagaagtgtgtgttctacacag--------------------------------------------

upper sequence: Vv07s0031g00350.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: EFJ24354 (Selaginella moellendorffii), 5'ss of exon 3
GCTGCTCAAACTCATCAACGCCAAGAACACCATGGAAATCGGCGTTTACACCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAGgtaagaaaaaatcatcacccatcaagacaaaatcaaagaaaaaacactctgtttggtttcatagaaaaccaaggaaatgcagagaaaaattttgaccatt
|||  | ||  |||| ||||||||||||||||| ||||||||||| | ||| ||||| || || |||  ||| || || || || || || || |||||||| | || |||            |   ||  |  ||  |        |||     |                                            
GCTAGTAAAGATCATGAACGCCAAGAACACCATCGAAATCGGCGTCTTCACGGGCTATTCTCTTCTCAGCACAGCGCTGGCGCTGCCAGAGGATGGAAAGgtgaaaacaaagtcctggatcgaagttcacgactaagaagtgtgtgttctacacag--------------------------------------------

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|37185325|gb|CF604678.1|CF604678
EST:     CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAG                         ATACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC
genomic: CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAGgtaagaaaaa ... aatgattcagATACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC
EST: gi|71859221|gb|DT008276.1|DT008276
EST:     CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAG                         ATACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC
genomic: CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAGgtaagaaaaa ... aatgattcagATACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC
EST: gi|37185179|gb|CF604532.1|CF604532
EST:     CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAG                         ATACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC
genomic: CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAGgtaagaaaaa ... aatgattcagATACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC
EST: gi|71857191|gb|DT006246.1|DT006246
EST:     CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAG                         GTACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC
genomic: CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAGgtaagaaaaa ... aatgattcagATACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC
EST: gi|71858580|gb|DT007635.1|DT007635
EST:     CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAG                         ATACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC
genomic: CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAGgtaagaaaaa ... aatgattcagATACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC
EST: gi|352785883|gb|FQ475886.1|FQ475886
EST:     CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAG                         ATACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC
genomic: CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAGgtaagaaaaa ... aatgattcagATACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC
EST: gi|30128852|gb|CB914191.1|CB914191
EST:     CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAG                         ATACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC
genomic: CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAGgtaagaaaaa ... aatgattcagATACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC
EST: gi|110728674|gb|EE104447.1|EE104447
EST:     CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAG                         ATACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC
genomic: CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAGgtaagaaaaa ... aatgattcagATACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC
EST: gi|71855811|gb|DT004866.1|DT004866
EST:     CGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGGAAAG                         ATACTGGCTATG
genomic: CGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGG-AAAGgtaagaaaaa ... aatgattcagATACTGGCTATG
EST: gi|110701151|gb|EE078431.1|EE078431
EST:     CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAG                         ATACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC
genomic: CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAGgtaagaaaaa ... aatgattcagATACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC
EST: gi|37189880|gb|CF609229.1|CF609229
EST:     CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAG                         ATACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC
genomic: CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAGgtaagaaaaa ... aatgattcagATACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC
EST: gi|71856551|gb|DT005606.1|DT005606
EST:     CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAG                         ATACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC
genomic: CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAGgtaagaaaaa ... aatgattcagATACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC
EST: gi|29782008|gb|CB346952.2|CB346952
EST:     CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAG                         ATACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC
genomic: CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAGgtaagaaaaa ... aatgattcagATACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC
EST: gi|30124789|gb|CB910128.1|CB910128
EST:     CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAG                         ATACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC
genomic: CCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAGgtaagaaaaa ... aatgattcagATACTGGCTATGGACATCAACCGTGAAAATTACGAATTGGGTCTTCCAATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCTCAAACTCATCAACGCCAAGAACACCATGGAAATCGGCGTTTACACCGGCTACTCCCTCCTCGCCACCGCCCTCGCTCTTCCCGACGACGGAAAGgtaagaaaaaatcatcacccatcaagacaaaatcaaagaaaaaacactctgtttggtttcatagaaaaccaaggaaatgcagagaaaaattttgaccatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggaaat