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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCCCTGCACTTACTCTGAAGACAGCACTCCTTTCTGTACAAGCCTTGCTCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAGgtctagtttgcttctagtcttcctacattatctccttatttattttagtcttattttcttgttaattaaattagcagctgtctatggtcattccattatc...

Basic information

species Vitis vinifera
transcript Vv17s0000g00610.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g00610.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os01g70140.1 (Oryza sativa), 5'ss of exon 3
GAGCCCTGCACTTACTCTGAAGACAGCACTCCTTTCTGTACAAGCCTTGCTCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAGgtctagtttgctt--ctagtcttcctacattatctccttatttattttagtcttattttcttgttaattaaattagcagctgtctatggtcattccattatc
|||||| || |||||  ||||||| ||||| |||||  | |||||  |||| |||||||||  ||||||||||||||| || ||||| || || |||||||||| |  | |||  ||| |   | |    | | |    ||      | || ||    | || |  |||||   || |  | |  || | |  | | |    
GAGCCCAGCCCTTACATTGAAGACGGCACTGCTTTCCCTCCAAGCTCTGCTTTCTGCCCCTGCACCTGATGATCCTCAGGATGCTGTCGTTGCACAACAGgtctggactacttgactatttagcttcatattttttagcataccaccttgttttgaactattatgcattaag--agtaaatttacattgcctcttcttggaa

upper sequence: Vv17s0000g00610.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA06G17470.3 (Glycine max), 5'ss of exon 3
GAGCCCTGCACTTACTCTGAAGACAGCACTCCTTTCTGTACAAGCCTTGCTCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAGgtctagtttgcttctagtcttcctacattatctccttatttattttagtcttattttcttgttaattaaattagcagctgtctatggtcattccattatc--
|||||| ||||| ||||||||||| ||||| |||||||| |||||  | |||||||| ||||| ||||||||||||||||| || |||||||| || |||||||   |   |  |  |  |       | ||||     || |   |   || || |  | |   |||  |  | | ||| | | | | | |  |||     
GAGCCCAGCACTCACTCTGAAGACTGCACTTCTTTCTGTGCAAGCACTTCTCTCTGCTCCTCAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactctttctt--ttgtgtagttgtgtctctactcttgtgaaaagtttcttcttatatcctttatgtgtggaactgccaaagcttaatatattgaaga

upper sequence: Vv17s0000g00610.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA04G37620.3 (Glycine max), 5'ss of exon 4
GAGCCCTGCACTTACTCTGAAGACAGCACTCCTTTCTGTACAAGCCTTGCTCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAGgtctagtttgcttctagtcttcctacattatctccttatttattttagtcttattttcttgttaattaaattagcagctgtctatggtcattccattatc--
|||||| ||||| ||||||||||| ||||| |||||||| |||||  | |||||||| || || ||||||||||||||||| || |||||||| || |||||||   |  |||   ||  |       | ||||     |||    |   || || |  | |   ||   |  | | ||| | | |  || |  |||     
GAGCCCAGCACTCACTCTGAAGACTGCACTTCTTTCTGTGCAAGCACTTCTCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgact--ctttctgttgtgtagttgtgtctctactcttaggaaaagtttcttcttatatcctttgcttatggaactgccaaagcacagtatattgaaga

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|161716905|gb|FC068127.1|FC068127
EST:     TCTCTGCCCCTCAACCTGATGATCCTCAAGATGCTGTGGTGGCTCAACAG                         TATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
genomic: TCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAGgtctagtttg ... gatgttgcagTATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
EST: gi|30298293|gb|CB975087.1|CB975087
EST:     TCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAG                         TATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
genomic: TCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAGgtctagtttg ... gatgttgcagTATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
EST: gi|294965161|gb|GW836992.1|GW836992
EST:     TCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGG-TCAACAG                         TATCTTAAAGACTATCAAACCTATGTTGGCA-AGCTCGATATTGGACAGAA
genomic: TCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAGgtctagtttg ... gatgttgcagTATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
EST: gi|30298360|gb|CB975154.1|CB975154
EST:     GCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAG                         TATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
genomic: GCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAGgtctagtttg ... gatgttgcagTATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
EST: gi|110391172|gb|EC956130.1|EC956130
EST:     TCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAG                         TATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
genomic: TCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAGgtctagtttg ... gatgttgcagTATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
EST: gi|110396526|gb|EC962216.1|EC962216
EST:     TCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAG                         TATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
genomic: TCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAGgtctagtttg ... gatgttgcagTATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
EST: gi|110401583|gb|EC968197.1|EC968197
EST:     TCTCTGCCCCTCAACCTGATGATCCTCAAGATGCTGTGGTGGCTCAACAG                         TATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
genomic: TCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAGgtctagtttg ... gatgttgcagTATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
EST: gi|32460677|gb|CD801851.1|CD801851
EST:     GATGATCCTCAAGACGCGCTGTGGTGGCTCAACAG                         TATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
genomic: GATGATCCTCAAGA--CGCTGTGGTGGCTCAACAGgtctagtttg ... gatgttgcagTATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
EST: gi|30295997|gb|CB972791.1|CB972791
EST:     GCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAG                         TATCTTAAAGGCTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
genomic: GCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAGgtctagtttg ... gatgttgcagTATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
EST: gi|161714263|gb|FC064160.1|FC064160
EST:     TCTCTGCCCCTCAACCTGATGATCCTCAAGATGCTGTGGTGGCTCAACAG                         TATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
genomic: TCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAGgtctagtttg ... gatgttgcagTATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
EST: gi|83274440|gb|DV938537.1|DV938537
EST:     TCTCTGCCCCTCAACCTGATGATCCTCAAGATGCTGTGGTGGCTCAACAG                         TATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
genomic: TCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAGgtctagtttg ... gatgttgcagTATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
EST: gi|83275178|gb|DV939274.1|DV939274
EST:     TCTCTGCCCCTCAACCTGATGATCCTCAAGATGCTGTGGTGGCTCAACAG                         TATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
genomic: TCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAGgtctagtttg ... gatgttgcagTATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
EST: gi|351028328|gb|FQ427224.1|FQ427224
EST:     TCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAG                         TATCTTAAAGACTATCAGACCTATGTTGGCACAACTCGATATTGGACAGAA
genomic: TCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAGgtctagtttg ... gatgttgcagTATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
EST: gi|77581774|gb|DV219842.1|DV219842
EST:     TCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAG                         TATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
genomic: TCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAGgtctagtttg ... gatgttgcagTATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
EST: gi|77583170|gb|DV220622.1|DV220622
EST:     TCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAG                         TATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
genomic: TCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAGgtctagtttg ... gatgttgcagTATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
EST: gi|71890757|gb|DT039812.1|DT039812
EST:     TCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAG                         TATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
genomic: TCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAGgtctagtttg ... gatgttgcagTATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
EST: gi|77588446|gb|DV223434.1|DV223434
EST:     TCTCTGCCCCTCAACCTGATGATCCTCAAGATGCTGTGGTGGCTCAACAG                         TATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
genomic: TCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAGgtctagtttg ... gatgttgcagTATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
EST: gi|77578362|gb|DV217970.1|DV217970
EST:     TCTCTGCCCCTCAACCTGATGATCCTCAAGATGCTGTGGTGGCTCAACAG                         TATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
genomic: TCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAGgtctagtttg ... gatgttgcagTATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
EST: gi|110412172|gb|EC977911.1|EC977911
EST:     TCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAG                         TATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA
genomic: TCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAGgtctagtttg ... gatgttgcagTATCTTAAAGACTATCAGACCTATGTTGGCACAGCTCGATATTGGACAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCCCTGCACTTACTCTGAAGACAGCACTCCTTTCTGTACAAGCCTTGCTCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAGgtctagtttgcttctagtcttcctacattatctccttatttattttagtcttattttcttgttaattaaattagcagctgtctatggtcattccattatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aattaaa