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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATGgtatacctcattacaccaatctagtttcggtggatttgtttcaggcagttgattgttttctcatcagttaatcatcaataaattgcacatctatgacaga...

Basic information

species Vitis vinifera
transcript Vv08s0007g03250.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g03250.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os08g44400.3 (Oryza sativa), 5'ss of exon 6
GTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATGgtatacctcattacaccaatctagtttcggtggatttgtttcaggcagttgattgttttctcatcagttaatcatcaataaattgcacatctatgacaga
||||||||||||||||| ||||| ||||||||||| |||| ||| || || ||  |||  |  |||||||||    |  ||| || |  ||   | |   |     |||  | ||    |  |  |   ||| |   ||   | |   |     |               
GTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATGgtg---cctatttcatctctcatctgtacatctccctgtccctggggcctcctactaacctcctgcatttgcccttgcttttcag---------------

upper sequence: Vv08s0007g03250.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G022866_T02 (Zea mays), 5'ss of exon 6
GTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATGgtatacctcattacaccaatctagtttcggtggatttgtttcaggcagttgattgttttctcatcagttaatcatcaataaattgcacatctatgacaga-------
||||||||||||||||| || || ||||||||||| |||||||| || || ||| | | ||  | ||||||| |     |||  ||  ||||  |||       |||| |       ||||||    | |  ||  ||     |  |      |     | ||   | ||       
GTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAATATCTAGCTGATACATATGgtgtgt---attcaacacatctccttttcact--tttgctcttaaaggttgatc--ctccctatttgtgggggaaaaggcttgtctcggtttaaccctgagacccca

upper sequence: Vv08s0007g03250.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM5G825090_T03 (Zea mays), 5'ss of exon 6
GTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATGgtatacctcattacaccaatctagtttcggtggatttgtttcaggcagttgattgttttctcatcagttaatcatcaataaattgcacatctatgacaga-------
|| |||||||||||||| || || ||||||||||| |||||||| || || ||| | | ||  | ||||||| |     |||  ||  ||||  |||       |||| |       |||| |    | |  ||  ||     |  |      |     | |||  | ||       
GTAGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAATATCTAGCTGATACATATGgtgtgt---attcaacacatctccttttcact--tttgctcttaaaggttgttc--ctccctatttgtgggggaaaaggcttgtcttggtttatccccgagacccca

upper sequence: Vv08s0007g03250.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM5G825090_T05 (Zea mays), 5'ss of exon 6
GTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATGgtatacctcattacaccaatctagtttcggtggatttgtttcaggcagttgattgttttctcatcagttaatcatcaataaattgcacatctatgacaga-------
|| |||||||||||||| || || ||||||||||| |||||||| || || ||| | | ||  | ||||||| |     |||  ||  ||||  |||       |||| |       ||||||    | |  ||  ||     |  |      |     | ||   | ||       
GTAGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAATATCTAGCTGATACATATGgtgtgt---attcaacacatctccttttcact--tttgctcttaaaggttgatc--ctccctatttgtgggggaaaaggcttgtctcggtttaaccctgagacccca

upper sequence: Vv08s0007g03250.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA0084S00210.1 (Glycine max), 5'ss of exon 6
GTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATGgtatacctcattacac-caatctagtttcggtggatttgtttcaggca-gttgattgttttctcatcagttaatcatcaataaattgcacatctatgacaga
|| || ||||||||||| | | ||||||||||||| ||||||||||||  |||||||||||  ||||||||| |   || |   |   | |||   ||| ||  || || ||  | || || |  | |||||   |    |    ||| ||||| |  |  |  ||    | 
GTTGACCCAAACACAGGCGCTTCAATGTATGAATCAGATGACATAATTCGGTATTTGGTTGACAAATATGgtttgtgtcttcgtatatattctctattctgta-atgtgcttatgccatgtagtcttttttcctgttgcatttcaatctataaaatataattacatatatg-

upper sequence: Vv08s0007g03250.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA13G22160.1 (Glycine max), 5'ss of exon 6
GTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATGgtatacctcattacaccaatctagtttcggtggatttgtttcaggca-gttgattgttttctcatcagttaatcatcaataaattgcacatctatgacaga
|| || ||||||||||| | | ||||||||||||| ||||||||||||  |||||||||||  ||||||||| |   || |   |   ||    |||       | || ||  | || || |  | |||||   |    |    ||| ||||| |  |  |  ||    | 
GTTGACCCAAACACAGGCGCTTCAATGTATGAATCAGATGACATAATTCGGTATTTGGTTGACAAATATGgtttgtgtcttcctatatatacccttttctgtattgtgcttatgccatgtagtcttttttcctgttgcatttcaatctataaaatataattacatatgtg-

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|30253288|gb|CB970839.1|CB970839
EST:     TGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATG                         GTGATGGAAATGTCCCTTTTATGTTGTCACTTGGTCTACTAACG
genomic: TGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATGgtatacctca ... ttttctatagGTGATGGAAATGTCCCTTTTATGTTGTCACTTGGTCTACTAACG
EST: gi|349822639|gb|FQ412903.1|FQ412903
EST:     TGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATG                         GTGATGGAAATGTCCCTTTTATGTTGTCACTTGGTCTACTAACG
genomic: TGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATGgtatacctca ... ttttctatagGTGATGGAAATGTCCCTTTTATGTTGTCACTTGGTCTACTAACG
EST: gi|27755146|gb|CB035901.1|CB035901
EST:     TGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATG                         GTGATGGAAATGTCCCTTTTATGTTGTCACTTGGTCTACTAACG
genomic: TGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATGgtatacctca ... ttttctatagGTGATGGAAATGTCCCTTTTATGTTGTCACTTGGTCTACTAACG
EST: gi|30253209|gb|CB970760.1|CB970760
EST:     TGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATG                         GTGATGGAAATGTCCCTTTTATGTTGTCACTTGGTCTACTAACG
genomic: TGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATGgtatacctca ... ttttctatagGTGATGGAAATGTCCCTTTTATGTTGTCACTTGGTCTACTAACG
EST: gi|351019188|gb|FQ429348.1|FQ429348
EST:     TGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATG                         GTGATGGAAATGTCCCTTTTATGTTGTCACTTGGTCTACTAACG
genomic: TGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATGgtatacctca ... ttttctatagGTGATGGAAATGTCCCTTTTATGTTGTCACTTGGTCTACTAACG
EST: gi|110413628|gb|EC979423.1|EC979423
EST:     TGCAATGTATGAATCAGATGACATAATTAAGTATTTGGTCGGGAAATATG                         GTGATGGAAATGTCCCTTTTATGTTGTCACTTGGTCTACTAACG
genomic: TGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATGgtatacctca ... ttttctatagGTGATGGAAATGTCCCTTTTATGTTGTCACTTGGTCTACTAACG
EST: gi|110423056|gb|EC989391.1|EC989391
EST:     TGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATG                         GTGATGGAAATGTCCCTTTTATGTTGTCACTTGGTCTACTAACG
genomic: TGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATGgtatacctca ... ttttctatagGTGATGGAAATGTCCCTTTTATGTTGTCACTTGGTCTACTAACG
EST: gi|28959489|gb|CB339745.1|CB339745
EST:     TGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATG                         GTGATGGAAATGTCCCTTTTATGTTGTCACTTGGTCTACTAACG
genomic: TGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATGgtatacctca ... ttttctatagGTGATGGAAATGTCCCTTTTATGTTGTCACTTGGTCTACTAACG
EST: gi|349811972|gb|FQ410769.1|FQ410769
EST:     TGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATG                         GTGATGGAAATGTCCCTTTTATGTTGTCACTTGGTCTACTAACGACCTTGA
genomic: TGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATGgtatacctca ... ttttctatagGTGATGGAAATGTCCCTTTTATGTTGTCACTTGGTCTACTAACGACTTTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATGgtatacctcattacaccaatctagtttcggtggatttgtttcaggcagttgattgttttctcatcagttaatcatcaataaattgcacatctatgacaga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caataaa