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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCCGTGTTGGAGCAGATGAAGCTCCACCTTGCCACCGACGCCGGTAAACAACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAGgtccctctctctctctctctccctctgtttccttgtgtatagacgtatttttatcctaatcctaatgtaatacttttgttgccggatcgtag

Basic information

species Vitis vinifera
transcript Vv18s0001g10520.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g10520.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os06g10890.2 (Oryza sativa), 5'ss of exon 1
CGCCG-TGTTGGAGCAGATGAAGCTCCACCTTGCCACCGACGCCGGTAAACAACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAGgtccctctctctctctctctccctctgtttccttgtgtatagacgtatttttatcctaatcctaat--gtaatacttttgttgccggatcgtag
 || | |  | |||||||||   |||||| | |||||||||||||| ||  |  || |||||||| ||||||||||||| ||| ||||||||||||| ||||||  | ||||  ||| || || | |  ||   ||    |  |          || | |||||  |  ||    |   | | || |        
-GCAGCTCCTCGAGCAGATGCGCCTCCACATGGCCACCGACGCCGGCAAGGACATCGCCAAGAAGGTCGGCCTCGTCTACCAGTTCAACATCGCCCCCAAGgtcaatatctccttctatccccttttaattgggtggaattgaagcgccccccgtcttgatcctgtttagtggcgcgcctttcgcag--------

upper sequence: Vv18s0001g10520.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA17G36080.1 (Glycine max), 5'ss of exon 1
CGCCGTGTTGGAGCAGATGAAGCTCCACCTTGCCACCGACGCCGGTAAACAACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAGgtccctctctctctctctctccctctgtttccttgtgtatagacgtatttttatcctaatcctaatgtaatacttttgttgccggatcgtag
 ||  |  |||||||||||||||  ||||| ||||||||||| || |||||| ||||||| || || || ||||| |||||| |  |||| || ||||||||   |   | ||  | |     |    |   |  |  ||     |||  ||||     ||  | || |  | ||   || |  ||      
-GCGATAATGGAGCAGATGAAGCAACACCTCGCCACCGACGCTGGCAAACAAGTCACCAATAAAATTGGACTCGTTTATCAGTTTCACATTGCTCCTAAGGtaattagttttcattattcgtttaacctaattaattaattactttatcattatttcggtctcattgaatgagttggatttctaga------

upper sequence: Vv18s0001g10520.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA14G09100.1 (Glycine max), 5'ss of exon 1
CGCCGTGTTGGAGCAGATGAAGCTCCACCTTGCCACCGACGCCGGTAAACAACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAGgtccctctctctctctctctccctctgtttccttgtgtatagacgtatttttatcctaatcctaatg------taatacttttgttgccgga-tcgtag------------------
|||  |  |||||||||||||||  ||||| ||||||||| | || |||||| ||||||| || || || ||||| ||||||||  | || || ||||||||     | |||   | | |     || | | || |  ||  |  |   |||| ||||||   | ||      ||||  |  |  ||||||  || | |                  
CGCGATAATGGAGCAGATGAAGCAGCACCTCGCCACCGACTCAGGCAAACAAGTCACCAAAAAAATTGGACTCGTTTATCAGATTCAAATTGCTCCTAAGgttagatt-tcttattgtttattaatgat-cattattcatctattttcgtttaacctaatttaattgattaattaattatcattatgccggtctcattgaatgagttgaatttctag

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|110692307|gb|EE071401.1|EE071401
EST:     AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAG                         AAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
genomic: AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAGgtccctctct ... cggatcgtagAAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
EST: gi|110731553|gb|EE106064.1|EE106064
EST:     AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAG                         AAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
genomic: AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAGgtccctctct ... cggatcgtagAAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
EST: gi|30137388|gb|CB922726.1|CB922726
EST:     ATCAGATCAACATCGCCCCTAAG                         AAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
genomic: ATCAGATCAACATCGCCCCTAAGgtccctctct ... cggatcgtagAAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
EST: gi|110702006|gb|EE080226.1|EE080226
EST:     AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAG                         AAAGTTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
genomic: AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAGgtccctctct ... cggatcgtagAAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
EST: gi|30128318|gb|CB913657.1|CB913657
EST:     AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAG                         AAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
genomic: AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAGgtccctctct ... cggatcgtagAAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
EST: gi|110406594|gb|EC972173.1|EC972173
EST:     AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAG                         AAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
genomic: AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAGgtccctctct ... cggatcgtagAAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
EST: gi|110428740|gb|EC995219.1|EC995219
EST:     AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAG                         AAAGTTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
genomic: AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAGgtccctctct ... cggatcgtagAAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
EST: gi|71871632|gb|DT020687.1|DT020687
EST:     AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAG                         AAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
genomic: AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAGgtccctctct ... cggatcgtagAAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
EST: gi|351025342|gb|FQ434355.1|FQ434355
EST:     AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAG                         AAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
genomic: AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAGgtccctctct ... cggatcgtagAAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
EST: gi|110730854|gb|EE108410.1|EE108410
EST:     AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAG                         AAAGTTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
genomic: AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAGgtccctctct ... cggatcgtagAAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
EST: gi|110401310|gb|EC967917.1|EC967917
EST:     AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAG                         AAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
genomic: AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAGgtccctctct ... cggatcgtagAAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
EST: gi|30125163|gb|CB910502.1|CB910502
EST:     AGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAG                         AAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
genomic: AGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAGgtccctctct ... cggatcgtagAAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
EST: gi|110377019|gb|EC942080.1|EC942080
EST:     AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAG                         AAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
genomic: AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAGgtccctctct ... cggatcgtagAAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
EST: gi|110421606|gb|EC987905.1|EC987905
EST:     AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAG                         AAAGTTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
genomic: AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAGgtccctctct ... cggatcgtagAAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
EST: gi|110422438|gb|EC988763.1|EC988763
EST:     TACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAG                         AAAGTTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
genomic: AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAGgtccctctct ... cggatcgtagAAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
EST: gi|110373216|gb|EC937434.1|EC937434
EST:     AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAG                         AAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
genomic: AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAGgtccctctct ... cggatcgtagAAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
EST: gi|110424832|gb|EC991205.1|EC991205
EST:     AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAG                         AAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
genomic: AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAGgtccctctct ... cggatcgtagAAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
EST: gi|30133262|gb|CB918601.1|CB918601
EST:     AGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAG                         AAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
genomic: AGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAGgtccctctct ... cggatcgtagAAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
EST: gi|110380104|gb|EC945346.1|EC945346
EST:     AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAG                         AAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
genomic: AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAGgtccctctct ... cggatcgtagAAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
EST: gi|34319348|gb|CF372102.1|CF372102
EST:     AACTCACCAAAAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAG                         AAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
genomic: AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAGgtccctctct ... cggatcgtagAAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
EST: gi|110429212|gb|EC995701.1|EC995701
EST:     AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAG                         AAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA
genomic: AACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAGgtccctctct ... cggatcgtagAAAATTGGATTCAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCCGTGTTGGAGCAGATGAAGCTCCACCTTGCCACCGACGCCGGTAAACAACTCACCAAGAAGATCGGCCTCGTCTATCAGATCAACATCGCCCCTAAGgtccctctctctctctctctccctctgtttccttgtgtatagacgtatttttatcctaatcctaatgtaatacttttgttgccggatcgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA