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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATAAGCTTGCACAATTTTCCCGAGGGAATGGCTGTGTTCCTTGGATCAATGAAGgtaatatctgatcttttacattattctgggagtcttgagatgtgctataaacctttttccttcactgtcagaatacaatctcttatctgttttagctgtt...

Basic information

species Vitis vinifera
transcript Vv06s0004g01860.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G050484_T01 (Zea mays), 5'ss of exon 6
GCATAAGCTTGCACAATTTTCCCGAGGGAATGGCTGTGTTCCTTGGATCAATGAAGgtaatatctgatc----tttta----cattattctgggagtcttgagatgtgctataaacctttt---tccttcactgtcagaata-caatctcttatctgttttagctgtt
| || |||||||| ||| |||| |||||||||||||| || ||||||||  | ||||||||| || |      || |     ||||||      | ||   |  ||| |||   |||||||   |  |  | |     |||| || ||| || | ||           
GAATTAGCTTGCATAATCTTCCAGAGGGAATGGCTGTATTTCTTGGATCTGTCAAGgtaataccttagtacagttatgccagcattatagcttaaatcactaactgt-ctaaccaccttttgggttttgaattactgaaataacattcttttctttg-----------

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA13G41580.5 (Glycine max), 5'ss of exon 6
GCATAAGCTTGCACAATTTTCCCGAGGGAATGGCTGTGTTCCTTGGATCAATGAAGgtaatatctgatcttttacattattctgggagtcttgagatgtgctataaacctttttc-cttcactgtcagaatacaatctcttatctgttt--tagctgtt----------------------------------------
||||||| |||||||||||||| || |||||||| ||||||||||||||  | ||||||       | || ||    |  |   |||  |   | || |  ||| ||   ||    | | |||   |   ||    |  | || || ||  ||   ||                                         
GCATAAGTTTGCACAATTTTCCAGAAGGAATGGCGGTGTTCCTTGGATCCTTAAAGgtacccatgaacctattgatgtgcttatggatccgccacat-tattattaattgttgaaacattacttatattttatccaccttgatgtgcttgttaatagtgccactttaatttgatgttttgtgacatgcgttttcaacag

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA15G03820.2 (Glycine max), 5'ss of exon 6
GCATAAGCTTGCACAATTTTCCCGAGGGAATGGCTGTGTTCCTTGGATCAATGAAGgtaatatctgatcttttacattattctgggagtcttgagatgtgctataaacc-tttttccttcactgtcagaatacaatctcttatctgttt--tagctgtt---------------------------------------
||||||| |||||||||||||| || |||||||| ||||||||||||||  | ||||||       | || ||    |  |   |||      | || |  ||| ||   ||    | | |||   |   ||    | || || || ||  ||    |                                        
GCATAAGTTTGCACAATTTTCCAGAAGGAATGGCAGTGTTCCTTGGATCCTTAAAGgtacccatgaacctattgatgtgcttatggatctgcaacat-tattattaattgttgaagcattacttatattgtatccaccctgatatgcttgttaataatggcacttcaatttgatgtttgtgacatgctttttcaacag

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT3G20870.1 (Arabidopsis thaliana), 5'ss of exon 6
GCATAAGCTTGCACAATTTTCCCGAGGGAATGGCTGTGTTCCTTGGATCAATGAAGgtaatatctg---atcttttacatta------ttctgggagtcttgagatgtgctataaacctttttccttcactgtcagaataca-atctcttatctgttttagctgtt------------------------------
|||||||||||||||||||||| || || |||||||| || || |||||||| ||||| |    |    | | |  | |  |      ||| |||||  |  |    | |||  ||  | | ||  | ||| |  ||  ||   | || | |  || |||  | |                               
GCATAAGCTTGCACAATTTTCCAGAAGGGATGGCTGTATTTCTCGGATCAATAAAGgtgaggattaaaaaacatgaaaaacagaaaatttcagggagcatgcatgcattctaacaatatatctctat-actatttgataacctgtgtcatctacgtattaa-tatcaatatttgcttgttggattctacttcacag

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: EFJ32545 (Selaginella moellendorffii), 5'ss of exon 6
GCATAAGCTTGCACAATTTTCCCGAGGGAATGGCTGTGTTCCTTGGATCAATGAAGgtaatatctgatcttttacattattctgggagtcttgagatgtgctataaacctttttccttcactgtcagaatacaatctcttatctgttttagctgtt
| |||||||||||||||||||| ||||||||||||||||||||||| || |||||||||   |   |   |     |||||     |   |  |      |  ||  | ||  | | |  | |                                 
GAATAAGCTTGCACAATTTTCCTGAGGGAATGGCTGTGTTCCTTGGGTCCATGAAGgta---tgaaacactaccgcttattgaaaaaacttccaa-----ccttacgcgttgctacatttcag---------------------------------

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: EFJ16604 (Selaginella moellendorffii), 5'ss of exon 6
GCATAAGCTTGCACAATTTTCCCGAGGGAATGGCTGTGTTCCTTGGATCAATGAAGgtaatatctgatcttttacattattctgggagtcttgagatgtgctataaacctttttccttcactgtcagaatacaatctcttatctgttttagctgtt
| |||||||||||||| ||||| |||||||||||||||||||||||||| |||||||||   |   |   |     |||||     |   |  |      |  ||  | ||  | | |  | |                                 
GAATAAGCTTGCACAACTTTCCTGAGGGAATGGCTGTGTTCCTTGGATCCATGAAGgta---tgaaacactaccgcttattgaaaaaacttccaa-----ccttacgcgttgctacatttcag---------------------------------

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|30251805|gb|CB969538.1|CB969538
EST:     TGGATCAATGAAG                         GGCCTTCGGGTTGGACTAAACTTGGCANTGGCCATTGCTTTGCACAACATC
genomic: TGGATCAATGAAGgtaatatctg ... tcttttgtagGGCCTTCGGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATC
EST: gi|30251808|gb|CB969541.1|CB969541
EST:     GAATGGCTGTGTTCCTTGGATCAATGAAG                         GGCCTTCGGGTCGGACTATCCTTGGNTCTNGCCATTGCTTTGCACAACATC
genomic: GAATGGCTGTGTTCCTTGGATCAATGAAGgtaatatctg ... tcttttgtagGGCCTTCGGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATC
EST: gi|110693804|gb|EE070356.1|EE070356
EST:     GCTTGCACAATTTTCCCGAGGGAATGGCTGTGTTCCTTGGATCAATGAAG                         GGCCTTCGGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATC
genomic: GCTTGCACAATTTTCCCGAGGGAATGGCTGTGTTCCTTGGATCAATGAAGgtaatatctg ... tcttttgtagGGCCTTCGGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATC
EST: gi|110689440|gb|EE065664.1|EE065664
EST:     GCTTGCACAATTTTCCCGAGGGAATGGCTGTGTTCCTTGGATCAATGAAG                         GGCCTTCGGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATC
genomic: GCTTGCACAATTTTCCCGAGGGAATGGCTGTGTTCCTTGGATCAATGAAGgtaatatctg ... tcttttgtagGGCCTTCGGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATC
EST: gi|110698572|gb|EE076222.1|EE076222
EST:     GCTTGCACAATTTTCCCGAGGGAATGGCTGTGTTCCTTGGATCAATGAAG                         GGCCTTCGGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATC
genomic: GCTTGCACAATTTTCCCGAGGGAATGGCTGTGTTCCTTGGATCAATGAAGgtaatatctg ... tcttttgtagGGCCTTCGGGTTGGACTAAACTTGGCACTGGCCATTGCTTTGCACAACATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATAAGCTTGCACAATTTTCCCGAGGGAATGGCTGTGTTCCTTGGATCAATGAAGgtaatatctgatcttttacattattctgggagtcttgagatgtgctataaacctttttccttcactgtcagaatacaatctcttatctgttttagctgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaataca