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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCTGTGGCACCAGTTAAAGGAAATGCAGTGCTTTTTTGGAGCATGgtttgttccttgatactacttcatataataccatgttctttagcatacacatctatctaatcacaaacctctcagccctttcctacctcaaatatataataattggatggaatgaaggtagttatggtgcactaaccacacgataatttgatttgtttggattctttcag

Basic information

species Vitis vinifera
transcript Vv05s0062g01220.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0062g01220.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA20G39250.1 (Glycine max), 5'ss of exon 11
GCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCTGTGGCACCAGTTAAAGGAAATGCAGTGCTTTTTTGGAGCATGgtttgttccttgatactacttcatataataccatgttctttagcatacacatctatctaatcacaaacctct-cagccctttcctacctcaaatatataataattggatggaatgaaggtagttatggtgcactaaccacacgataatttgatttgtttggattctttcag
|||||||| |||   ||| |||||||||||||   ||| | |||| | ||||||  |||| |||||||||||||||||||||| ||||| |||||| ||    | |   | |||  |||   ||  | | |     ||   | ||   | |||  | |||      ||    ||| | |  | |    || |||||                                                                    
GCTGGTTCAGGTGAATGTAGCTGTGGTGGGAAACTTGTCAAAGGGCTATCTGTGAAACCAATTAAAGGAAATGCAGTGCTTTTCTGGAGTATGgttagtgtaattagtttgcttattatgg-acattatccacggacaccta-atgattataaggagaaagtaagacaattatttacaaaataaggctta-aataa--------------------------------------------------------------------

upper sequence: Vv05s0062g01220.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA10G44480.1 (Glycine max), 5'ss of exon 11
GCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCTGTGGCACCAGTTAAAGGAAATGCAGTGCTTTTTTGGAGCATGgtttgttccttgatactacttcatataataccatgttctttagcatacacatctatctaatcacaaacctctcagccctttcctacctcaaatatataataattggatggaatgaaggtagttatggtgcactaaccacacgataatttgatttgtttggattctttcag
|||||||| |||   ||  |||||||||||||   ||| | |||| | ||||||   ||  |||||||||||||||||||||| ||||| |||||| ||    | |   | |||  |||      |  ||       || |||    | ||||| |  |   |   |    |    ||   ||| ||| ||  || |    ||  | ||                                                      
GCTGGTTCAGGTGAATGCAGCTGTGGTGGGAAACTTGTCAAAGGGCTATCTGTGAAGCCGATTAAAGGAAATGCAGTGCTTTTCTGGAGTATGgttagtgtaattagtttgcttattatgg----acatt-------atccacggacacctaataatga---ttataagggtaaagtaagacaagtatttacaaaataa--ggcttaaa------------------------------------------------------

upper sequence: Vv05s0062g01220.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA10G44480.2 (Glycine max), 5'ss of exon 11
GCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCTGTGGCACCAGTTAAAGGAAATGCAGTGCTTTTTTGGAGCATGgtttgttccttgatactacttcatataataccatgttctttagcatacacatctatctaatcacaaacctctcagccctttcctacctcaaatatataataattggatggaatgaaggtagttatggtgcactaaccacacgataatttgatttgtttggattctttcag
          ||   ||  |||||||||||||   ||| | |||| | ||||||   ||  |||||||||||||||||||||| ||||| |||||| ||    | |   | |||  |||      |  ||       || |||    | ||||| |  |   |   |    |    ||   ||| ||| ||  || |    ||  | ||                                                      
----------GTGAATGCAGCTGTGGTGGGAAACTTGTCAAAGGGCTATCTGTGAAGCCGATTAAAGGAAATGCAGTGCTTTTCTGGAGTATGgttagtgtaattagtttgcttattatgg----acatt-------atccacggacacctaataatga---ttataagggtaaagtaagacaagtatttacaaaataa--ggcttaaa------------------------------------------------------

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|110370486|gb|EC929820.1|EC929820
EST:     GGTTGTCTGTGGCACCAGTTAAAGGAAATGCAGTGCTTTTTTGGAGCATG                         GGACTAGATGGACAATCAGACCCAAATAGCATCCATGGCGGATGCGAAGTA
genomic: GGTTGTCTGTGGCACCAGTTAAAGGAAATGCAGTGCTTTTTTGGAGCATGgtttgttcct ... attctttcagGGACTAGATGGACAATCAGACCCAAATAGCATCCATGGCGGATGCGAAGTA
EST: gi|110427318|gb|EC993753.1|EC993753
EST:     GGTTGTCTGTGGCACCAGTTAAAGGAAATGCAGTGCTTTTTTGGAGCATG                         GGACTAGATGGACAATCAGACCCAAATAGCATCCATGGCGGATGCGAAGTA
genomic: GGTTGTCTGTGGCACCAGTTAAAGGAAATGCAGTGCTTTTTTGGAGCATGgtttgttcct ... attctttcagGGACTAGATGGACAATCAGACCCAAATAGCATCCATGGCGGATGCGAAGTA
EST: gi|349820405|gb|FQ406961.1|FQ406961
EST:     GGTTGTCTGTGGCACCAGTTAAAGGAAATGCAGTGCTTTTTTGGAGCATG                         GGACTAGATGGA
genomic: GGTTGTCTGTGGCACCAGTTAAAGGAAATGCAGTGCTTTTTTGGAGCATGgtttgttcct ... attctttcagGGACTAGATGGA
EST: gi|34319741|gb|CF372495.1|CF372495
EST:     GGTTGTCTGTGGCCCCAGTTAAAGGAAATGCAGTGCTTTTTTGGAGCATG                         GGACTAGATGGACAATCAGACCCAAATAGCATCCATGGCGGATGCGAAGTA
genomic: GGTTGTCTGTGGCACCAGTTAAAGGAAATGCAGTGCTTTTTTGGAGCATGgtttgttcct ... attctttcagGGACTAGATGGACAATCAGACCCAAATAGCATCCATGGCGGATGCGAAGTA
EST: gi|110415165|gb|EC981042.1|EC981042
EST:     GGTTGTCTGTGGCACCAGTTAAAGGAAATGCAGTGCTTTTTTGGAGCATG                         GGACTAGATGGACAATCAGACCCAAATAGCATCCATGGCGGATGCGAAGTA
genomic: GGTTGTCTGTGGCACCAGTTAAAGGAAATGCAGTGCTTTTTTGGAGCATGgtttgttcct ... attctttcagGGACTAGATGGACAATCAGACCCAAATAGCATCCATGGCGGATGCGAAGTA
EST: gi|30297955|gb|CB974749.1|CB974749
EST:     GGTTGTCTGTGGCACCAGTTAAAGGAAATGCAGTGCTTTTTTGGAGCATG                         GGACTAGATGGACAATCAGACCCAAATAGCATCCATGGCGGATGCGAAGTA
genomic: GGTTGTCTGTGGCACCAGTTAAAGGAAATGCAGTGCTTTTTTGGAGCATGgtttgttcct ... attctttcagGGACTAGATGGACAATCAGACCCAAATAGCATCCATGGCGGATGCGAAGTA
EST: gi|351042433|gb|FQ442900.1|FQ442900
EST:     GGTTGTCTGTGGCACCAGTTAAAGGAAATGCAGTGCTTTTTTGGAGCATG                         GGACTAGATGGACAATCAAACCCAA-TAGCATCCATGGCGGA
genomic: GGTTGTCTGTGGCACCAGTTAAAGGAAATGCAGTGCTTTTTTGGAGCATGgtttgttcct ... attctttcagGGACTAGATGGACAATCAGACCCAAATAGCATCCATGGCGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCTGTGGCACCAGTTAAAGGAAATGCAGTGCTTTTTTGGAGCATGgtttgttccttgatactacttcatataataccatgttctttagcatacacatctatctaatcacaaacctctcagccctttcctacctcaaatatataataattggatggaatgaaggtagttatggtgcactaaccacacgataatttgatttgtttggattctttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA