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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATGgtaatttctcattttactaatattggttttttttgcttattattatttaagccttgtcagaggcaatgcagtaagagagttctgatgtgagcacaattca...

Basic information

species Vitis vinifera
transcript Vv13s0019g03470.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g03470.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G098153_T01 (Zea mays), 5'ss of exon 2
GTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATGgtaattt-ctcattttactaatattggttttttttgcttattattatttaagccttgtcagaggcaatgcagtaagagagttctgatgtgagcacaattca--
|| ||  | || ||||| ||||| ||||| ||||     || |||||||||||||| || ||||||||||| |||||||||| |    | ||    |         | ||      | |  | |||||||    || || |   | || | |||    |   |  ||||||   | | |    
GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAGGTGAACCCCAAGGAAGTCATCGTCGGATGgtgagcaacccaccccatcgcctcacgattccacaccctcgttttattta--ttttttctggctccat-cggtatatcaacacatatgtgaatgccagtgctc

upper sequence: Vv13s0019g03470.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA18G03340.1 (Glycine max), 5'ss of exon 2
-GTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATGgtaatttct-cattttactaatattggtttttttt-gcttattattatttaagccttgtcagaggcaatgcagtaagagagttctgatgtgagcacaattca
 |||||||||||||| || ||||| || ||||||||| |||||||||| || ||||||||||||||| |||| || |||||||||||||   | |||   ||  |   ||||     | ||||||| ||   |  ||     || |   ||    |  | | || | |  |    |      |
GGTTGCATTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAAGTGAATCCAAAGGAAATCATAGTAGGATGgtaatttcaatactttttaaaggtctattttccccaggttattataatggtattctcaat-gaagtgttggcccagaaaacttttaa-atccatatggccta

upper sequence: Vv13s0019g03470.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA02G42210.1 (Glycine max), 5'ss of exon 2
GTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATGgtaatttctcattttactaa-----tattggtttt---ttttgcttattattatttaagccttgtcagaggcaatgcagtaagagagttctgatgtgagcacaattca
|| || |||||||| || || || |||| ||||||||||||||||||||||||||| ||||||||||| || || ||||||||| | || ||| |  |||     || |  |||    || ||   ||| |  |   |    |||||| || |||| || |  | |    || | |  |         
GTCGCTTTGGATATTGAGTATCAACATAGTATGTTATTATCCCACCAGAAGGTGAACCCAAAGGAAGTTATAGTTGGATGgtaagtcct-attcttttaaccctttactattttaaagttctgtgcattgtgttcacaatggtgtcagtgggaatgtagaattaaataggtggtctttgtt-------

upper sequence: Vv13s0019g03470.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA11G35020.1 (Glycine max), 5'ss of exon 2
GTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATGgtaatttctcattttactaatattggttttttttgcttattattatttaagccttgtcagaggcaatgcagtaagagagttctgatgtgagcacaattca----
||||| |||||||| || ||||| || ||||||||| |||||||||| || ||||||||||||||| |||| || ||||||||||| |     ||  ||| |   || | |                    ||     | |||  || ||  | |  | ||   |||           ||    
GTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAAGTGAATCCAAAGGAAATCATAGTAGGATGgtaattccaatactttttaaaa---gtctatccccacccccccccccccccccccccaaaaggttat-caaaatggtattttcaatgaagtgttggcccagaaa

upper sequence: Vv13s0019g03470.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA14G06690.1 (Glycine max), 5'ss of exon 2
GTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATGgtaatttctcattttactaatattggttttttttgcttattat-tatttaagccttgtcagaggcaatgcagtaagagagttctg-atgtgagcacaattca
|| || |||||||| || || || |||| ||||||||||||||||||||||||||| ||||||||||| || || || |||||| | ||  | ||   |   ||   | ||||    |    | ||||  |  |        | |||||        || |||   | |||  |    ||  
GTCGCTTTGGATATTGAGTATCACCATAGTATGTTATTATCCCACCAGAAGGTGAACCCAAAGGAAGTTATAGTTGGGTGgtaagtcctattcttttgaccctttactattttaaagttccgtgtattgtattcacaatgttgtcaatgggaatgtggaattcaataggtggtctttgtt--

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|110706072|gb|EE083646.1|EE083646
EST:     ATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATG                         GTATTCAACTGGTTTAGGAGTCACTGGCGGTAGTGCATTAATCCATGAATT
genomic: ATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATGgtaatttctc ... atgtttgcagGTATTCAACTGGTTTAGGAGTCACTGGCGGTAGTGCATTAATCCATGAATT
EST: gi|110380965|gb|EC946269.1|EC946269
EST:     ATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATG                         GTATTCAACTGGTTTAGGAGTCACTGGCGGTAGTGCATTAATCCATGAATT
genomic: ATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATGgtaatttctc ... atgtttgcagGTATTCAACTGGTTTAGGAGTCACTGGCGGTAGTGCATTAATCCATGAATT
EST: gi|110688899|gb|EE067979.1|EE067979
EST:     ATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATG                         GTATTCAACTGGTTTAGGAGTCACTGGCGGTAGTGCATTAATCCATGAATT
genomic: ATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATGgtaatttctc ... atgtttgcagGTATTCAACTGGTTTAGGAGTCACTGGCGGTAGTGCATTAATCCATGAATT
EST: gi|110401608|gb|EC968223.1|EC968223
EST:     ATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATG                         GTATTCAACTGGTTTAGGAGTCACTGGCGGTAGTGCATTAATCCATGAATT
genomic: ATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATGgtaatttctc ... atgtttgcagGTATTCAACTGGTTTAGGAGTCACTGGCGGTAGTGCATTAATCCATGAATT
EST: gi|110712101|gb|EE089334.1|EE089334
EST:     ATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATG                         GTATTCAACTGGTTTAGGAGTCACTGGCGGTAGTGCATTAATCCATGAATT
genomic: ATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATGgtaatttctc ... atgtttgcagGTATTCAACTGGTTTAGGAGTCACTGGCGGTAGTGCATTAATCCATGAATT
EST: gi|110387531|gb|EC952206.1|EC952206
EST:     ATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATG                         GTATTCAACTGGTTTAGGAGTCACTGGCGGTAGTGCATTAATCCATGAATT
genomic: ATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATGgtaatttctc ... atgtttgcagGTATTCAACTGGTTTAGGAGTCACTGGCGGTAGTGCATTAATCCATGAATT
EST: gi|110375382|gb|EC940363.1|EC940363
EST:     ATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATG                         GTATTCAACTGGTTTAGGAGTCACTGGCGGTAGTGCATTAATCCATGAATT
genomic: ATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATGgtaatttctc ... atgtttgcagGTATTCAACTGGTTTAGGAGTCACTGGCGGTAGTGCATTAATCCATGAATT
EST: gi|110726721|gb|EE102749.1|EE102749
EST:     ATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATG                         GTATTCAACTGGTTTAGGAGTCACTGGCGGTAGTGCATTAATCCATGAATT
genomic: ATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATGgtaatttctc ... atgtttgcagGTATTCAACTGGTTTAGGAGTCACTGGCGGTAGTGCATTAATCCATGAATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATGgtaatttctcattttactaatattggttttttttgcttattattatttaagccttgtcagaggcaatgcagtaagagagttctgatgtgagcacaattca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaggcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagagag