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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTGACAGGAAACTGAAGAACACATACGATCATCTTCTTTTCAGCAGgtcctgctcatcttttgaaataaattttatcccttaaagtcagcttgggcatgtagaagaagtatattaatgcttttgtttacaaaatctgctcatctca...

Basic information

species Vitis vinifera
transcript Vv09s0002g00100.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00100.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: LOC_Os03g08570.1 (Oryza sativa), 5'ss of exon 11
GTTTGACAGGAAACTGAAGAACACATACGATCATCTTCTTTTCAGCAGgtcctgctcatcttttgaaataaattttatc-ccttaaagtcagcttgggcatgtagaagaagtatattaatgcttttgtttacaaaatctgctcatctca--------------------------------------------------------------------------------------------------
|||||| || ||||||||||||||||| || || ||||||||||||||||    ||  |  ||    || | ||||     | |        ||   |||| |       |  ||| | || |||  |  || ||| |   |  | |                                                                                                    
GTTTGATAGAAAACTGAAGAACACATATGACCACCTTCTTTTCAGCAGgtgtctcttctaattcctcatcagttttgctgtcctttcactgcctcatgcatttgctctgtgc-tatgactggttt-atgaactaaaacgatttgtattgcccaaattgggcacattctatcctgattttgtatacattcttgattaataccaaatatcatatgtcccatgtattgatcttgttcccttttctttcag

upper sequence: Vv09s0002g00100.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GRMZM2G410515_T01 (Zea mays), 5'ss of exon 11
GTTTGACAGGAAACTGAAGAACACATACGATCATCTTCTTTTCAGCAGgtcctgctcatcttttgaaataaattttatcccttaaagtcag-cttgggcatg---tagaagaagtatattaatgcttttgtttacaaaatctgctcatct-ca-----------------------------------
||||||||| |||||||| |||||||| || || |||||||||||||||| |  ||| |   |  |  |||    | |    |  | | |  |||||  |||   |   |  |  || ||     |  | ||         ||  ||||| ||                                   
GTTTGACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAGgtacctctcctggctgtagttaatgcatttattgtgcaataaatcttggttatgattttttatcaacatgttttatgtgctattctggttgaatgtccatctgcagtattaaataccatgtctttttcttttcttttcag

upper sequence: Vv09s0002g00100.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA11G36810.1 (Glycine max), 5'ss of exon 10
GTTTGACAGGAAACTGAAGAACACATACGATCATCTTCTTTTCAGCAGgtcctgctcatcttttgaaataaattttatcccttaaagtcagcttgggcatgtagaagaagtatattaatgcttttgtttacaaaatctgctcatctca-
||||||||| ||||||||||||||||| ||||| ||||| || |||||||| | | ||   ||||||| |  | | ||  ||  |||  |         |||  |   | | |  |  |   ||| | |      |     ||| |   
GTTTGACAGAAAACTGAAGAACACATATGATCACCTTCTCTTTAGCAGgtcttccacaaactttgaaacacctgtaatgtctggaagggatagaaatgctgttcatttaatgt-ctgttttgtttttctgatgcgtagatgcatattga

upper sequence: Vv09s0002g00100.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA18G00720.2 (Glycine max), 5'ss of exon 6
GTTTGACAGGAAACTGAAGAACACATACGATCATCTTCTTTTCAGCAGgtcctgctcatcttttgaaataaattttatcccttaaagtcagcttgggcatgtagaagaagtatattaatgcttttgtttacaaaatctgctcatctca-
||||||||| ||||||||||||||||| ||||| ||||| || |||||||| | ||||   ||||||| |  | | ||  ||  |||  |         |||  |   | |    |  |   ||| | |   | ||      || |   
GTTTGACAGAAAACTGAAGAACACATATGATCACCTTCTCTTTAGCAGgtcttcctcaaactttgaaacacctgtaatgtctggaagggatagaaattctgttcatttaatgc-ctgttttgtttttctgatacatagatgtatattga

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|110392879|gb|EC957437.1|EC957437
EST:     GTTTGACAGGAAACTGAAGAACACATACGATCATCTTCTTTTCAGCAG                         AAGTCCCCTTCTGAGTGTGTATGCTGACATGTCCGTAACATGTAAG
genomic: GTTTGACAGGAAACTGAAGAACACATACGATCATCTTCTTTTCAGCAGgtcctgctca ... ccccatgcagAAGTCCCCTTCTGAGTGTGTATGCTGACATGTCCGTAACATGTAAG




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTGACAGGAAACTGAAGAACACATACGATCATCTTCTTTTCAGCAGgtcctgctcatcttttgaaataaattttatcccttaaagtcagcttgggcatgtagaagaagtatattaatgcttttgtttacaaaatctgctcatctca

- - - - - -  CTGAAG
- - - - - - - TGAAGA
- - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaagaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacaaaa