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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAACTACAGGGCTGTTCGTTGCCTTATATTAACAACATTGAACAGTGAGAGAAGCTCAATTCTTATAGAGCATTTCATGGAGACTGGCCAAGgtgacctacatgatcttgctcttctatagcctgctggtttttataggtccaaaactatttgtgaattaacattcttcacttaactattcatagaaactga...

Basic information

species Vitis vinifera
transcript Vv01s0011g00500.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g00500.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA01G07190.2 (Glycine max), 5'ss of exon 11
CAAACTACAGGGCTGTTCGTTGCCTTATATTAACAACATTGAACAGTGAGAGAAGCTCAATTCTTATAGAGCATTTCATGGAGACTGGCCAAGgtgacctacatgatcttgctcttctatagcctgctggtttttataggtccaaaactatttgtg-aattaacattcttcacttaactattcatagaa-actga
|||||||| | |||||||| ||||||  ||| |   |||| |||  ||| || ||||| |||||| |  ||||||||||||||||||||||||||    |   || |     |||||  |       |      ||||  |   |   |  |  |  |||     || || |  | || ||  | ||   ||  |
CAAACTACCGAGCTGTTCGGTGCCTTGCATTGAACTCATTAAACCCTGAAAGGAGCTCTATTCTTTTGCAGCATTTCATGGAGACTGGCCAAGgta--ttgtctgtttccattcttcattccttatatccacaatatacctttgagtttgataatctaatctgtttttttaatcttaccataaacaggccacata

upper sequence: Vv01s0011g00500.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA02G13010.1 (Glycine max), 5'ss of exon 7
CAAACTACAGGGCTGTTCGTTGCCTTATATTAACAACATTGAACAGTGAGAGAAGCTCAATTCTTATAGAGCATTTCATGGAGACTGGCCAAGgtgacctacat-gatcttgctcttctatagcctgctggttttt---ataggtccaaaactatttgtgaattaacattcttcacttaactattcatagaaactga
                                                     ||||| |||||| |  ||||||||||||||||||||||||||    |   |  ||||   ||   | |    ||||  | |     |||  ||    ||  ||  | |  ||  | || |     || ||     ||| | || 
----------------------------------------------------GAGCTCTATTCTTTTTCAGCATTTCATGGAGACTGGCCAAGgtattgtctgttaatctgtttccattcttcattgcttatatccacaatatatctttgacgtttgataatctattactcctggtggaattac----agacattgt
















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|71879732|gb|DT028787.1|DT028787
EST:     CAGTGAGAGAAGCTCAATTCTTATAGAGCATTTCATGGAGACTGGCCAAG                         TTTTATCCCCACAAGAGGTCTCTAAGATGGAACATGTTCTACCTTTATGGG
genomic: CAGTGAGAGAAGCTCAATTCTTATAGAGCATTTCATGGAGACTGGCCAAGgtgacctaca ... ttgtttccagTTTTATCCCCACAAGAGGTCTCTAAGATGGAACATGTTCTACCTTTATGGG
EST: gi|71877796|gb|DT026851.1|DT026851
EST:     CAGTGAGAGAAGCTCAATTCTTATAGAGCATTTCATGGAGACTGGCCAAG                         TTTTATCCCCACAAGAGGTCTCTAAGATGGAACATGTTCTACCTTTATGGG
genomic: CAGTGAGAGAAGCTCAATTCTTATAGAGCATTTCATGGAGACTGGCCAAGgtgacctaca ... ttgtttccagTTTTATCCCCACAAGAGGTCTCTAAGATGGAACATGTTCTACCTTTATGGG
EST: gi|71878342|gb|DT027397.1|DT027397
EST:     CAGTGAGAGAAGCTCAATTCTTATAGAGCATTTCATGGAGACTGGCCAAG                         TTTTATCCCCACAAGAGGTCTCTAAGATGGAACATGTTCTACCTTTATGGG
genomic: CAGTGAGAGAAGCTCAATTCTTATAGAGCATTTCATGGAGACTGGCCAAGgtgacctaca ... ttgtttccagTTTTATCCCCACAAGAGGTCTCTAAGATGGAACATGTTCTACCTTTATGGG
EST: gi|71878071|gb|DT027126.1|DT027126
EST:     CAGTGAGAGAAGCTCAATTCTTATAGAGCATTTCATGGAGACTGGCCAAG                         TTTTATCCCCACAAGAGGTCTCTAAGATGGAACATGTTCTACCTTTATGGG
genomic: CAGTGAGAGAAGCTCAATTCTTATAGAGCATTTCATGGAGACTGGCCAAGgtgacctaca ... ttgtttccagTTTTATCCCCACAAGAGGTCTCTAAGATGGAACATGTTCTACCTTTATGGG
EST: gi|71879077|gb|DT028132.1|DT028132
EST:     CAGTGAGAGAAGCTCAATTCTTATAGAGCATTTCATGGAGACTGGCCAAG                         TTTTATCCCCACAAGAGGTCTCTAAGATGGAACATGTTCTACCTTTATGGG
genomic: CAGTGAGAGAAGCTCAATTCTTATAGAGCATTTCATGGAGACTGGCCAAGgtgacctaca ... ttgtttccagTTTTATCCCCACAAGAGGTCTCTAAGATGGAACATGTTCTACCTTTATGGG
EST: gi|71880088|gb|DT029143.1|DT029143
EST:     CAGTGAGAGAAGCTCAATTCTTATAGAGCATTTCATGGAGACTGGCCAAG                         TTTTATCCCCACAAGAGGTCTCTAAGATGGAACATGTTCTACCTTTATGGG
genomic: CAGTGAGAGAAGCTCAATTCTTATAGAGCATTTCATGGAGACTGGCCAAGgtgacctaca ... ttgtttccagTTTTATCCCCACAAGAGGTCTCTAAGATGGAACATGTTCTACCTTTATGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAACTACAGGGCTGTTCGTTGCCTTATATTAACAACATTGAACAGTGAGAGAAGCTCAATTCTTATAGAGCATTTCATGGAGACTGGCCAAGgtgacctacatgatcttgctcttctatagcctgctggtttttataggtccaaaactatttgtgaattaacattcttcacttaactattcatagaaactga

- - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atagaaa