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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgggttgttattgaatttgtcatttcattaacaaggatctttatgctggaaagcatgttatagttcagttattgttaaaccggaatctctaat...

Basic information

species Vitis vinifera
transcript Vv06s0004g04800.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04800.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os01g62420.5 (Oryza sativa), 5'ss of exon 5
AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgggttgttattgaatttgtcatttcattaacaaggatctttatgctggaaagcatgttatagttcagttattgttaaaccggaatctctaat-----------------------------------------------------------------------------
| ||  | ||    |||   ||| |||||||||| |||||||| |||||||||||||| || || ||||||||||||||||||||||| ||||| |||   ||       ||  | | ||        |||| || |   | ||   |    |      | |||   || | || | |        || ||||||                                                                             
AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttctaacatagagcaattacatcacgattagcatgttccctt-cacatttatctgcctcataaaccaat-atgggttttttcctatatctaatgtctttcttgaccgatgcctggtacctgattctgcaattctgttcattcgaattatttgaaatatgcatgacattag

upper sequence: Vv06s0004g04800.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G146206_T02 (Zea mays), 5'ss of exon 6
AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtct----------gggttgttattgaat-------ttgtcatttcattaacaaggatctttatgctggaaagcatgttatagttcagttat-tgttaa-accggaatctctaat----------------------------------------
||||| | |||   |||   |||||||| ||||| |||||||| |||||||| ||||| || || || |||||||| ||||||||||| ||||| |||   ||          | |   | | || ||       ||  ||  || |  | |      |  ||  ||     |  | |||  || | |||  | |  | | |    |   ||||                                        
AAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGGCTATTGGTACCGGCAAAGTTGCAACTCCTGCTCAGGCTCAGGAGgtatagcttcttatgcacgagcaataactgcatgattttttttccacatcgtagatagttgcttccat-ttgtgtctcccggtattcttgatttacatatcgatatcaatgttcttaattctgctttgtgtatcatttgagatgtgcatggtattgtag

upper sequence: Vv06s0004g04800.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA13G41120.1 (Glycine max), 5'ss of exon 6
AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgggt---tgttattgaatttgtcatttcattaacaaggatctttatgctggaaagcatgttatagttcagt-tattgttaaaccggaatctctaat
  ||| | ||||  ||||| ||| | |||||||| ||||| || |||||||||||||| || |||||||||||||| ||||||||||| || || ||| |  ||  |   | || || |   |   |||   ||    |  |  |    ||    | |    ||||| ||  |  | || ||   |    || |     
CTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCAACTCCTGCTCAGGCTCAAGAGgtatgcttgtctatattttgttaacagtactattgttttggtgaaaacttgctcgccattatggtgattatatttttgaattttattgttctcacatatt----

upper sequence: Vv06s0004g04800.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA15G04290.1 (Glycine max), 5'ss of exon 6
AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgggt---tgttattgaatttgtcatttcattaacaaggatctttatgctggaaagcatgttatagttcagttattgttaaaccggaatctctaat
  ||| | ||||  ||||| ||| | |||||||| || || || |||||||||||||| || ||||||||||| || ||||||||||| || || ||| |  ||  |   | || || |   |   |||   ||    |  |  |   |||    | || |||| |  ||  ||   ||| ||         ||| | 
CTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTACGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCTACTCCTGCTCAGGCTCAAGAGgtatgcttgcctatattttgttaacagtacaattgttttggtgaaaacttgcttgccactatgc-tgttttttttttgtg--tgtgaattttattgttctcac

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|110415564|gb|EC981483.1|EC981483
EST:     TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA                         GTTCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
genomic: TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgg ... tatgtgtcagGTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
EST: gi|351028511|gb|FQ444792.1|FQ444792
EST:     TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA                         GTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
genomic: TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgg ... tatgtgtcagGTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
EST: gi|30129525|gb|CB914864.1|CB914864
EST:     TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA                         GTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAG
genomic: TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgg ... tatgtgtcagGTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAG
EST: gi|110389346|gb|EC954175.1|EC954175
EST:     TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA                         GTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
genomic: TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgg ... tatgtgtcagGTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
EST: gi|22015534|gb|BQ800568.1|BQ800568
EST:     TTTGGCCCATTGGCACTGGGAAGGTTGCAACCCCTGCTCAGGCACAGGAA                         GTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
genomic: TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgg ... tatgtgtcagGTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
EST: gi|34551021|gb|CF519221.1|CF519221
EST:     TTTGGGCTATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA                         GTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
genomic: TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgg ... tatgtgtcagGTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
EST: gi|33409412|gb|CF215039.1|CF215039
EST:     TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA                         GTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
genomic: TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgg ... tatgtgtcagGTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
EST: gi|110378426|gb|EC943557.1|EC943557
EST:     TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA                         GTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
genomic: TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgg ... tatgtgtcagGTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
EST: gi|110692722|gb|EE068329.1|EE068329
EST:     TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA                         GTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
genomic: TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgg ... tatgtgtcagGTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
EST: gi|110395870|gb|EC961544.1|EC961544
EST:     TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA                         GTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
genomic: TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgg ... tatgtgtcagGTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
EST: gi|349826936|gb|FQ419027.1|FQ419027
EST:     TTTGGGCCATTGGCACTGGAAAGGTTGCAGCCCCTGCTCAGGCACAGGAA                         GTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
genomic: TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgg ... tatgtgtcagGTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
EST: gi|110726667|gb|EE102647.1|EE102647
EST:     TTTGGGCCAATGGCACTCGAAAGGTTGCCACCCCTGCTCAGGCAGAGAAA                         GTTCAGTGTGAA
genomic: TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgg ... tatgtgtcagGTCCATTGTGAA
EST: gi|71871008|gb|DT020063.1|DT020063
EST:     TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA                         GTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
genomic: TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgg ... tatgtgtcagGTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
EST: gi|110404715|gb|EC970203.1|EC970203
EST:     TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA                         GTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
genomic: TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgg ... tatgtgtcagGTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
EST: gi|161720486|gb|FC070598.1|FC070598
EST:     TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA                         GTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
genomic: TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgg ... tatgtgtcagGTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
EST: gi|32461078|gb|CD802252.1|CD802252
EST:     AAAGGTTGCAACCCCTGCTCAGGCACAGGAA                         GTCCATTGTGTGAATTGAGGAAATGGCTTCATGATAATGCGGGAGATGAAG
genomic: AAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgg ... tatgtgtcagGTCCA-T-TGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAG
EST: gi|161714171|gb|FC062916.1|FC062916
EST:     TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA                         GTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGA-GTT
genomic: TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgg ... tatgtgtcagGTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
EST: gi|110364963|gb|EC928597.1|EC928597
EST:     TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA                         GTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
genomic: TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgg ... tatgtgtcagGTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
EST: gi|110411583|gb|EC977303.1|EC977303
EST:     TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA                         GTTCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
genomic: TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgg ... tatgtgtcagGTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
EST: gi|33409496|gb|CF215123.1|CF215123
EST:     TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA                         GTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT
genomic: TTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgg ... tatgtgtcagGTCCATTGTGAATTGAGGAAATGGCTTCATGATAATGCTGGAGATGAAGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgggttgttattgaatttgtcatttcattaacaaggatctttatgctggaaagcatgttatagttcagttattgttaaaccggaatctctaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaagga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaagca