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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcatgctaaatccaaaagagcctctgacttgaaaccctacacaacgaaactaagtagcaaggaaaaattgcagGAAGGACTATTACCAAGAAGGCAGCCATGTTTATGGTGAATTGAATGTAATGGAGGCATTTCGCAAAGCTTTGACCACATGGGCAAGATGGGTTGATGCC

Basic information

species Vitis vinifera
transcript Vv08s0007g06680.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g06680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G28840.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------gtaagtgcatgctaaatccaaaagagcctctga--cttgaaaccctacacaacga-aactaagtag-caaggaaaaattgcagGAAGGACTATTACCAAGAAGGCAGCCATGTTTATGGTGAATTGAATGTAATGGAGGCATTTCGCAAAGCTTTGACCACATGGGCAAGATGGGTTGATGCC
                                                   |     | | || | || ||    |  |   |   ||  || || | ||   |  |||||| | | | | ||||| ||  |||||||||||||||||||| || |||||||| |||| |||| |||||||  ||||||||||||| |  ||| | || || |||   |||||| ||||||||
gtaaatgcattacaatttctcttagatgtgattgcagttctggctctttattctcaaccttcttattctaattctgttttctaagattacaagccaaaaccttgttaactaacttgtccatgaaaatttctagGAAGGACTATTACCAAGAGGGTAGCCATGTCTATGATGAACTGAATGTTTTGGAGGCATTTCGAAGGGCTATAACAACTTGGAGTAGATGGATTGATGCC

upper sequence: Vv08s0007g06680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G16780.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------gtaagtgcatgctaaa---tccaaaagagcctctgacttgaaaccctacacaacga---------aactaagtag-caaggaaaaattgcagGAAGGACTATTACCAAGAAGGCAGCCATGTTTATGGTGAATTGAATGTAATGGAGGCATTTCGCAAAGCTTTGACCACATGGGCAAGATGGGTTGATGCC
                                               |    | ||| || ||   ||  |   |   | ||  ||  |    ||||   | |         |||||| ||| | | | ||||||  |||||||||||||||||||| || |||||||| |||| |||  |||||||  ||||||||||||| |  ||| | || || |||   |||||| | ||||||
gtaaatggaaaaatgcattagaaattcttagatgtgattgtagttctggcttttcattctcaaccttcttatttatattttgttttctatgattacaagtcaagaccttgttaactaactagtccaagtaaaattctagGAAGGACTATTACCAAGAGGGTAGCCATGTCTATGATGAGCTGAATGTTTTGGAGGCATTTCGAAGGGCTATAACAACTTGGAGTAGATGGATCGATGCC

upper sequence: Vv08s0007g06680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G33110.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------------------------------------------gtaagtgcatgctaaatccaaaagagcctctgacttgaaaccctacacaacgaaactaagtagca-aggaaaaattgcagGAAGGACTATTACCAAGAAGGCAGCCATGTTTATGGTGAATTGAATGTAATGGAGGCATTTCGCAAAGCTTTGACCACATGGGCAAGATGGGTTGATGCC
                                                                                       |  ||   | | ||    | | || ||     ||||  |   |  |||   |   ||| | ||  | || || || |||| ||||||||||||||||||| |||||||| |||| |||||| || ||  | ||||||||  | | |||||| || || |||   |  ||||||||||||
gtaattacaatcaacttccctttggagtgattgcaattgacactgttaactgtttcgttatttacctgtatacttatacataattgttttgtaagttccaagattagaggaaccctacccttgtta---tgaacatgaactttaaattgcgcatgacaattttcagGCAGGACTATTACCAAGAAGGTAGCCATGTGTATGCTGAATTAAACGTTCTTGAGGCATTCAGAAGAGCTTTAACGACTTGGAGCAAGTGGGTTGATGCC

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|71861366|gb|DT010421.1|DT010421
EST:     ATCATCTTCAATACAGGACATTGGTGGACTCATGATAAAACTTCCAAAGG                         GAAGGACTATTACCAAGAAGGCAGCCATGTTTATGGTGAATTGAATGTAAG
genomic: ATCATCTTCAATACAGGACATTGGTGGACTCATGATAAAACTTCCAAAGGgtaagtgcat ... aaaattgcagGAAGGACTATTACCAAGAAGGCAGCCATGTTTATGGTGAATTGAATGTAAT
EST: gi|71863474|gb|DT012529.1|DT012529
EST:     ATCATCTTCAATACAGGACATTGGTGGACTCATGATAAAACTTCCAAAGG                         GAAGGACTATTACCAAGAAGGCAGCCATGTTTATGGTGAATTGAATGTAAT
genomic: ATCATCTTCAATACAGGACATTGGTGGACTCATGATAAAACTTCCAAAGGgtaagtgcat ... aaaattgcagGAAGGACTATTACCAAGAAGGCAGCCATGTTTATGGTGAATTGAATGTAAT
EST: gi|71863998|gb|DT013053.1|DT013053
EST:     ATCATCTTCAATACAGGACATTGGTGGACTCATGATAAAACTTCCAAAGG                         GAAGGACTATTACCAAGAAGGCAGCCATGTTTATGGTGAATTGAATGTAAT
genomic: ATCATCTTCAATACAGGACATTGGTGGACTCATGATAAAACTTCCAAAGGgtaagtgcat ... aaaattgcagGAAGGACTATTACCAAGAAGGCAGCCATGTTTATGGTGAATTGAATGTAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcctctgacttgaaaccctacacaacgaaactaagtagcaaggaaaaattgcagGAAGGACTATTACCAAGAAGGCAGCCATGTTTATGGTGAATTGAATGTAATGGAGGCATTTCGCAAAGCTTTGACCACATGGGCAAGATGGGTTGATGCC
   ctctgac  putative branch site (score: 3)
                                            aaaaatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgcatgctaaatccaaaagagcctctgacttgaaaccctacacaacgaaactaagtagcaaggaaaaattgcagGAAGGACTATTACCAAGAAGGCAGCCATGTTTATGGTGAATTGAATGTAATGGAGGCATTTCGCAAAGCTTTGACCACATGGGCAAGATGGGTTGATGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG