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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatatggttcattatggttattttctcttttgatcttcctcagcagttaccactgcattgccataaaactgggtggtgatctgttcttttctttgcttcttttcatattttctagGATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGACAGGAATCTTGCAGAGAACACTCTAAAGGCAATTAAGAAGATTGACAAAG

Basic information

species Vitis vinifera
transcript Vv08s0007g03850.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g03850.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G19410.2 (Glycine max), 3'ss of exon 1
gtaaatatggttcattatggttat-tttctcttttgatcttcctcagcagttaccactgcattgccataaaactgggtggtgatctgttcttttctttgcttcttttcatatt-ttctagGATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGACAGGAATCTTGCAGAGAACACTCTAAAGGCAATTAAGAAGATTGACAAAG
||||||    || | | || ||   ||||| |   | ||||   ||   |||        | | |  |    || |||   ||   | |      ||      ||| |||  | ||  |||| |||||||||||||||||||||||||| || ||||||||||||||||||||||||||||| |||||    || ||||| |||   |||||||| ||| 
gtaaat-caattaactttgtttccctttctgtcagggtcttatacatgtgttgtt----tactactgt----cttggtttggagaagcttcagcattattacatttacatgctgtttcagGACTCAACCTTTGAGTTTGAGAGAAAGCGAAACAGGCCAGAGAGATATGACAGGAATCTTGCTGAGAATGTCCTCAAGGCCATTCCAAAGATTGATAAAA

upper sequence: Vv08s0007g03850.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G09780.1 (Glycine max), 3'ss of exon 4
gtaaatatggttcattatggttattttctcttttgatcttcctcagcagttaccactgcattgccataaaactgggtggtgatctgttcttttctttgcttcttttcatattttctagGATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGACAGGAATCTTGCAGAGAACACTCTAAAGGCAATTAAGAAGATTGACAAAG---------------
                                                                                                   || | ||  | ||||  |||| ||||| |||||||||||||||||| | |||||||| || |||||||||||||||||||| |||||    || ||||| |||   |||||||| ||                 
--------------------------------------------------------------------------------------------------gttatatttttgtttt--aggactcaacttttgagTTTGAGAGAAAGAGAAATAGGCCTGAAAGATATGACAGGAATCTTGCGGAGAATGTCCTCAAGGCCATTCCTAAGATTGATAAGATCAGAGTCTCGAGGG

upper sequence: Vv08s0007g03850.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G05270.1 (Glycine max), 3'ss of exon 3
gtaaatatggttcattatggttattttctcttttgatcttcctcagcagttaccactgcattgccataaaactgggtggtgatctgttcttttctttgcttcttttcatattttctagGATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGACAGGAATCTTGCAGAGAACACTCTAAAGGCAATTAAGAAGATTGACAAAG
                        |      || ||| |||   | | | |   | |  | |  | |  |  || |               |||   |||  | |   | | || ||||| ||||||||||||||||||||||| || || ||||| || |||||||||||||||||||| |||||    || ||||| |||   |||||||| ||| 
-----------------------gtaatgacttggatattcgatacctggt--taatttaatttccttgacttgagaaac-----------ttcacagctgttatatttttgttttagGACTCAACCTTTGAGTTTGAGAGAAAACGAAACAGGCCTGAAAGATATGACAGGAATCTTGCGGAGAATGTCCTGAAGGCCATTCCTAAGATTGATAAAA

upper sequence: Vv08s0007g03850.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G09090.1 (Glycine max), 3'ss of exon 3
gtaaatatggttcattatggttat-tttctcttttgatcttcctcagcagttaccactgcattgccataaaactgggtggtgatctgttcttttctttgcttcttttcatatt-ttctagGATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGACAGGAATCTTGCAGAGAACACTCTAAAGGCAATTAAGAAGATTGACAAAG
||||||    || | | || ||   ||||| |  || ||||   ||   |||        | | |  |    || |||   ||   | |      ||    | ||| |||  | ||  |||| || ||||||||||||||||||||||| || || || ||||||||||||||||||||||| |||||    || ||||| |||   |||||||| ||| 
gtaaatgaaattaactttgtttgcctttctgtcatggtcttatacatgtgttgtt----tactactgt----cttggtttggagaagcttcagcattattatatttacatgctgtttcagGACTCGACCTTTGAGTTTGAGAGAAAGCGAAACAGACCTGAGAGATATGACAGGAATCTTGCTGAGAATGTCCTCAAGGCCATTCCAAAGATTGATAAAA

upper sequence: Vv08s0007g03850.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G30680.2 (Glycine max), 3'ss of exon 3
gtaaatatggttcattatggttattttctcttttgatcttcctcagcagttaccactgcattgccataaaactgggtggtgatctgttcttttctttgcttcttttcatattttctagGATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGACAGGAATCTTGCAGAGAACACTCTAAAGGCAATTAAGAAGATTGACAAAG
                        |   |  || ||| |     | | | |   | |  |||||| | |   ||||               |||   |||  | |   | | || ||||| ||||| |||||||||||||||||| | || ||||| || |||||||||||||||||||| |||||    || ||||| |||   |||||||| ||  
-----------------------gtaattacttggatatcagatacctgct-taatttaattgccttgat-ttgggcaaa----------cttcacagctgttatatttttgttttagGACTCAACTTTTGAGTTTGAGAGAAAGAGAAACAGGCCTGAAAGATATGACAGGAATCTTGCGGAGAATGTCCTCAAGGCCATTCCTAAGATTGATAAGA

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|26262309|gb|CA813372.1|CA813372
EST:     TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAG                         GATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
genomic: TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAGgtaaatatgg ... tattttctagGATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
EST: gi|110401381|gb|EC967989.1|EC967989
EST:     TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAG                         GATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
genomic: TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAGgtaaatatgg ... tattttctagGATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
EST: gi|71876723|gb|DT025778.1|DT025778
EST:     TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAG                         GATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
genomic: TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAGgtaaatatgg ... tattttctagGATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
EST: gi|71890437|gb|DT039492.1|DT039492
EST:     TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAG                         GATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
genomic: TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAGgtaaatatgg ... tattttctagGATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
EST: gi|110418414|gb|EC984567.1|EC984567
EST:     TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAG                         GATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
genomic: TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAGgtaaatatgg ... tattttctagGATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
EST: gi|110400284|gb|EC966842.1|EC966842
EST:     TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAG                         GATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
genomic: TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAGgtaaatatgg ... tattttctagGATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
EST: gi|351028971|gb|FQ434972.1|FQ434972
EST:     TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAG                         GATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
genomic: TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAGgtaaatatgg ... tattttctagGATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
EST: gi|77587193|gb|DV222731.1|DV222731
EST:     TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAG                         GATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
genomic: TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAGgtaaatatgg ... tattttctagGATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
EST: gi|71882405|gb|DT031460.1|DT031460
EST:     TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAG                         GATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
genomic: TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAGgtaaatatgg ... tattttctagGATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
EST: gi|71882718|gb|DT031773.1|DT031773
EST:     TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAG                         GATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
genomic: TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAGgtaaatatgg ... tattttctagGATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
EST: gi|71881638|gb|DT030693.1|DT030693
EST:     TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAG                         GATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
genomic: TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAGgtaaatatgg ... tattttctagGATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
EST: gi|71868891|gb|DT017946.1|DT017946
EST:     TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAG                         GATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
genomic: TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAGgtaaatatgg ... tattttctagGATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
EST: gi|71866642|gb|DT015697.1|DT015697
EST:     TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAG                         GATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
genomic: TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAGgtaaatatgg ... tattttctagGATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
EST: gi|110375172|gb|EC940133.1|EC940133
EST:     TAAAATGGACAAAGGCTTACAGGCGGTTGCATGGAAAGGATATGACACAG                         GATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
genomic: TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAGgtaaatatgg ... tattttctagGATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
EST: gi|349823493|gb|FQ414903.1|FQ414903
EST:     TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAG                         GATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC
genomic: TAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAAAGGATATGACACAGgtaaatatgg ... tattttctagGATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccataaaactgggtggtgatctgttcttttctttgcttcttttcatattttctagGATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGACAGGAATCTTGCAGAGAACACTCTAAAGGCAATTAAGAAGATTGACAAAG
                   tctgttcttttctttg  CT-rich tract
                                    ttcttttcatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatatggttcattatggttattttctcttttgatcttcctcagcagttaccactgcattgccataaaactgggtggtgatctgttcttttctttgcttcttttcatattttctagGATTCAACCTTTGAGTTTGAGAGAAAGCGGAATAGGCCAGAGAGATATGACAGGAATCTTGCAGAGAACACTCTAAAGGCAATTAAGAAGATTGACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG