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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatatattgaattaaacttgtgttcttttcagtttctggtgttgtggttagaaaccttaaaagtgtcattgctttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAG

Basic information

species Vitis vinifera
transcript Vv06s0004g06920.t01
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 21
gttatatattgaattaaacttgtgttcttttcagtttctg--gtgttgtggttagaa-accttaaaagtgtcattgctttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAG
||| |    ||| ||| |  |    |       || |  |   |  | |||||        ||||   |    ||  ||  ||  |||| || ||||| || ||||||||||| ||| ||||||||||||||||||||||  || | ||||||
gttttcacatgacttagatgtaaacttgcccttgtataggccctactatggttgatttgttttaattcttgagtttgttcattacagGCAGTTTTGAGGGCATTATATGCTTATTTTACTGACAGGCCTTTGAAAGAAATTGCAGATATTGAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 32
gttatatattgaattaaacttgtgtt--cttttcagtttctggtgttgtggttagaa-accttaaaagtgtcattgctttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAG
||| |    |||| || |  |    |  |  ||   | |    |  |  ||||         |||   |    ||  ||  ||  |||| || ||||| || ||||||||||| ||| ||||||||||||||||||||||  || | ||||||
gttttcacatgaactagatgtaaacttgcccttttatatgccctcctacggttgacttgttctaattcttgagtttgttcattacagGCTGTTTTGAGGGCATTATATGCTTATTTTACTGACAGGCCTTTGAAAGAAATTGCAGATATTGAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 23
------gttatatattgaattaaacttgtgttcttttc-agtttctggtgttg-tggttagaaaccttaaaagtgtca---ttgctttg--ttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAG-
      |  |    || |  |||| |  || |  |    | ||| |   ||||   |||  ||  | | |   | |     ||| || |  ||| |||| || ||||| ||  |||||||||| |||||||||||||||||||| ||||| || || || ||| 
ttgtacgcaagtcgttaagctaaattcatgcttgtaaagaatttatatggttgactgttctaattcgtgaggtttttcgatttgtttcgcattgcaggCAGTTTTGAGGGCACTATATGCTTATTTTGCTGACAGGCCTTTGAACGAAATTCCGCATATAGAGG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 22
-------gttatatattgaattaaacttgtgttcttttcagtttctggtgtt--gtggttagaaaccttaaaagtgt--cattgcttt---gttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAG
       |  |   ||| |  || | |  || |  |      ||    || |     |||  || || | |   | |  |||   |||    ||| |||| || ||||| ||  |||||||||| ||||||||||| |||||||| ||||| || || || | |
gttgtatgcaagtcattaagctacattcatgcttgtaaagactttatatggttgactgttctaatccgtgaggtttttccatacgtttcacattgcagGCAGTTTTGAGGGCACTATATGCTTATTTTGCTGACAGACCTTTGAACGAAATTCCGCATATAGCG

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|352764397|gb|FQ472754.1|FQ472754
EST:     TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG                         GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
genomic: TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAGgttatatatt ... tttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
EST: gi|71882349|gb|DT031404.1|DT031404
EST:     TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG                         GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
genomic: TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAGgttatatatt ... tttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
EST: gi|352769630|gb|FQ468558.1|FQ468558
EST:     TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG                         GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTT-GAAAGAA
genomic: TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAGgttatatatt ... tttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
EST: gi|71888454|gb|DT037509.1|DT037509
EST:     TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG                         GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
genomic: TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAGgttatatatt ... tttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
EST: gi|352768928|gb|FQ468119.1|FQ468119
EST:     TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCCG                         GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
genomic: TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAGgttatatatt ... tttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
EST: gi|71889378|gb|DT038433.1|DT038433
EST:     TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG                         GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
genomic: TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAGgttatatatt ... tttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
EST: gi|71887336|gb|DT036391.1|DT036391
EST:     TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG                         GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
genomic: TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAGgttatatatt ... tttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
EST: gi|71887343|gb|DT036398.1|DT036398
EST:     TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG                         GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
genomic: TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAGgttatatatt ... tttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
EST: gi|71890359|gb|DT039414.1|DT039414
EST:     TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG                         GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
genomic: TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAGgttatatatt ... tttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
EST: gi|34362375|gb|CF403960.1|CF403960
EST:     TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG                         GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
genomic: TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAGgttatatatt ... tttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
EST: gi|71887083|gb|DT036138.1|DT036138
EST:     TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG                         GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
genomic: TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAGgttatatatt ... tttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
EST: gi|110360631|gb|EC923892.1|EC923892
EST:     TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG                         GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
genomic: TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAGgttatatatt ... tttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
EST: gi|110415443|gb|EC981352.1|EC981352
EST:     TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG                         GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
genomic: TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAGgttatatatt ... tttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
EST: gi|77581485|gb|DV219679.1|DV219679
EST:     TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG                         GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
genomic: TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAGgttatatatt ... tttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
EST: gi|352781433|gb|FQ468277.1|FQ468277
EST:     TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG                         GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTT-GAAAGAA
genomic: TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAGgttatatatt ... tttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
EST: gi|71888451|gb|DT037506.1|DT037506
EST:     TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG                         GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
genomic: TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAGgttatatatt ... tttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
EST: gi|71881182|gb|DT030237.1|DT030237
EST:     TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG                         GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
genomic: TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAGgttatatatt ... tttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
EST: gi|71885715|gb|DT034770.1|DT034770
EST:     TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG                         GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
genomic: TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAGgttatatatt ... tttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
EST: gi|27582400|gb|CB005095.1|CB005095
EST:     TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG                         GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
genomic: TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAGgttatatatt ... tttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
EST: gi|352774206|gb|FQ474729.1|FQ474729
EST:     TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG                         GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTT-GAAAGAA
genomic: TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAGgttatatatt ... tttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA
EST: gi|352768854|gb|FQ468045.1|FQ468045
EST:     TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG                         GCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTT-GAAAGAA
genomic: TCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAGgttatatatt ... tttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagtttctggtgttgtggttagaaaccttaaaagtgtcattgctttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAG
                                         ttgcttt  CT-rich tract
                             ttaaaagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatatattgaattaaacttgtgttcttttcagtttctggtgttgtggttagaaaccttaaaagtgtcattgctttgttgtagGCGGTATTGAGAGCGTTATATGCTTACTTTGCTGACAGGCCTTTGAAAGAAATCCCACACATTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA