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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgctttagtattgtgattgcgcatttgcatttgcattttctgattgcaggtgccataaaaatgaatttctgaatgttggttctttctgttgacttgcagTCACTAATGATTGCTTCGATTCCTAATATAATAGGATGGCTTGCAATATCATTTGCCCAA

Basic information

species Vitis vinifera
transcript Vv04s0023g01860.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g01860.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G06280.1 (Glycine max), 3'ss of exon 3
--------gtgctttagt-attgtgattgcgcattt-gcatttgcattttctgattgcaggt----gccataaaaatgaatttctgaatgttggttctttctgttgac-ttgcagTCACTAATGATTGCTTCGATTCCTAATATAATAGGATGGCTTGCAATATCATTTGCCCAA
         || |||| | |||   | ||    ||| | | |     ||||  |   |||          | || |   |||  ||| | ||||    || | |  |  ||||||||| | ||||||||| ||||||| ||||||||||| |||||||| || || |||||| ||
gtattttattgatttatttatttgtagtgtatgttttgaagtcagtctttcaaaggacagtctatgaatgtgaagagtgattggtgatttttggcgtgttttttgaatgttgcagTCATTGATGATTGCTGCGATTCCCAATATAATAGGGTGGCTTGCTATTTCTTTTGCCAAA

upper sequence: Vv04s0023g01860.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G16220.1 (Glycine max), 3'ss of exon 5
--------gtgctttagt-attgtgattgcgcatttgcatttgcattttctgattgcaggtgccataaaaatgaa------tttctgaatgttggt-tctttctgttgac-ttgcagTCACTAATGATTGCTTCGATTCCTAATATAATAGGATGGCTTGCAATATCATTTGCCCAA
         || |||| | |||   | |||   |||  |  |  || ||   |  | |  | | || ||  ||||      ||  ||| | ||||  | ||| | || |  ||||||||| | ||||||||| |||| || ||||||||||| |||||||| || || |||||| ||
gtattttattgatttattcatttgtagtgcatgttttgaagtcaatctttcaaaggaaaat-ctatgaatgtgaagagtgattggtgatttttggcgtgttttttttaatgttgcagTCATTGATGATTGCTGCGATCCCCAATATAATAGGGTGGCTTGCTATTTCTTTTGCCAAA

upper sequence: Vv04s0023g01860.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G25310.1 (Glycine max), 3'ss of exon 3
---------gtgctttagtattgtgattgcgcatttgcatttgcattttctgattgcaggtgc-----cataaaaatgaatttctgaatgttggttctttctgttgac-ttgcagTCACTAATGATTGCTTCGATTCCTAATATAATAGGATGGCTTGCAATATCATTTGCCCAA
          |  ||    |||   | |||   |||  |  |   | ||   |  | |  |         | || |   |||  ||| | ||||    || | |  |  ||||||||| | ||||||||| |||| || ||||||||||| |||||||| || || |||||| ||
gtattttatttatttattcatttgtagtgcatgttttgaagtcagtctttcaaaggaaaatttatgaatgtgaagagtgattgatgatttttggcgtgttttttgaatgttgcagTCATTGATGATTGCTGCGATCCCCAATATAATAGGGTGGCTTGCTATTTCTTTTGCCAAA

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|71885483|gb|DT034538.1|DT034538
EST:     TTGGGGCAATAGCCAGTGGTCAGATTGCGGAATACATCGGCAGGAAAGGG                         TCACTAATGATTGCTTCGATTCCTAATATAATAGGATGGCTTGCAATATCA
genomic: TTGGGGCAATAGCCAGTGGTCAGATTGCGGAATACATCGGCAGGAAAGGGgtatgatcga ... tgacttgcagTCACTAATGATTGCTTCGATTCCTAATATAATAGGATGGCTTGCAATATCA
EST: gi|161706203|gb|FC054967.1|FC054967
EST:     TTGGGGCAATAGCCAGTGGTCAGATTGCGGAATACATCGGCAGGAAAGGG                         TCACTAATGATTGCTTCGATTCCTAATATAATAGGATGGCTTGCAATATCA
genomic: TTGGGGCAATAGCCAGTGGTCAGATTGCGGAATACATCGGCAGGAAAGGGgtatgatcga ... tgacttgcagTCACTAATGATTGCTTCGATTCCTAATATAATAGGATGGCTTGCAATATCA
EST: gi|71882686|gb|DT031741.1|DT031741
EST:     TTGGGGCAATAGCCAGTGGTCAGATTGCGGAATACATCGGCAGGAAAGGG                         TCACTAATGATTGCTTCGATTCCTAATATAATAGGATGGCTTGCAATATCA
genomic: TTGGGGCAATAGCCAGTGGTCAGATTGCGGAATACATCGGCAGGAAAGGGgtatgatcga ... tgacttgcagTCACTAATGATTGCTTCGATTCCTAATATAATAGGATGGCTTGCAATATCA
EST: gi|71885656|gb|DT034711.1|DT034711
EST:     TTGGGGCAATAGCCAGTGGTCAGATTGCGGAATACATCGGCAGGAAAGGG                         TCACTAATGATTGCTTCGATTCCTAATATAATAGGATGGCTTGCAATATCA
genomic: TTGGGGCAATAGCCAGTGGTCAGATTGCGGAATACATCGGCAGGAAAGGGgtatgatcga ... tgacttgcagTCACTAATGATTGCTTCGATTCCTAATATAATAGGATGGCTTGCAATATCA
EST: gi|71882039|gb|DT031094.1|DT031094
EST:     TTGGGGCAATAGCCAGTGGTCAGATTGCGGAATACATCGGCAGGAAAGGG                         TCACTAATGATTGCTTCGATTCCTAATATAATAGGATGGCTTGCAATATCA
genomic: TTGGGGCAATAGCCAGTGGTCAGATTGCGGAATACATCGGCAGGAAAGGGgtatgatcga ... tgacttgcagTCACTAATGATTGCTTCGATTCCTAATATAATAGGATGGCTTGCAATATCA
EST: gi|71882706|gb|DT031761.1|DT031761
EST:     TTGGGGCAATAGCCAGTGGTCAGATTGCGGAATACATCGGCAGGAAAGGG                         TCACTAATGATTGCTTCGATTCCTAATATAATAGGATGGCTTGCAATATCA
genomic: TTGGGGCAATAGCCAGTGGTCAGATTGCGGAATACATCGGCAGGAAAGGGgtatgatcga ... tgacttgcagTCACTAATGATTGCTTCGATTCCTAATATAATAGGATGGCTTGCAATATCA
EST: gi|71889871|gb|DT038926.1|DT038926
EST:     TTGGGGCAATAGCCAGTGGTCAGATTGCGGAATACATCGGCAGGAAAGGG                         TCACTAATGATTGCTTCGATTCCTAATATAATAGGATGGCTTGCAATATCA
genomic: TTGGGGCAATAGCCAGTGGTCAGATTGCGGAATACATCGGCAGGAAAGGGgtatgatcga ... tgacttgcagTCACTAATGATTGCTTCGATTCCTAATATAATAGGATGGCTTGCAATATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaggtgccataaaaatgaatttctgaatgttggttctttctgttgacttgcagTCACTAATGATTGCTTCGATTCCTAATATAATAGGATGGCTTGCAATATCATTTGCCCAA
                                          tgttgac  putative branch site (score: 3)
                                   ttctttctgtt  CT-rich tract
          ataaaaatgaatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctttagtattgtgattgcgcatttgcatttgcattttctgattgcaggtgccataaaaatgaatttctgaatgttggttctttctgttgacttgcagTCACTAATGATTGCTTCGATTCCTAATATAATAGGATGGCTTGCAATATCATTTGCCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - tgattgc
- - - - - - - - - - -gcatttg
- - - - - - - - - - - catttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ataaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaatg