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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacattgttgtgtttttttagtgttgactggataaaaattcaaacatagcccacttttatgtgttgatgtgaagcatccattgacttccaagttttacagGTTCTGCGGTTGGATTCAAGTTGGACAGTCTTTTAAAACTCACTGATACACGTGCCTCTAACAGCAAGATGACACTTATGCATTATCTTTGTAAG

Basic information

species Vitis vinifera
transcript Vv17s0000g06640.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA05G00820.1 (Glycine max), 3'ss of exon 12
----------------------------------------------aacattgttgtgtttttttagtgtt---gactggataaaaattcaaac-----atagccca-cttttatgtgttgatgtga------agcatccattgacttccaagttttacagGTTCTGCGGTTGGATTCAAGTTGGACAGTCTTTTAAAACTCACTGATACACGTGCCTCTAACAGCAAGATGACACTTATGCATTATCTTTGTAAG
                                               |  ||| |   | | ||      |    ||  | |   || || |         || | | ||||||| || | |||| |      || ||| | ||  |||  | |||| |||| ||||| ||||||||||||||||| ||||||||||| |||||||| || ||||| |||||||| || |||||||| |||||||||||||| |||
gtaagtccgtaagtctgttatagttatgtcagtttcattctcattatatgttgctagatgtattagacacttgacacatggtgccaactctatttgttagcagtcaatcttttatatgattatgttagatcttagtatcaaatgttttc--atttttgcagGATCTGCTGTTGGATTCAAGTTGGATAGTCTTTTAAAGCTCACTGACACTCGTGCTTCTAACAGTAAAATGACACTGATGCATTATCTTTGCAAG

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA17G11100.1 (Glycine max), 3'ss of exon 14
------------------------------aacattgttgtgtttttttagtgttgactg-gataaaaattcaa-acatagc-ccacttttatgtgttgat-gtgaagcatccat-tgact------------------------tccaagttttacagGTTCTGCGGTTGGATTCAAGTTGGACAGTCTTTTAAAACTCACTGATACACGTGCCTCTAACAGCAAGATGACACTTATGCATTATCTTTGTAAG
                              |   |  || |  || |||  || |   ||   || | | |  | |||| |  |||  | ||| ||||  | || || | |  || ||| |                        |   | |||| |||| ||||| ||||||||||||||||| ||||||||||| |||||||| || ||||| |||||||| || |||||||| |||||||||||||| |||
gtaagtctgtaagtctttggtagttatgtaagtttcattctcattatttgttgctagatgtagtagacacttgacacatggtgccaactctatttgttagtagtcaatcttttatatgattctgttagatcttagtatcaaatgttttcatttttgcagGATCTGCAGTTGGATTCAAGTTGGATAGTCTTTTAAAGCTCACTGACACTCGTGCTTCTAACAGTAAAATGACACTGATGCATTATCTTTGCAAG

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA06G21190.1 (Glycine max), 3'ss of exon 14
aacattgttgtgtttttttagtgt-tgactggataaaaattcaaacatagcccacttttatgtgttgatgtgaagcatccattga---cttccaagttttacagGTTCTGCGGTTGGATTCAAGTTGGACAGTCTTTTAAAACTCACTGATACACGTGCCTCTAACAGCAAGATGACACTTATGCATTATCTTTGTAAG
    |  |||    || ||  | | | | |  | |||  ||      |     |  | | ||  || || |  |       |  |   ||||||  || |||||| ||||| |||||||||||||| || |||||| ||||||| ||||| || ||||| || ||||| || |||||||| ||||||| |||||| |||
----tacttggcccttcttcatatgttagtaaagaaattttatttgtttttttatatatctgatttcatatacaatgagtgtgaaatgcttccactttgtacagGATCTGCTGTTGGATTCAAGTTAGATAGTCTTCTAAAACTAACTGAAACTCGTGCTTCAAACAGTAAAATGACACTCATGCATTTTCTTTGCAAG

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA04G32990.1 (Glycine max), 3'ss of exon 15
------------------------------------------------------------------------------------------------aacattgttgtgttttttta-gtgttgactggataaaaattcaaacatagcccacttttatgtgttgatgtgaagcatccattga---cttccaagttttacagGTTCTGCGGTTGGATTCAAGTTGGACAGTCTTTTAAAACTCACTGATACACGTGCCTCTAACAGCAAGATGACACTTATGCATTATCTTTGTAAG
                                                                                                 | | |  | |||   || |  ||||      |  ||| ||||    |     |  | |       |||   |        |  |    |||||  || |||||| ||||| |||||||||||||| || |||||||||||||| || || || ||||| || ||||| || |||||||| ||||||| |||||| |||
gtatgtctttttttagtaatagaaatgtctttattaccattcacttctggttatgggaaatatatatggtgctacttctgtctatttttaaaattagataatact-tgtcccttcatatgttagt--aaagaaatttcattttttttaaatatctgatctccgataaaatatgagtgtgaaatgtttccactttgtacagGATCTGCTGTTGGATTCAAGTTAGATAGTCTTTTAAAACTAACCGAAACTCGTGCTTCAAACAGTAAAATGACACTAATGCATTTTCTTTGCAAG

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT5G07740.1 (Arabidopsis thaliana), 3'ss of exon 11
---aacattgtt-gtgtttttttagtgttgactggataaaaattcaaacatagcccacttttatgtgttgatgtgaagcatccat---tgac----------ttccaagttttacagGTTCTGCGGTTGGATTCAAGTTGGACAGTCTTTTAAAACTCACTGATACACGTGCCTCTAACAGCAAGATGACACTTATGCATTATCTTTGTAAG
   |  ||| ||  |||| || | ||  |   |   |    |   | |||| ||    | || ||| |  | |   | | |   |   |||            |     || | ||||  |||| ||||||||||||||||||||| | |  ||| | | ||||||||||||  |||||||||||||||| || |||||||||||||| |||
gtaagtattatttatgttattcttgttctacatctttttgcaca-agacattgctagttgttttgtctgtacggataacctttgtggttgatatgatccttgctttgctttctgcagGCGCTGCTGTTGGATTCAAGTTGGACAGTTTATCGAAATTAAGTGATACACGTGCTGCTAACAGCAAGATGACTCTCATGCATTATCTTTGCAAG

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT5G07650.1 (Arabidopsis thaliana), 3'ss of exon 22
----------------------------------------------------aacattgttgtgtttttttagtgttgactggataaaaa--------------ttcaaacatagccca-----cttttatgtgttgatgtgaagcatccattgacttccaagttttacagGTTCTGCGGTTGGATTCAAGTTGGACAGTCTTTTAAAACTCACTGATACACGTGCCTCTAACAGCAAGATGACACTTATGCATTATCTTTGTAAG
                                                    ||||||  ||||||   |  | | | | |  |  |||               || || | | ||        || || ||| ||      | |||     |     |    || |  |||   ||| || |||||||||||| | ||| | || | | | |  || ||| ||||  |||||||||||||||| || |||||||||||||| |||
gtgagtattacattatcttttggctttaagatatctcctaacgcaacacaataacattcgtgtgttcaatgtgagctaagttaacgaaaggaatggcgcctttgtttaatcgttgcattatgtcctcttttgttttatctgaacgcaaatcctttgcactgctttctgtagGCAGTGCCGTGGGATTCAAGTTGAAAAGTTTATTGATATTAAGCGACACATGTGCACCTAACAGCAAGATGACTCTCATGCATTATCTTTGCAAG

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT5G07780.1 (Arabidopsis thaliana), 3'ss of exon 8
----aacattgttgtgtttttttagtgttgactggataaaaattcaaacatagcccacttttatgtgttgatgtgaagcatccattgacttccaagttttacagGTTCTGCGGTTGGATTCAAGTTGGACAGTCTTTTAAAACTCACTGATACACGTGCCTCTAACAGCAAGATGACACTTATGCATTATCTTTGTAAG
    ||    |   |  |||  | |  |    |  |      ||    |  | |  |  ||  | ||| | ||  ||  | || |   |||     || |  |||    || || ||||||| |||||| ||| | || | | | |  || ||||||||   ||||||||||||||| || |||||||||||||| |||
aaagaatggcgcctttgtttcattgcatcatatatacttttgttttgtctgaacgtaaattctt-tgtggttgataaagacccttgttctttt---ttctgaagGCAGGGCAGTGGGATTCAGGTTGGATAGTTTATTGATATTAAGCGAGACACGTGCTGATAACAGCAAGATGACTCTCATGCATTATCTTTGCAAG

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|110700830|gb|EE077830.1|EE077830
EST:     GAAGAAAATTCTTTACCTCGGGAATACATTGAACCAAGGAACTGCAAGGG                         GTTCTGCGGTTGGATTCAAGTTGGACAGTCTTTTAAAACTCACTGATACAC
genomic: GAAGAAAATTCTTTACCTCGGGAATACATTGAACCAAGGAACTGCAAGGGgtgaggactt ... agttttacagGTTCTGCGGTTGGATTCAAGTTGGACAGTCTTTTAAAACTCACTGATACAC
EST: gi|110700821|gb|EE077821.1|EE077821
EST:     GAAGAAAATTCTTTACCTCGGGAATACATTGAACCAAGGAACTGCAAGGG                         GTTCTGCGGTTGGATTCAAGTTGGACAGTCTTTTAAAACTCACTGATACAC
genomic: GAAGAAAATTCTTTACCTCGGGAATACATTGAACCAAGGAACTGCAAGGGgtgaggactt ... agttttacagGTTCTGCGGTTGGATTCAAGTTGGACAGTCTTTTAAAACTCACTGATACAC
EST: gi|110700879|gb|EE077921.1|EE077921
EST:     GAAGAAAATTCTTTACCTCGGGAATACATTGAACCAAGGAACTGCAAGGG                         GTTCTGCGGTTGGATTCAAGTTGGACAGTCTTTTAAAACTCACTGATACAC
genomic: GAAGAAAATTCTTTACCTCGGGAATACATTGAACCAAGGAACTGCAAGGGgtgaggactt ... agttttacagGTTCTGCGGTTGGATTCAAGTTGGACAGTCTTTTAAAACTCACTGATACAC
EST: gi|110700824|gb|EE077817.1|EE077817
EST:     GAAGAAAATTCTTTACCTCGGGAATACATTGAACCAAGGAACTGCAAGGG                         GTTCTGCGGTTGGATTCAAGTTGGACAGTCTTTTAAAACTCACTGATACAC
genomic: GAAGAAAATTCTTTACCTCGGGAATACATTGAACCAAGGAACTGCAAGGGgtgaggactt ... agttttacagGTTCTGCGGTTGGATTCAAGTTGGACAGTCTTTTAAAACTCACTGATACAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagcccacttttatgtgttgatgtgaagcatccattgacttccaagttttacagGTTCTGCGGTTGGATTCAAGTTGGACAGTCTTTTAAAACTCACTGATACACGTGCCTCTAACAGCAAGATGACACTTATGCATTATCTTTGTAAG
                                 cattgac  putative branch site (score: 3)
       acttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacattgttgtgtttttttagtgttgactggataaaaattcaaacatagcccacttttatgtgttgatgtgaagcatccattgacttccaagttttacagGTTCTGCGGTTGGATTCAAGTTGGACAGTCTTTTAAAACTCACTGATACACGTGCCTCTAACAGCAAGATGACACTTATGCATTATCTTTGTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - -tgttgtg
- - - - - - - - - - - - tgactgg
- - - - - - - - - - - - - - - -ataaaaa
- - - - - - - - - - - - - - - - - - - - caaacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acttcca