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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttatttgttttatctttatttttcatccttgcttttagttcttcagtttaatctcaattggatgatgggaatattggttggatttgtgtttgcccgcagCTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTGCTCTTACGGTAGAGCCCAAAGCCCCGGAGTTTACGCCTTTAGAT

Basic information

species Vitis vinifera
transcript Vv01s0026g01720.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g01720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G16200.1 (Glycine max), 3'ss of exon 1
--tttatttgttttatctttatttttcatccttgcttttagttcttcagtttaatc---tcaattggatgatgggaatattggttggatttgtgtttgcccgcagCTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTGCTCTTACGGTAGAGCCCAAAGCCCCGGAGTTTACGCCTTTAGAT
  |||     ||| |     |      ||  ||  |  || || |    | |  |    | |  |   |  | ||  |  |||||  || ||||||     | |||||||| ||||||||||| ||||||| | || || ||||||||||| ||||| |||||  |    || |   |||| || || | |||  | |||
ggttttccaatttaaaaacaaaaaactatttttaatagtacttatgtgttcttgttgtgtaatgtacttatttggttttctggtttaatgtgtgttcagtTGGAGCTTTGCCGCCTAGGGTTTATGTTGGTTACTCCATTTACAAAGGGAAGGCTGCGCTTACATTGACTCCTAGGCCCCCCGAATTCATGCCACTCGAT

upper sequence: Vv01s0026g01720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G40850.2 (Glycine max), 3'ss of exon 1
--------tttatttgttttatctttatttttcatccttgcttttagttcttcagtttaatctcaattggatgatgggaatattggttggatttgtgtttgcccgcagCTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTGCTCTTACGGTAGAGCCCAAAGCCCCGGAGTTTACGCCTTTAGAT
         | ||   |  |   ||  ||||   |  |   |||| ||| |    |  | | | |  |   |  | ||  |  |||||  || ||||||     | |||||||| ||||||||||| ||||||| | || || ||||||||||| ||||| |||||  |    || |   ||||||| || | |||  | || 
gacagtcactaatggatggtgggttagttttgtgttatgtgtttttgttgtgtgat--actgtgatgtacttatttggttttctggtttaatgtgtgttcagTTGGAGCTTTGCCGCCTAGGGTTTATGTTGGTTACTCCATTTACAAAGGGAAGGCTGCGCTTACATTGACTCCTAGGCCCCCGGAATTCATGCCGCTCGA-

upper sequence: Vv01s0026g01720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT2G02740.1 (Arabidopsis thaliana), 3'ss of exon 1
tttatttgttttatctttatt-tttcatccttg-----cttttagttcttcagtttaatctcaattggatgatgggaatattggttggatttgtgtttgc--ccgcagCTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTGCTCTTACGGTAGAGCCCAAAGCCCCGGAGTTTACGCCTTTAGAT
    |  | |||    | ||| ||| | | |||          || | |  | || |     | || ||   |  |  | || ||| | ||||  |||    | | ||  |     |||||  |||  || ||||||||||| |||||||||||||||||||||||| |||| ||   ||| || ||||||  | |||| || 
---gtagggttttcactcattgtttgagctttgaaaaatgggaagctttgaaattcagaa--agtttgaaattttgtttgtttgtttgttttggttttatagCTGAAGTATCTTCTCCTAGATTTTACGTGGGTCATTCGATTTACAAAGGGAAAGCTGCTCTTACGATAGAACCACGAGCACCAGAGTTTGTGGCTTTGGA-

upper sequence: Vv01s0026g01720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G14410.1 (Arabidopsis thaliana), 3'ss of exon 1
------------------------------------------------------------------------------------------------tttatttgttttatctttatttttcatc------cttgcttttagttcttcagtttaatctcaattggatgatgggaatattggttg---gatttgtgtt--tgcccgcagCTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTGCTCTTACGGTAGAGCCCAAAGCCCCGGAGTTTACGCCTTTAGAT
                                                                                                ||| |    || |   ||    | ||          |  |||||  |||  || |  | |||   | | |||||   |  |  |||    | || |  ||  |  | | ||  ||||   ||||  |||  || |||||||||||||||||||||||||||||  | || || || || | ||| || ||||||  | ||||||| 
gtaagccatctcacttggttactttagggttttagcttgcttaattaagaaattggaagcttaaaaacacaaaagggtactcttaattacgagaaatttgtaaccttgaagcttgaaatccaaaaagagaactctttttatatctatagatggagctcg--taggtgatgtttacttgtgttctttgtttcgatttgatagCTGAAGGATTGCCTGCTAGATTTTACGTGGGTCATTCGATATACAAAGGGAAAGCTGCGTTAACAGTGGACCCAAGAGCACCAGAGTTTGTGGCTTTAGA-

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|110411392|gb|EC977103.1|EC977103
EST:     GCAGAACATCACTCGCAGACAACCTCCAAATGACTCTTCTTTTGGAGGAG                         CTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTG
genomic: GCAGAACATCACTCGCAGACAACCTCCAAATGACTCTTCTTTTGGAGGAGgtgagactga ... ttgcccgcagCTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTG
EST: gi|352785896|gb|FQ475899.1|FQ475899
EST:     GCAGAACATCACTCGCAGACAACCTCCAAATGACTCTTCTTTTGGAGGAG                         CTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTG
genomic: GCAGAACATCACTCGCAGACAACCTCCAAATGACTCTTCTTTTGGAGGAGgtgagactga ... ttgcccgcagCTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTG
EST: gi|351028060|gb|FQ425961.1|FQ425961
EST:     GCAGAACATCACTCGCAGACAACCTCCAAATGACTCTTCTTTTGGAGGAG                         CTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAGGCTG
genomic: GCAGAACATCACTCGCAGACAACCTCCAAATGACTCTTCTTTTGGAGGAGgtgagactga ... ttgcccgcagCTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTG
EST: gi|26257143|gb|CA808206.1|CA808206
EST:     GCAGAACATCACTCGCAGACAACCTCCAAATGACTCTTCTTTTGGAGGAG                         CTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTG
genomic: GCAGAACATCACTCGCAGACAACCTCCAAATGACTCTTCTTTTGGAGGAGgtgagactga ... ttgcccgcagCTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTG
EST: gi|110723587|gb|EE101073.1|EE101073
EST:     GCAGAACATCACTCGCAGACAACCTCCAAATGACTCTTCTTTTGGAGGAG                         CTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTG
genomic: GCAGAACATCACTCGCAGACAACCTCCAAATGACTCTTCTTTTGGAGGAGgtgagactga ... ttgcccgcagCTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTG
EST: gi|28959463|gb|CB339732.1|CB339732
EST:     GCAGAACATCACTCGCAGACAACCTCCAAATGACTCTTCTTTTGGAGGAG                         CTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTG
genomic: GCAGAACATCACTCGCAGACAACCTCCAAATGACTCTTCTTTTGGAGGAGgtgagactga ... ttgcccgcagCTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTG
EST: gi|26257138|gb|CA808201.1|CA808201
EST:     GCAGAACATCACTCGCAGACAACCTCCAAATGACTCTTCTTTTGGAGGAG                         CTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTG
genomic: GCAGAACATCACTCGCAGACAACCTCCAAATGACTCTTCTTTTGGAGGAGgtgagactga ... ttgcccgcagCTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTG
EST: gi|110690593|gb|EE067826.1|EE067826
EST:     GCAGAACATCACTCGCAGACAACCTCCAAATGACTCTTCTTTTGGAGGAG                         CTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTG
genomic: GCAGAACATCACTCGCAGACAACCTCCAAATGACTCTTCTTTTGGAGGAGgtgagactga ... ttgcccgcagCTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTG
EST: gi|28958978|gb|CB339490.1|CB339490
EST:     GCAGAACATCACTCGCAGACAACCTCCAAATGACTCTTCTTTTGGAGGAG                         CTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTG
genomic: GCAGAACATCACTCGCAGACAACCTCCAAATGACTCTTCTTTTGGAGGAGgtgagactga ... ttgcccgcagCTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTG
EST: gi|351043541|gb|FQ431015.1|FQ431015
EST:     GCAGAACATCACTCGCAGACAACCTCCAAATGACTCTTCTTTTGGAGGAG                         CTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTG
genomic: GCAGAACATCACTCGCAGACAACCTCCAAATGACTCTTCTTTTGGAGGAGgtgagactga ... ttgcccgcagCTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttaatctcaattggatgatgggaatattggttggatttgtgtttgcccgcagCTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTGCTCTTACGGTAGAGCCCAAAGCCCCGGAGTTTACGCCTTTAGAT
 gtttaat  putative branch site (score: 4)
                                            tttgccc  putative PPT
                         aatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttatttgttttatctttatttttcatccttgcttttagttcttcagtttaatctcaattggatgatgggaatattggttggatttgtgtttgcccgcagCTTTGCAGCCTAGGGTTTTTGTTGGTCATTCGATATACAAAGGGAAAGCTGCTCTTACGGTAGAGCCCAAAGCCCCGGAGTTTACGCCTTTAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - -tcatcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggttgg