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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctaaatgccaccaattataaagcagatgaatatgatctgtattgctgccatcatcctgggttgctatactaatgtattctattctttgccactaagcagGAGGAACGCAAAATGGAAGTCTGCACAAGCAGCTGTAATTCCTAATTTCCATCTCCCAATGCGTAGTTTTGAAGTTAAAAATAG

Basic information

species Vitis vinifera
transcript Vv15s0048g00750.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0048g00750.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G40460.1 (Glycine max), 3'ss of exon 1
gctaaatgccaccaattataaagcagatgaat-atgatctgtattgctgcca-tcatcctgggttgctatactaatgtattctattctttgccactaagcagGAGGAACGCAAAATGGAAGTCTGCACAAGCAGCTGTAATTCCTAATTTCCATCTCCCAATGCGTAGTTTTGAAGTTAAAAATAG
      |   | || |  | |   | ||  ||   | |    |    ||||| || | |    ||    ||      | ||  | | ||||||  ||      |||| | || | |||| | ||||||||||||| || |  || |||||||||||||||||||| ||||||||  | ||||||||
----ggttttatcagt-gtcatatatatatattgcgctgcagaaaaatgccactctttccaaattttggtatgttgatgttaaaatatttgcctttattattcagGAGCTCATATTGGAGGCCTGCACAAGCAGCCGTGAAGCCCAATTTCCATCTCCCAATGCGCAGTTTTGAGTTAAAAAATAG

upper sequence: Vv15s0048g00750.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G45380.1 (Glycine max), 3'ss of exon 1
gctaaatgccaccaattataaagcagatgaatat-gatctgtattgctgccatcatcctgggttgctatactaatgtattctattctttgccactaagcagGAGGAACGCAAAATGGAAGTCTGCACAAGCAGCTGTAATTCCTAATTTCCATCTCCCAATGCGTAGTTTTGAAGTTAAAAATAG
  | |    | |||  ||||  |    || |||  | |    |      |  |  | |    ||    ||    ||      | | |||| |  ||   |  |||| | ||   |||| | || ||||||||||||| |   | |||||||||||||||||||| ||||||||  | ||||||| 
--ttatcagcgccatatatat-gtgtgtgtataccggtgcagaaaataccactttttccaaattttggtatgtttgatgctaaatatttgtctttattaatcaGGAGCTCATGTTGGAGGCCTACACAAGCAGCTGTGAAGTCCAATTTCCATCTCCCAATGCGCAGTTTTGAGTTAAAAAATA-
















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|349818845|gb|FQ409379.1|FQ409379
EST:     GACTCAACTCTCCAGTTTCCGCGTCCTAACTGCGGCGATATCAACAAGAG                         GAGGAATGCCAAATGGAAGTCTGCACAAGCAGCTGTAATTCCTAATTTCCA
genomic: GACTCAACTCTCCAGTTTCCGCGTCCTAACTGCGGCGATATCAACAAGAGgttaatctga ... cactaagcagGAGGAACGCAAAATGGAAGTCTGCACAAGCAGCTGTAATTCCTAATTTCCA
EST: gi|349815681|gb|FQ400837.1|FQ400837
EST:     GACTCAACTCTCCAGTTTCCGCGTCCTAACTGCGGCGATATCAACAAGAG                         GAGGAATGCCAAATGGAAGTCTGCACAAGCAGCTGTAATTCCTAATTTCCA
genomic: GACTCAACTCTCCAGTTTCCGCGTCCTAACTGCGGCGATATCAACAAGAGgttaatctga ... cactaagcagGAGGAACGCAAAATGGAAGTCTGCACAAGCAGCTGTAATTCCTAATTTCCA
EST: gi|349813360|gb|FQ413618.1|FQ413618
EST:     GACTCAACTCTCCAGTTTCCGCGTCCTAACCGCGGCGATATCAACAAGAG                         GAGGAATGCCAAATGGAAGTCTGCACAAGCAGCTGTAATTCCTAATTTCCA
genomic: GACTCAACTCTCCAGTTTCCGCGTCCTAACTGCGGCGATATCAACAAGAGgttaatctga ... cactaagcagGAGGAACGCAAAATGGAAGTCTGCACAAGCAGCTGTAATTCCTAATTTCCA
EST: gi|161711157|gb|FC061163.1|FC061163
EST:     GACTCAACTCTCCAGTTTCCGCGTCCTAACTGCGGCGATATCAACAAGAG                         GAGGAATGCAAAATGGAAGTCTGCACAAGCAGCTGTAATTCCTAATTTCCA
genomic: GACTCAACTCTCCAGTTTCCGCGTCCTAACTGCGGCGATATCAACAAGAGgttaatctga ... cactaagcagGAGGAACGCAAAATGGAAGTCTGCACAAGCAGCTGTAATTCCTAATTTCCA
EST: gi|349819155|gb|FQ412049.1|FQ412049
EST:     GACTCAACTCTCCAGTTTCCGCGTCCTAACTGCGGCGATATCAACAAGAG                         GAGGAATGCCAAATGGAAGTCTGCACAAGCAGCTGTAATTCCTAATTTCCA
genomic: GACTCAACTCTCCAGTTTCCGCGTCCTAACTGCGGCGATATCAACAAGAGgttaatctga ... cactaagcagGAGGAACGCAAAATGGAAGTCTGCACAAGCAGCTGTAATTCCTAATTTCCA
EST: gi|349813204|gb|FQ411444.1|FQ411444
EST:     GACTCAACTCTCCAGTTTCCGCGTCCTAACTGCGGCGATATCAACAAGAG                         GAGGAATGCCAAATGGAAGTCTGCACAAGCAGCTGTAATTCCTAATTTCCA
genomic: GACTCAACTCTCCAGTTTCCGCGTCCTAACTGCGGCGATATCAACAAGAGgttaatctga ... cactaagcagGAGGAACGCAAAATGGAAGTCTGCACAAGCAGCTGTAATTCCTAATTTCCA
EST: gi|349820595|gb|FQ404090.1|FQ404090
EST:     GACTCAACTCTCCAGTTTCCGCGTCCTAACTGCGGCGATATCAACAAGAG                         GAGGAATGCCAAATGGAAGTCTGCACAAGCAGCTGTAATTCCTAATTTCCA
genomic: GACTCAACTCTCCAGTTTCCGCGTCCTAACTGCGGCGATATCAACAAGAGgttaatctga ... cactaagcagGAGGAACGCAAAATGGAAGTCTGCACAAGCAGCTGTAATTCCTAATTTCCA
EST: gi|349823087|gb|FQ400066.1|FQ400066
EST:     GACTCAACTCTCCAGTTTCCGCGTCCTAACTGCGGCGATATCAACAAGAG                         GAGGAATGCCAAATGGAAGTCTGCACAAGCAGCTGTAATTCCTAATTTCCA
genomic: GACTCAACTCTCCAGTTTCCGCGTCCTAACTGCGGCGATATCAACAAGAGgttaatctga ... cactaagcagGAGGAACGCAAAATGGAAGTCTGCACAAGCAGCTGTAATTCCTAATTTCCA
EST: gi|349823336|gb|FQ402535.1|FQ402535
EST:     GACTCAACTCTCCAGTTTCCGCGTCCTAACTGCGGCGATATCAACAAGAG                         GAGGAATGCCAAATGGAAGTCTGCACAAGCAGCTGTAATTCCTAATTTCCA
genomic: GACTCAACTCTCCAGTTTCCGCGTCCTAACTGCGGCGATATCAACAAGAGgttaatctga ... cactaagcagGAGGAACGCAAAATGGAAGTCTGCACAAGCAGCTGTAATTCCTAATTTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgccatcatcctgggttgctatactaatgtattctattctttgccactaagcagGAGGAACGCAAAATGGAAGTCTGCACAAGCAGCTGTAATTCCTAATTTCCATCTCCCAATGCGTAGTTTTGAAGTTAAAAATAG
                      tactaat  putative branch site (score: 1)
                                ttctattctttgcc  putative PPT
                    tatactaatgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctaaatgccaccaattataaagcagatgaatatgatctgtattgctgccatcatcctgggttgctatactaatgtattctattctttgccactaagcagGAGGAACGCAAAATGGAAGTCTGCACAAGCAGCTGTAATTCCTAATTTCCATCTCCCAATGCGTAGTTTTGAAGTTAAAAATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - ccaccaa
- - - - - - - - - - aagcaga
- - - - - - - - - - - - - - - - - - - - - - - -gccatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgggttg