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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatttttccttcagtgaattaatcagcatagcatccctagcttagaagaaagcaatggacaactgagctttgtaattggtttttttatgaatttatgcagATAATGAGTAATGGAATATTCAAGAGCCCCATACACAGGGTTGTGACAAACTCAGAAAGGATGAGGATATCAGTAGCTATGTTTAATGAACCTGAGCCAG

Basic information

species Vitis vinifera
transcript Vv11s0118g00390.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0118g00390.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G11690.1 (Glycine max), 3'ss of exon 3
aatttttccttcagtgaattaatcagcatagcatc--cctagctt--agaagaaagcaatggacaactgagctttgtaattggtttttttatgaatttatgcagATAATGAGTAATGGAATATTCAAGAGCCCCATACACAGGGTTGTGACAAACTCAGAAAGGATGAGGATATCAGTAGCTATGTTTAATGAACCTGAGCCAG
 |||||    | | |   ||  |  |   | |||   |  |  ||  ||  | | | | ||  ||  |||    ||   ||| |    ||    |||  ||||||| ||||||||||||||||||||||||   || |||||||||||||| ||  |||||| | ||||||| || ||||| ||||||||||| || ||| | |
-attttgtacttactttcttg-ttggtgcatcattaactaaattttgaggcgtaggaagtgttcagttgaagaatgc--ttgatgaaattggtgattcttgcagATCATGAGTAATGGAATATTCAAGAGCATAATGCACAGGGTTGTGACCAATACAGAAAAGCTGAGGATGTCTGTAGCAATGTTTAATGAGCCAGAGGCCG
















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|77581502|gb|DV219695.1|DV219695
EST:     TTCCTGTAATTCCCCATGCTCTTGTTGTCAACCTTGGGGATCAGATGCAG                         ATAATGAGTAATGGAATATTCAAGAGCCCCATACACAGGGTTGTGACAAAC
genomic: TTCCTGTAATTCCCCACGCTCTTGTTGTCAACCTTGGGGATCAGATGCAGgtatatatat ... atttatgcagATAATGAGTAATGGAATATTCAAGAGCCCCATACACAGGGTTGTGACAAAC
EST: gi|34363907|gb|CF405492.1|CF405492
EST:     TTCCTGTAATTCCCCCCGCTCTTGTTGTCACCCTTGGGGATCAGATGCAG                         ATAATGAGTAATGGAATATTCAAGAGCCCCATACACAGGGTTGTGACAAAC
genomic: TTCCTGTAATTCCCCACGCTCTTGTTGTCAACCTTGGGGATCAGATGCAGgtatatatat ... atttatgcagATAATGAGTAATGGAATATTCAAGAGCCCCATACACAGGGTTGTGACAAAC
EST: gi|30128117|gb|CB913456.1|CB913456
EST:     TTCCTGTAATTCCCCACGCTCTTGTTGTCAACCTTGGGGATCAGATGCAG                         ATAATGAGTAATGGAATATTCAAGAGCCCCATACACAGGGTTGTGACAAAC
genomic: TTCCTGTAATTCCCCACGCTCTTGTTGTCAACCTTGGGGATCAGATGCAGgtatatatat ... atttatgcagATAATGAGTAATGGAATATTCAAGAGCCCCATACACAGGGTTGTGACAAAC
EST: gi|71890065|gb|DT039120.1|DT039120
EST:     TTCCTGTAATTCCCCATGCTCTTGTTGTCAACCTTGGGGATCAGATGCAG                         ATAATGAGTAATGGAATATTCAAGAGCCCCATACACAGGGTTGTGACAAAC
genomic: TTCCTGTAATTCCCCACGCTCTTGTTGTCAACCTTGGGGATCAGATGCAGgtatatatat ... atttatgcagATAATGAGTAATGGAATATTCAAGAGCCCCATACACAGGGTTGTGACAAAC
EST: gi|22007034|gb|BQ792068.1|BQ792068
EST:     TTCCTGTAATTCCCCACGCTCTTGTTGTCAACCTTGGGGATCAGATGCAG                         ATAATGAGTAATGGAATATTCAAGAGCCCCATACACAGGGTTGTGACAAAC
genomic: TTCCTGTAATTCCCCACGCTCTTGTTGTCAACCTTGGGGATCAGATGCAGgtatatatat ... atttatgcagATAATGAGTAATGGAATATTCAAGAGCCCCATACACAGGGTTGTGACAAAC
EST: gi|110405393|gb|EC970934.1|EC970934
EST:     TTCCTGTAATTCCCCACGCTCTTGTTGTCAACCTTGGGGATCAGATGCAG                         ATAATGAGTAATGGAATATTCAAGAGCCCCATACACAGGGTTGTGACAAAC
genomic: TTCCTGTAATTCCCCACGCTCTTGTTGTCAACCTTGGGGATCAGATGCAGgtatatatat ... atttatgcagATAATGAGTAATGGAATATTCAAGAGCCCCATACACAGGGTTGTGACAAAC
EST: gi|30127645|gb|CB912984.1|CB912984
EST:     TTCCTGTAATTCCCCACGCTCTTGTTGTCAACCTTGGGGATCAGATGCAG                         ATAATGAGTAATGGAATATTCAAGAGCCCCATACACAGGGTTGTGACAAAC
genomic: TTCCTGTAATTCCCCACGCTCTTGTTGTCAACCTTGGGGATCAGATGCAGgtatatatat ... atttatgcagATAATGAGTAATGGAATATTCAAGAGCCCCATACACAGGGTTGTGACAAAC
EST: gi|71889585|gb|DT038640.1|DT038640
EST:     TTCCTGTAATTCCCCATGCTCTTGTTGTCAACCTTGGGGATCAGATGCAG                         ATAATGAGTAATGGAATATTCAAGAGCCCCATACACAGGGTTGTGACAAAC
genomic: TTCCTGTAATTCCCCACGCTCTTGTTGTCAACCTTGGGGATCAGATGCAGgtatatatat ... atttatgcagATAATGAGTAATGGAATATTCAAGAGCCCCATACACAGGGTTGTGACAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaaagcaatggacaactgagctttgtaattggtttttttatgaatttatgcagATAATGAGTAATGGAATATTCAAGAGCCCCATACACAGGGTTGTGACAAACTCAGAAAGGATGAGGATATCAGTAGCTATGTTTAATGAACCTGAGCCAG
                       tttgtaattggttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatttttccttcagtgaattaatcagcatagcatccctagcttagaagaaagcaatggacaactgagctttgtaattggtttttttatgaatttatgcagATAATGAGTAATGGAATATTCAAGAGCCCCATACACAGGGTTGTGACAAACTCAGAAAGGATGAGGATATCAGTAGCTATGTTTAATGAACCTGAGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - tccttca
- - - - - - - - - - - - - - - -catccct
- - - - - - - - - - - - - - - - - - - - - - - - aaagcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ggacaac