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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataataagtaatgactccaaagaagtgaccccactcatttcaatagatgcctcagcttttgtttttgcacttggttttctaattgttttattaatcacagGTCCTTGAAATATTGGAACTGTATAGACGTATATATGAAGAGTACTTGGCGATTCCTGTTATAAAGGGTAAGAAGAGTGAGATGGAGAAGTTTGCTGGTG

Basic information

species Vitis vinifera
transcript Vv07s0005g02620.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g02620.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA19G40930.1 (Glycine max), 3'ss of exon 7
ataataagtaatgactccaaagaagtgaccccactcatttcaatagatgcctcagcttttgtt--tttgcacttggttttctaattgttttattaatcacagGTCCTTGAAATATTGGAACTGTATAGACGTATATATGAAGAGTACTTGGCGATTCCTGTTATAAAGGGTAAGAAGAGTGAGATGGAGAAGTTTGCTGGTG
|  ||  | |     |         |    |||| ||        |||| | || ||||||    ||||   |   | |  |      | || |  |  ||||| ||||| ||  ||||| | ||||| |||||||| |||||||| |||||  ||||||| |||||||||||||| |||||| | ||||||||||||||||
actatctgcatgttattttgtattttccttccacccaagcaggctgatgtc-catcttttggaaatttgttttcaatatattctaaactatactgctt-cagGTTCTTGAGATTCTGGAATTATATAGGCGTATATACGAAGAGTATTTGGCAGTTCCTGTCATAAAGGGTAAGAAAAGTGAGCTTGAGAAGTTTGCTGGTG

upper sequence: Vv07s0005g02620.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA03G38340.1 (Glycine max), 3'ss of exon 7
ataataagtaatgactccaaagaagtgaccccactcatttcaatagatgcctcagcttttgtttttgcactt----ggttttctaattgttttattaatcacagGTCCTTGAAATATTGGAACTGTATAGACGTATATATGAAGAGTACTTGGCGATTCCTGTTATAAAGGGTAAGAAGAGTGAGATGGAGAAGTTTGCTGGTG
 ||        | |||    |    |    |||| ||     |  |||| | || ||||||    |    ||      | ||||||   | ||| |  |  ||||| ||||| ||  ||||| | ||||| |||||||| |||||||| |||||  ||||||| |||||||||||||| |||||| | ||||||||||||||||
-tatctgcatgttactttgtattt-tccttccacccaagcagactgatgtcccatcttttggaaatttgttttaaaaatattctaaac-tattactgctt-cagGTTCTTGAGATTCTGGAATTATATAGGCGTATATACGAAGAGTATTTGGCAGTTCCTGTCATAAAGGGTAAGAAAAGTGAGCTTGAGAAGTTTGCTGGTG
















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|30306282|gb|CB983076.1|CB983076
EST:     GGCAGGAGGGGCATACTGCTTTTGCTAAAAAGGAAGAGGCAGATAAAGAG                         GTCCTTGAAATATTGGAACTGTATAGACGTATATATGAAGAGTACTTGGCG
genomic: GGCAGGAGGGGCATACTGCTTTTGCTACAAAGGAAGAGGCAGATAAAGAGgtatggaatt ... ttaatcacagGTCCTTGAAATATTGGAACTGTATAGACGTATATATGAAGAGTACTTGGCG
EST: gi|294964991|gb|GW838794.1|GW838794
EST:     GGCAGGAGGGGCATACTGCTTTTGCTACAAAGGAAGAGGCAGATAAAGAG                         GTCCTTGAAATATTGGAACTGTATAGACGTATATATGAAGAGTACTTGGCG
genomic: GGCAGGAGGGGCATACTGCTTTTGCTACAAAGGAAGAGGCAGATAAAGAGgtatggaatt ... ttaatcacagGTCCTTGAAATATTGGAACTGTATAGACGTATATATGAAGAGTACTTGGCG
EST: gi|110712760|gb|EE088090.1|EE088090
EST:     GGCAGGAAGGGCATACTGCTTTTGCTACAAAGGANGAGGCAGATAAAGAG                         GTCCTTGAAATATTGAAACTGTATAGACGTATATATGAAGAGTACTTGGGC
genomic: GGCAGGAGGGGCATACTGCTTTTGCTACAAAGGAAGAGGCAGATAAAGAGgtatggaatt ... ttaatcacagGTCCTTGAAATATTGGAACTGTATAGACGTATATATGAAGAGTACTTGG-C
EST: gi|110427116|gb|EC993547.1|EC993547
EST:     GGCAGGAGGGGCATACTGCTTTTGCTACAAAGGAAGAGGCAGATAAAGAG                         GTCCTTGAAATATTGGAACTGTATAGACGTATATATGAAGAGTACTTGGCG
genomic: GGCAGGAGGGGCATACTGCTTTTGCTACAAAGGAAGAGGCAGATAAAGAGgtatggaatt ... ttaatcacagGTCCTTGAAATATTGGAACTGTATAGACGTATATATGAAGAGTACTTGGCG
EST: gi|29784140|gb|CB344515.2|CB344515
EST:     GGCAGGAGGGGCATACTGCTTTTGCTACAAAGGAAGAGGCAGATAAAGAG                         GTCCTNGGATTGAT-GGAACTGTATAGACGTATATATGAAGAGTACTTGAT
genomic: GGCAGGAGGGGCATACTGCTTTTGCTACAAAGGAAGAGGCAGATAAAGAGgtatggaatt ... ttaatcacagGTCCTTGAAAT-ATTGGAACTGTATAGACGTATATATGAAGAGTACTTGGC
EST: gi|161708997|gb|FC058789.1|FC058789
EST:     GGCAGGAGGGGCATACTGCTTTTGCTACAAAGGAAGAGGCAGATAAAGAG                         GTCCTTGAAATATTGGAACTGTATAGACGTATATATGAAGAGTACTTGGCG
genomic: GGCAGGAGGGGCATACTGCTTTTGCTACAAAGGAAGAGGCAGATAAAGAGgtatggaatt ... ttaatcacagGTCCTTGAAATATTGGAACTGTATAGACGTATATATGAAGAGTACTTGGCG
EST: gi|37190730|gb|CF610079.1|CF610079
EST:     GGCAGGAGGGGCATACTGCTTTTGCTACAAAGGAAGAGGCAGATAAAGAG                         GTCCTTGAAATATTGGAACTGTATAGACGTATATATGAAGAG
genomic: GGCAGGAGGGGCATACTGCTTTTGCTACAAAGGAAGAGGCAGATAAAGAGgtatggaatt ... ttaatcacagGTCCTTGAAATATTGGAACTGTATAGACGTATATATGAAGAG
EST: gi|110713336|gb|EE089170.1|EE089170
EST:     GGCAGGAGGGGCATACTGCTTTTGCTACAAAGGAAGAGGCAGATAAAGAG                         GTCCTTGAAATATTGGAACTGTATAGACGTATATATGAAGAGTACTTGGCG
genomic: GGCAGGAGGGGCATACTGCTTTTGCTACAAAGGAAGAGGCAGATAAAGAGgtatggaatt ... ttaatcacagGTCCTTGAAATATTGGAACTGTATAGACGTATATATGAAGAGTACTTGGCG
EST: gi|110712013|gb|EE089150.1|EE089150
EST:     TGCAGGAGGGGCAAACTGCTTTTGCTACAAAGGAAGAGGGAGATAAAGAG                         GTCCTTGAAATATTGGAAAC-GTATAGACGTAAAAATGAAGAGTACTTGGC
genomic: GGCAGGAGGGGCATACTGCTTTTGCTACAAAGGAAGAGGCAGATAAAGAGgtatggaatt ... ttaatcacagGTCCTTGAAATATTGGAA-CTGTATAGACGTATATATGAAGAGTACTTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgcctcagcttttgtttttgcacttggttttctaattgttttattaatcacagGTCCTTGAAATATTGGAACTGTATAGACGTATATATGAAGAGTACTTGGCGATTCCTGTTATAAAGGGTAAGAAGAGTGAGATGGAGAAGTTTGCTGGTG
                                           tattaat  putative branch site (score: 2)
                                        ttttatt  CT-rich tract
                             ttttctaattgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataataagtaatgactccaaagaagtgaccccactcatttcaatagatgcctcagcttttgtttttgcacttggttttctaattgttttattaatcacagGTCCTTGAAATATTGGAACTGTATAGACGTATATATGAAGAGTACTTGGCGATTCCTGTTATAAAGGGTAAGAAGAGTGAGATGGAGAAGTTTGCTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - gactcca
- - - - - - - - - - - - - - -cccactc
- - - - - - - - - - - - - - - - - - - - - - - -tgcctca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcacttg