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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaattatttcttgtgaatttcatttttcagctgttattagcttcttagattttggtgggtcagttattagttcttctaaacagttgaatggtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAAGAAATGGCTAAGAAGGTCAACGATTTATGTG

Basic information

species Vitis vinifera
transcript Vv09s0002g00170.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 1
-------------------------------------------------------------------aaattatttcttgtgaatttcatttttcagctgttatta--gcttctta--gattttggtgggtcagttattag--ttcttcta-aacag--ttgaa---tggtttatgca-----gGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAAGAAATGGCTAAGAAGGTCAACGATTTATGTG
                                                                      || |   |  || ||   | | | ||  | || |||   || || |    |  ||   | | | |||  |   | ||| ||  | ||  ||  |   |||||||||||     ||| ||||| ||||||||  |    ||||| ||| | ||||||||||| ||||||||||| || |||||||| ||||||||||
gttctgttgctgcctgcctagttattcaaattccaatcacacattgacctttttctgccatcacttctccttgtacttgatggatcaaaatatacacttttttttatgactgctcatctgtactgtctgtttaattaacaaaatccttttatgatagacttagactttggtttatgcaatgcagGGTTTGGGGCCTTATTCCACCAGCATAAAAAAAGCCGAGAAGGAAATCAAAGAAATGGCAAAAAAGGTCAATGATTTATGTG

upper sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G42370.1 (Glycine max), 3'ss of exon 1
--aaattattt-cttgtgaatttcatttttcagctgttattagcttcttagattttggtgggtcagttattagttcttctaaacagttgaatggtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAAGAAATGGCTAAGAAGGTCAACGATTTATGTG
  ||| |||   ||| |   | | | |  ||| |||| | |  ||  |||   ||       ||  ||  |  |     || ||  | |  |     |||||||| ||||| ||||||||  |    ||||| ||| | ||||||||||| ||||||||||| || |||||||| ||||||||||
tcaaaatatacacttttttttatgactgctcatctgt-actgtctgtttaa--ttaacaaaatccttttatgatagacttagactttggtttatgcaatgcagGGTTTGGGGCCTTATTCCACCAGCATAAAAAAAGCCGAGAAGGAAATCAAAGAAATGGCAAAAAAGGTCAATGATTTATGTG

upper sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 1
aaattatttcttgtgaatttcatttttcagctgttattagcttcttagattttggtgggtcagttattagttcttctaaacagttgaa--tggtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAAGAAATGGCTAAGAAGGTCAACGATTTATGTG
   |   |  | | |||  | | |  |  | | |   |  || |||  | || ||||| | |   ||   ||  |   |    ||||   |||||||||||||| ||||| ||||||||  ||   ||||| |||   ||||||||||| ||||| ||||| || |||||||| ||||||||||
-tctctgtcatagggaagctgactgatatgatatctattactccttgtactt-ggtggttgaaaaatccttttataacagactttgactttggtttatgcagGGTTTGGGGCCTTATTCCACAAGCATAAAAAAAGTCGAGAAGGAAATCAAAGACATGGCAAAAAAGGTCAATGATTTATGTG

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|351055270|gb|FQ441868.1|FQ441868
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|110381635|gb|EC934981.1|EC934981
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|46917525|gb|CN546854.1|CN546854
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|351037539|gb|FQ462522.1|FQ462522
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|71858037|gb|DT007092.1|DT007092
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|71863099|gb|DT012154.1|DT012154
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|352798958|gb|FQ480807.1|FQ480807
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|110700764|gb|EE077702.1|EE077702
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|71860941|gb|DT009996.1|DT009996
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|294966728|gb|GW837747.1|GW837747
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACTTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|352786546|gb|FQ479753.1|FQ479753
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|110710904|gb|EE087489.1|EE087489
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|351038545|gb|FQ464411.1|FQ464411
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|110424138|gb|EC990494.1|EC990494
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|110718922|gb|EE096307.1|EE096307
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|37183695|gb|CF603049.1|CF603049
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|71858529|gb|DT007584.1|DT007584
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|294963909|gb|GW836784.1|GW836784
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|161718866|gb|FC067339.1|FC067339
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|110688813|gb|EE067797.1|EE067797
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|71864317|gb|DT013372.1|DT013372
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|71859940|gb|DT008995.1|DT008995
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|351047798|gb|FQ459018.1|FQ459018
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|71861519|gb|DT010574.1|DT010574
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|110727512|gb|EE104359.1|EE104359
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|71861538|gb|DT010593.1|DT010593
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|71863095|gb|DT012150.1|DT012150
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|110686619|gb|EE064467.1|EE064467
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
EST: gi|161715740|gb|FC066144.1|FC066144
EST:     AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTAT                         GGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA
genomic: AGAACCCTCGGCCTCTTGATGAAGATGATATTGCTCTCCTTAAAACCTATgtaagtattc ... gtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagattttggtgggtcagttattagttcttctaaacagttgaatggtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAAGAAATGGCTAAGAAGGTCAACGATTTATGTG
                            ttctaaa  putative branch site (score: 2)
                  ttattagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaattatttcttgtgaatttcatttttcagctgttattagcttcttagattttggtgggtcagttattagttcttctaaacagttgaatggtttatgcagGGCTTGGGACCTTATTCTGCACCAATAAAGAAAACAGAGAAGGAAATTAAAGAAATGGCTAAGAAGGTCAACGATTTATGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - -ttcagct
- - - - - - - - - - - - - - - - - - - - - - - - - - tggtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacagt