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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagactacaaaggtttatgtgtaatttcacttttattgtctcctttgatcttatgatgaacttgtattgagctttataatttaacacagGAGCTGAGTTTTAAAAGCAAGCCAAATGTGTGGGCATACTTCTCTGTTAAG

Basic information

species Vitis vinifera
transcript Vv18s0001g04980.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM5G858094_T02 (Zea mays), 3'ss of exon 10
gttagactacaaaggtttatgtgtaatttcacttttattg---tctcctttgatcttatgatgaacttgtattgagctttataatttaacacagGAGCTGAGTTTTAAAAGCAAGCCAAATGTGTGGGCATACTTCTCTGTTAAG
|| ||  | | |      |||| | || |  | || |  |   |    |||| |   ||||  |    || ||||  |||    |||    |||||| | ||||||||||||||||| ||||| ||||| |||||||| || |||
gtaagttttctagatcacatgtattatatatcgttcaaagagattaagtttggttaaatgactag---gtcttgattttttatcttt----cagGAGATAAGTTTTAAAAGCAAGCCTAATGTTTGGGCCTACTTCTCAGTAAAG

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AC197672.3_FGT002 (Zea mays), 3'ss of exon 10
-----gttagactacaaaggtttatgt------gtaatttcacttttattgtctcctttgatcttat---gatgaacttgtattgagctttataatttaacacagGAGCTGAGTTTTAAAAGCAAGCCAAATGTGTGGGCATACTTCTCTGTTAAG
     | || |   | || ||||   |       |  | |   |   |||||  | |||    ||      |||| |  || |||   |||||| ||||     |||| | ||||||||||||||||| ||||| ||||| |||||||| || |||
tccatggtatatatctaaagtttggatcttttaatggtatagatccaattgttccatttatgtttggttacatgaccaggtcttggtttttatatttta-----gGAGATAAGTTTTAAAAGCAAGCCTAATGTTTGGGCCTACTTCTCAGTAAAG

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 8
gttagactacaaaggtttatgtgtaatttcacttttattgtctcctttgatcttatgatgaacttgtattgagctttataatttaacacagGAGCTGAGTTTTAAAAGCAAGCCAAATGTGTGGGCATACTTCTCTGTTAAG
|||| | |||||  ||  |   | ||| |||  |||     || | || |||   |    |||||||| |||| |  |  ||||    |||||||| || |||||||||||||||||||||||||||||||||||||| |||
gtta-attacaa--gtccaacagcaatctcatctttta---cttcattcatccagt----aacttgtactgagttcaagtatttg-tgcagGAGCTTAGCTTTAAAAGCAAGCCAAATGTGTGGGCATACTTCTCTGTCAAG

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 8
gttagactacaaaggtttatgtgtaatttcacttttattgtctcctttgatcttatgatgaacttgtattgagctttataatttaacacagGAGCTGAGTTTTAAAAGCAAGCCAAATGTGTGGGCATACTTCTCTGTTAAG
|||| |||||||  ||  |   | ||| |||  |||     || | || |||   |    |||||||| |||| |  |  ||||    |||||||| |  |||||||||||||||||||||||||| ||||||||||| |||
gtta-actacaa--gtccaacagcaatatcatctttta---cttcattcatccagt----aacttgtactgagttcaagtatttg-tgcagGAGCTTAACTTTAAAAGCAAGCCAAATGTGTGGGCGTACTTCTCTGTCAAG

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G36160.1 (Arabidopsis thaliana), 3'ss of exon 9
-----gttaga-ctacaaaggtttatgtgtaatttcacttttattgtctcctttgatcttatgatgaacttgtattgagctttataatttaacacagGAGCTGAGTTTTAAAAGCAAGCCAAATGTGTGGGCATACTTCTCTGTTAAG
     || | | ||    |     | ||| || ||||  || | ||    || ||    |  |    ||||||||          || ||   ||||||| |||||||||| |||||||||||||||||||| ||||||||||| |||
gtaatgtgatatctgtggaatgcaaagtgaaagttca--ttcactgagaactctg----tgggtaacacttgtatg---------aacttgcaacagGAGTTGAGTTTTAAGAGCAAGCCAAATGTGTGGGCGTACTTCTCTGTCAAG

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G36180.1 (Arabidopsis thaliana), 3'ss of exon 9
gttagactacaaaggtttatgtgtaat-ttcacttttattgtctcctttgatcttatgatgaacttgtattgagctttat-aatttaacacagGAGCTGAGTTTTAAAAGCAAGCCAAATGTGTGGGCATACTTCTCTGTTAAG
     | |   |   | | |||| |||    | |||||  ||||    | |   |  |  |   |   | |    | ||| || ||   ||||||  |||||||||| |||||||||||| ||||| | ||||||||||| |||
---gtaatgtgata-tatctgtggaatgcaaaattttaaagtctatgataactgtgcggggg--tgacact----tgtatgaacttgcaacagGAATTGAGTTTTAAGAGCAAGCCAAATATGTGGTCGTACTTCTCTGTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtctcctttgatcttatgatgaacttgtattgagctttataatttaacacagGAGCTGAGTTTTAAAAGCAAGCCAAATGTGTGGGCATACTTCTCTGTTAAG
                                            atttaac  putative branch site (score: 3)
                                      tttataatttaacaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagactacaaaggtttatgtgtaatttcacttttattgtctcctttgatcttatgatgaacttgtattgagctttataatttaacacagGAGCTGAGTTTTAAAAGCAAGCCAAATGTGTGGGCATACTTCTCTGTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG