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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgataagcaatgaaattgtcaatactttgtgtttctcatgatgtgttttacattgcattcagtaacgagtatattcatgcattgattcttttctgatgtattcatccttcattcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGTTAAACCAGCAGAGAATGGGG

Basic information

species Vitis vinifera
transcript Vv00s0313g00030.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0313g00030.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G057037_T01 (Zea mays), 3'ss of exon 3
gtgagtgataagcaatgaaattgtcaatactttgtgtttctcatgatgtgttttacattgcattcagtaacgagtatattcatgcattgattcttttctgatgtattcatccttcattcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGTTAAACCAGCAGAGAATGGGG
                | ||||     |||||  | | | | ||||||     ||  || |  |   |   ||  | ||| ||  ||| |   | || |  | || |  |              ||  ||||| | |||| |    |||||||||||||| ||||||||||| || || ||||| || |||||||||
----------------gtaatt-----tacttcttttatgtgatgatgaaacata-gttcctcttcctgttgaagaaattaattaattaaacatcttttattttaatgtt--------------agAATTACCTCTGGAACCAAGTGGATACATCCAAGTATTTCTTGATGGTGGATTGAACCAACAAAGAATGGGG
















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|38516635|gb|CF983810.1|CF983810
EST:     TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         GCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
EST: gi|34549653|gb|CF517885.1|CF517885
EST:     TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         GCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
EST: gi|71858527|gb|DT007582.1|DT007582
EST:     TTTGGCCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         GCTTACCACAGGAAAC
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAAC
EST: gi|37183648|gb|CF603002.1|CF603002
EST:     TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         C
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcag-
EST: gi|37183648|gb|CF603002.1|CF603002
EST:     TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         C
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcag-
EST: gi|37183648|gb|CF603002.1|CF603002
EST:     TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         C
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcag-
EST: gi|30128462|gb|CB913801.1|CB913801
EST:     TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         GCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
EST: gi|352764443|gb|FQ472800.1|FQ472800
EST:     TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         GCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
EST: gi|161708098|gb|FC056489.1|FC056489
EST:     TTTGGCCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         GCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGG
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGG
EST: gi|71854764|gb|DT003819.1|DT003819
EST:     TTTGGCCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         GCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
EST: gi|71859639|gb|DT008694.1|DT008694
EST:     TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         GCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
EST: gi|161716901|gb|FC068123.1|FC068123
EST:     TTTGGTCAACCAAGGATGGGAAGCCTGTGAATTATCTGCAAGCACCCCTG                         GCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
EST: gi|110724909|gb|EE101147.1|EE101147
EST:     TTTGGCCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         GCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
EST: gi|110710320|gb|EE086550.1|EE086550
EST:     TTTGGCCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         GCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
EST: gi|161714330|gb|FC062631.1|FC062631
EST:     TTTGGCCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCTCTG                         GCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
EST: gi|33409871|gb|CF215498.1|CF215498
EST:     TTTGGCCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         GCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
EST: gi|71855588|gb|DT004643.1|DT004643
EST:     TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         GCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
EST: gi|351032719|gb|FQ462433.1|FQ462433
EST:     TTTGGCCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         GCTTACCACAGGAAACTCAAGGATGCATCCAAGTGTTTCTTGATGGAGGGT
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
EST: gi|30136929|gb|CB922267.1|CB922267
EST:     TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         GCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
EST: gi|352782495|gb|FQ470398.1|FQ470398
EST:     TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         GCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
EST: gi|352794755|gb|FQ475253.1|FQ475253
EST:     TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         GCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
EST: gi|352785495|gb|FQ477709.1|FQ477709
EST:     TTTGGCCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         GCTTACCACAGGAAACTCAAGGATACATCCAAGTGTTTCTTGATGGAGGGT
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
EST: gi|351016529|gb|FQ423956.1|FQ423956
EST:     TTTGGCCAACCAAGGGTGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         GCTTACCACAGGAAACTCAAGGATACATCCAAGTGTTTCTTGATGGAGGGT
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
EST: gi|351018711|gb|FQ425613.1|FQ425613
EST:     TTTGGCCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         GCTTACCACAGGAAACTCAAGGATACATCCAAGTGTTTCTTGATGGAGGGT
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
EST: gi|71857101|gb|DT006156.1|DT006156
EST:     TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         GCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
EST: gi|351013796|gb|FQ433948.1|FQ433948
EST:     TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         GCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
EST: gi|161718121|gb|FC068890.1|FC068890
EST:     TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         GCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
EST: gi|71857389|gb|DT006444.1|DT006444
EST:     TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         GCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
EST: gi|352773927|gb|FQ473059.1|FQ473059
EST:     TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTG                         GCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT
genomic: TTTGGTCAACCAAGGATGGAAAGCCTGTGAATTATCTGCAAGCACCCCTGgtgagtgata ... ttcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtatattcatgcattgattcttttctgatgtattcatccttcattcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGTTAAACCAGCAGAGAATGGGG
                        ttctgat  putative branch site (score: 3)
                                  ttcatccttcattc  putative PPT
                  attctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgataagcaatgaaattgtcaatactttgtgtttctcatgatgtgttttacattgcattcagtaacgagtatattcatgcattgattcttttctgatgtattcatccttcattcaaagcagGCTTACCACAGGAAACTCAGGGATACATCCAAGTGTTTCTTGATGGAGGGTTAAACCAGCAGAGAATGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG