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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttgccattaattgtgaagtttgagtatgatgtttacagaagttggtgtcacataaatgctactgctcaatggggattaatctatttttgttaattcagGTACCTCTAGTAGCTTCAAACCGCATTGGGAAGGAAATAATCCAGACAGAGCATGGAAATACTGAAATCACATTCTATGGAAACTCTTTTATAGCAG

Basic information

species Vitis vinifera
transcript Vv06s0080g00560.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0080g00560.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA08G07960.1 (Glycine max), 3'ss of exon 7
gcttgccattaattgtgaagtttgagtatgatgtttacagaagttggtgtca-cataaatgct---actgctcaatggg---gattaatctatttttgttaattcagGTACCTCTAGTAGCTTCAAACCGCATTGGGAAGGAAATAATCCAGACAGAGCATGGAAATACTGAAATCACATTCTATGGAAACTCTTTTATAGCAG
  | | ||||  || |      | | ||| | |  |  |     | |||||| ||| ||||||   ||| | |||       ||| ||   ||||| |  ||| ||||||||||| || || |||||  | || || ||||| |||||  |||| ||||||||||| | ||| || ||||||||||||||||| || |||||||
--tcgtcatttttttta-----taaatatcaaggatgtaaccacttgtgtcaacattaatgcttaaacttcccaacatatttgatcaaataattttggaaaatgcagGTACCTCTTGTGGCATCAAATAGGATAGGAAAGGAGATAATTGAGACTGAGCATGGAAAAAGTGAGATAACATTCTATGGAAACTCCTTCATAGCAG

upper sequence: Vv06s0080g00560.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT2G27450.2 (Arabidopsis thaliana), 3'ss of exon 7
--gcttgccattaattgtgaagtttgagta---tgatgtttacagaagttggtgtcacataaatgctactgctcaatgggg-attaatctatttttgttaattcagGTACCTCTAGTAGCTTCAAACCGCATTGGGAAGGAAATAATCCAGACAGAGCATGGAAATACTGAAATCACATTCTATGGAAACTCTTTTATAGCAG
  |  |    ||  ||  |   |||        |     || |  || |  |  ||| ||   |  | ||  | | || || | ||||  | ||| | |  ||||||||||||||||||| ||||| ||||| ||||||||||||||  | || |||||||||  || | | ||||| ||||| ||||  || || || || |
atgtatctagtttgttccgttatttctactgattagaacttgccaaaatgtgcttcaaatggtt--tgctaatgagtgaggcaataat--actttgggt--ttcagGTACCTCTAGTAGCCTCAAATCGCATAGGGAAGGAAATAATTGAAACTGAGCATGGACCTAGTCAGATCACTTTCTACGGAACTTCCTTCATTGCCG
















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|30320849|gb|CD004111.1|CD004111
EST:     CTTGTGATCACTGGAAGCGAGTGATGCAAGGGCATGCTGGGGCTAATTTG                         GTACCTCTAGTAGCTTCAAACCGCATTGGGAAGGAAATAATCCAGACAGAG
genomic: CTTGTGATCACTGGAAGCGAGTGATGCAAGGGCATGCTGGGGCTAATTTGgtaagttaac ... gttaattcagGTACCTCTAGTAGCTTCAAACCGCATTGGGAAGGAAATAATCCAGACAGAG
EST: gi|30321318|gb|CD004580.1|CD004580
EST:     CTTGTGATCACTGGAAGCGAGTGATGCAAGGGCATGCTGGGGCTAATTTG                         GTACCTTTAGTAGCTTCAAACCGCATTGGGAAGGAAATAATCCAGACAGAG
genomic: CTTGTGATCACTGGAAGCGAGTGATGCAAGGGCATGCTGGGGCTAATTTGgtaagttaac ... gttaattcagGTACCTCTAGTAGCTTCAAACCGCATTGGGAAGGAAATAATCCAGACAGAG
EST: gi|22014795|gb|BQ799829.1|BQ799829
EST:     CTTGTGATCACTGGAAGCGAGTGATGCAAGGGCATGCTGGGGCTAATTTG                         GTACCTCTAGTAGCTTCAAACCGCATTGGGAAGGAAATAATCCAGACAGAG
genomic: CTTGTGATCACTGGAAGCGAGTGATGCAAGGGCATGCTGGGGCTAATTTGgtaagttaac ... gttaattcagGTACCTCTAGTAGCTTCAAACCGCATTGGGAAGGAAATAATCCAGACAGAG
EST: gi|30134451|gb|CB919789.1|CB919789
EST:     CTTGTGATCACTGGAAGCGAGTGATGCAAGGGCATGCTGGGGCTAATTTG                         GTACCTCTAGTAGCTTCAAACCGCATTGGGAAGGAAATAATCCAGACAGAG
genomic: CTTGTGATCACTGGAAGCGAGTGATGCAAGGGCATGCTGGGGCTAATTTGgtaagttaac ... gttaattcagGTACCTCTAGTAGCTTCAAACCGCATTGGGAAGGAAATAATCCAGACAGAG
EST: gi|26257496|gb|CA808559.1|CA808559
EST:     CTCGTGATCACTGGAAGCGAGTGATGCAAGGGCATGCTGGGGCTAATTTG                         GTACCTCTAGTAGCTTCAAACCGCATTGGGAAGGAAATAATCCAGACAGAG
genomic: CTTGTGATCACTGGAAGCGAGTGATGCAAGGGCATGCTGGGGCTAATTTGgtaagttaac ... gttaattcagGTACCTCTAGTAGCTTCAAACCGCATTGGGAAGGAAATAATCCAGACAGAG
EST: gi|110385570|gb|EC950109.1|EC950109
EST:     CTCGTGATCACTGGAAGCGAGTGATGCAAGGGCATGCTGGGGCTAATTTG                         GTACCTCTAGTAGCTTCAAACCGCATTGGGAAGGAAATAATCCAGACAGAG
genomic: CTTGTGATCACTGGAAGCGAGTGATGCAAGGGCATGCTGGGGCTAATTTGgtaagttaac ... gttaattcagGTACCTCTAGTAGCTTCAAACCGCATTGGGAAGGAAATAATCCAGACAGAG
EST: gi|352782096|gb|FQ469394.1|FQ469394
EST:     CTTGTGATCACTGGAAGCGAGTGATGCAAGGGCATGCTGGGGCTAATTTG                         GTACCTCTAGTACCTTCAAACCGC
genomic: CTTGTGATCACTGGAAGCGAGTGATGCAAGGGCATGCTGGGGCTAATTTGgtaagttaac ... gttaattcagGTACCTCTAGTAGCTTCAAACCGC
EST: gi|34543783|gb|CF512015.1|CF512015
EST:     TGTGATCACTGGAAGCGAGTGATGCAAGGGCATGCGAT-GGGCTAATTTG                         GTACCTCTAGTAGCTTCAAACCGCATTGGGAAGGAAATAATCCAGACAGAG
genomic: TGTGATCACTGGAAGCGAGTGATGCAAGGGCATGC--TGGGGCTAATTTGgtaagttaac ... gttaattcagGTACCTCTAGTAGCTTCAAACCGCATTGGGAAGGAAATAATCCAGACAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgtcacataaatgctactgctcaatggggattaatctatttttgttaattcagGTACCTCTAGTAGCTTCAAACCGCATTGGGAAGGAAATAATCCAGACAGAGCATGGAAATACTGAAATCACATTCTATGGAAACTCTTTTATAGCAG
                                            tgttaat  putative branch site (score: 3)
                                        tttttgtt  CT-rich tract
                               attaatctatttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttgccattaattgtgaagtttgagtatgatgtttacagaagttggtgtcacataaatgctactgctcaatggggattaatctatttttgttaattcagGTACCTCTAGTAGCTTCAAACCGCATTGGGAAGGAAATAATCCAGACAGAGCATGGAAATACTGAAATCACATTCTATGGAAACTCTTTTATAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
-cttgcca
- - - - - - - - - - - - - - - - - - - - - gttggtg
- - - - - - - - - - - - - - - - - - - - - - - - - -acataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctactgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatggg