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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attattactattctcttgttcgcattcataattgttgttcttatgacttcaatattgctaattgaggatttagtaaacttaatttgatttctttcctcagGCATGAGCTTCTACTATTTGAAGCCCTTCGAGAAGGCCTGGAAGAAGAAATGGATAGAGATCCCCGAGTATGCGTAATGGGTGAAGACGTGGGCCACTAT

Basic information

species Vitis vinifera
transcript Vv04s0043g00720.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0043g00720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G27260.1 (Glycine max), 3'ss of exon 3
-attattactattctcttgttcgcattcataattgttgttcttatgacttcaatattgctaattgaggatttagtaaacttaatttgatttctttcctcagGCATGAGCTTCTACTATTTGAAGCCCTTCGAGAAGGCCTGGAAGAAGAAATGGATAGAGATCCCCGAGTATGCGTAATGGGTGAAGACGTGGGCCACTAT
  ||  ||  ||| | || || |  | | || | |  |  || ||    | | |  ||   | ||| |||  |   |||   || ||  || | |  | |||||||| ||||| || ||||| ||||| || |||||  |||||||||||||||| || |||||  | ||||| || ||||| ||||| || || ||||||
agttgctaaaatttttttttttgtttgc-tattggcagcactgattgtgtgagttatgaccaatgatgatggaaataaccatatatgcattttatttttagGCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAAGAAGAAATGGAGAGGGATCCTTGTGTATGTGTCATGGGCGAAGATGTAGGTCACTAT

upper sequence: Vv04s0043g00720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G10200.1 (Glycine max), 3'ss of exon 3
attattactattctcttgttcgcattcataattgttgttcttatg-acttcaatattgctaattgaggatt-tagtaaacttaatttgatttctttcctcagGCATGAGCTTCTACTATTTGAAGCCCTTCGAGAAGGCCTGGAAGAAGAAATGGATAGAGATCCCCGAGTATGCGTAATGGGTGAAGACGTGGGCCACTAT
|  | | | |   ||    | |  || | ||   || || || |   ||   |  ||| ||      |||| ||   ||||  || ||  || | |  | |||||||| ||||| || ||||| ||||| || |||||  |||||||||||||||| || |||||  | ||||| || ||||| ||||| || || ||||||
acaagtgccaaattcaaagttg--ttaaaaaacattttttttgtttgctattaccttgttatgcactgattgtaactaactatatatgcattttatttttagGCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAAGAAGAAATGGAGAGGGATCCTTGTGTATGTGTCATGGGCGAAGATGTAGGTCACTAT

upper sequence: Vv04s0043g00720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA14G10550.1 (Glycine max), 3'ss of exon 3
--attattactattctcttgttcgcattcataattgttgttcttatgacttcaatattgctaattgaggatttagtaaacttaatttgatttctttcctcagGCATGAGCTTCTACTATTTGAAGCCCTTCGAGAAGGCCTGGAAGAAGAAATGGATAGAGATCCCCGAGTATGCGTAATGGGTGAAGACGTGGGCCACTAT
   | | ||| ||    ||| |   |    |  || |||||    |    | | |  ||   | | | |||  | | |||      ||  || | |  | |||||||| ||||| || ||||| ||||| || |||||  |||| ||||||||||| || |||||  | ||||| || ||||||||||| || || || |||
tagtcaatac-atgaaattgctaaaagcatttttttttgtttcc-tattatgagttatgaccaataatgatggaattaaccatgcatgcattttatttttagGCATGAACTTCTCCTTTTTGAGGCCCTACGTGAAGGTTTGGAGGAAGAAATGGAGAGGGATCCTTGTGTATGTGTCATGGGTGAAGATGTAGGTCATTAT

upper sequence: Vv04s0043g00720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G34960.1 (Glycine max), 3'ss of exon 3
attattactattctcttgttcgcattcataattgttg--ttcttatgacttcaatat-tgctaattgaggatttagtaaacttaatttgatttctttcctcagGCATGAGCTTCTACTATTTGAAGCCCTTCGAGAAGGCCTGGAAGAAGAAATGGATAGAGATCCCCGAGTATGCGTAATGGGTGAAGACGTGGGCCACTAT
 | | ||| ||    ||| |   |  |||  || |||  ||| |   | |   |  | |||  | | | |||  | | |||    | ||  || | |  | |||||||| ||||| || ||||| ||||| || |||||  |||| ||||||||||| || |||||  | ||||| || ||||||||||| || || || |||
-tcaatac-atgaagttgctaaaaa-cattttttttggtttcctcctattgtgaggtatgcccaataatgatggaattaaccatgtatgcattttatttttagGCATGAACTTCTCCTTTTTGAGGCCCTACGCGAAGGTTTGGAGGAAGAAATGGAGAGGGATCCTTGTGTATGTGTCATGGGTGAAGATGTAGGTCATTAT

upper sequence: Vv04s0043g00720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G30120.1 (Arabidopsis thaliana), 3'ss of exon 3
attattactattctcttgttcgcattcataattgttgttcttatgac-----ttcaatattgctaattgaggatttagtaaacttaatttgatttctttcctcagGCATGAGCTTCTACTATTTGAAGCCCTTCGAGAAGGCCTGGAAGAAGAAATGGATAGAGATCCCCGAGTATGCGTAATGGGTGAAGACGTGGGCCACTAT
    ||   | |  | || ||  |||||  ||   |||  | ||||      ||   | |    |||  |   | |    ||  |  | |  | |   |   ||| ||||| ||  | || || || || ||||  ||||| ||||||||||| ||||| |||||||| |  ||||| || ||||||||||| || ||||| || 
---ctttaaacttccatgctcatattcaatataagtgtcatgatgatgccttttttttgtcaaaaatacaaagtgtgaccaatct--tctcgtatgaatttacagACATGAACTATTGCTTTTCGAGGCTCTTCAGGAAGGTCTGGAAGAAGAGATGGACAGAGATCCACATGTATGTGTTATGGGTGAAGATGTTGGCCATTAC

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|110380102|gb|EC945344.1|EC945344
EST:     GTTGCAGCGAAGGCGGATGCTTCTGTGACCTCAACTGCATCTAAACCTGG                         GCATGAGCTTCTACTATTTGAAGCCCTTCGAGAAGGCCTGGAAGAAGAAAT
genomic: GTTGCAGCGAAGGCGGATGCTTCTGTGACCTCAACTGCATCTAAACCTGGgtttgtttct ... ctttcctcagGCATGAGCTTCTACTATTTGAAGCCCTTCGAGAAGGCCTGGAAGAAGAAAT
EST: gi|110701493|gb|EE079129.1|EE079129
EST:     GCGAAGGCGGATGCTTCTGTGACCTCAACTGCATCTAAACCTGG                         GCATGAGCTTCTACTATTTGAAGCCCTTCGAGAAGGCCTGGAAGAAGAAAT
genomic: GCGAAGGCGGATGCTTCTGTGACCTCAACTGCATCTAAACCTGGgtttgtttct ... ctttcctcagGCATGAGCTTCTACTATTTGAAGCCCTTCGAGAAGGCCTGGAAGAAGAAAT
EST: gi|110730292|gb|EE107208.1|EE107208
EST:     GCGAAGGCGGATGCTTCTGTGACCTCAACTGCATCTAAACCTGG                         GCATGAGCTTCTACTATTTGAAGCCCTTCGAGAAGGCCTGGAAGAAGAAAT
genomic: GCGAAGGCGGATGCTTCTGTGACCTCAACTGCATCTAAACCTGGgtttgtttct ... ctttcctcagGCATGAGCTTCTACTATTTGAAGCCCTTCGAGAAGGCCTGGAAGAAGAAAT
EST: gi|18458826|gb|BM437104.1|BM437104
EST:     GCTTCTGTGACCTCAACTGCATCTAAACCTGG                         GCATGAGCTTCTACTATTTGAAGCCCTTCGAGAAGGCCTGGAAGAAGAAAT
genomic: GCTTCTGTGACCTCAACTGCATCTAAACCTGGgtttgtttct ... ctttcctcagGCATGAGCTTCTACTATTTGAAGCCCTTCGAGAAGGCCTGGAAGAAGAAAT
EST: gi|110376240|gb|EC941289.1|EC941289
EST:     GCGAAGGCGGATGCTTCTGTGACCTCAACTGCATCTAAACCTGG                         GCATGAGCTTCTACTATTTGAAGCCCTTCGAGAAGGCCTGGAAGAAGAAAT
genomic: GCGAAGGCGGATGCTTCTGTGACCTCAACTGCATCTAAACCTGGgtttgtttct ... ctttcctcagGCATGAGCTTCTACTATTTGAAGCCCTTCGAGAAGGCCTGGAAGAAGAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttcaatattgctaattgaggatttagtaaacttaatttgatttctttcctcagGCATGAGCTTCTACTATTTGAAGCCCTTCGAGAAGGCCTGGAAGAAGAAATGGATAGAGATCCCCGAGTATGCGTAATGGGTGAAGACGTGGGCCACTAT
                                     tttgatttctttcctc  CT-rich tract
                      atttagtaaacttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attattactattctcttgttcgcattcataattgttgttcttatgacttcaatattgctaattgaggatttagtaaacttaatttgatttctttcctcagGCATGAGCTTCTACTATTTGAAGCCCTTCGAGAAGGCCTGGAAGAAGAAATGGATAGAGATCCCCGAGTATGCGTAATGGGTGAAGACGTGGGCCACTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - -gcattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agtaaac