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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctcctcaattacaaatctaaagtttttattttattgtttgtgtttcatttgtttaacttcttatcacatttagttattttaatttatgaatgatctcagGCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCTGTGGCACCAGTTAAAGGAAATGCAGTGCTTTTTTGGAGCATG

Basic information

species Vitis vinifera
transcript Vv05s0062g01220.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0062g01220.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA20G39250.1 (Glycine max), 3'ss of exon 10
--gctcctcaattacaaatctaa-agtttttattttattgtttgtgtttcatttgtttaacttcttatcacatttagttattttaatttatga-atgatctcagGCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCTGTGGCACCAGTTAAAGGAAATGCAGTGCTTTTTTGGAGCATG
    |  | |  || | || |   |   | |  | | |  ||   |||  |  | || | | |  |    |   | |||| |   || ||  | ||||| |||||||||||| |||   ||| |||||||||||||   ||| | |||| | ||||||  |||| |||||||||||||||||||||| ||||| |||
gtaatagttatctatatatgtgctaacctgttctctgtcattctagttggacattttgaccgtactgatgctgct-gttagt--gatatacaatatgat-tcagGCTGGTTCAGGTGAATGTAGCTGTGGTGGGAAACTTGTCAAAGGGCTATCTGTGAAACCAATTAAAGGAAATGCAGTGCTTTTCTGGAGTATG

upper sequence: Vv05s0062g01220.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA20G39250.2 (Glycine max), 3'ss of exon 10
--gctcctcaattacaaatctaa-agtttttattttattgtttgtgtttcatttgtttaacttcttatcacatttagttattttaatttatga-atgatctcagGCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCTGTGGCACCAGTTAAAGGAAATGCAGTGCTTTTTTGGAGCATG-------
    |  | |  || | || |   |   | |  | | |  ||   |||  |  | || | | |  |    |   | |||| |   || ||  | ||||| |||||||||||| |||   ||| |||||||||||||   ||| | |||| | ||||||  |||| |||||||||||||||||||||| ||||| |||       
gtaatagttatctatatatgtgctaacctgttctctgtcattctagttggacattttgaccgtactgatgctgct-gttagt--gatatacaatatgat-tcagGCTGGTTCAGGTGAATGTAGCTGTGGTGGGAAACTTGTCAAAGGGCTATCTGTGAAACCAATTAAAGGAAATGCAGTGCTTTTCTGGAGTATGGTTAGTG
















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|110370486|gb|EC929820.1|EC929820
EST:     TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATG                         GCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCT
genomic: TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATGgtaattagtt ... atgatctcagGCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCT
EST: gi|110427318|gb|EC993753.1|EC993753
EST:     TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATG                         GCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCT
genomic: TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATGgtaattagtt ... atgatctcagGCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCT
EST: gi|349820405|gb|FQ406961.1|FQ406961
EST:     TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATG                         GCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCT
genomic: TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATGgtaattagtt ... atgatctcagGCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCT
EST: gi|351036556|gb|FQ457269.1|FQ457269
EST:     TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATG                         GCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCT
genomic: TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATGgtaattagtt ... atgatctcagGCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCT
EST: gi|351046420|gb|FQ453036.1|FQ453036
EST:     TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATG                         GCTGGTTCTGGTTTTTG
genomic: TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATGgtaattagtt ... atgatctcagGCTGGTTCTGGTTTTTG
EST: gi|349811155|gb|FQ406107.1|FQ406107
EST:     TCATTTATTTGAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATG                         GCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGG
genomic: TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATGgtaattagtt ... atgatctcagGCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGG
EST: gi|34319741|gb|CF372495.1|CF372495
EST:     TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATG                         GCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCT
genomic: TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATGgtaattagtt ... atgatctcagGCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCT
EST: gi|349807356|gb|FQ401348.1|FQ401348
EST:     TCATTTATTTAAGTGATAATGTTGAAGGGGGAGAAACATATTTCCCTATG                         GCTGGTTCTGGGTTTTGTCGC
genomic: TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATGgtaattagtt ... atgatctcagGCTGGTTCTGGTTTTTGTCGC
EST: gi|351033401|gb|FQ462052.1|FQ462052
EST:     TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATG                         GCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCT
genomic: TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATGgtaattagtt ... atgatctcagGCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCT
EST: gi|30297955|gb|CB974749.1|CB974749
EST:     TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATG                         GCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCT
genomic: TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATGgtaattagtt ... atgatctcagGCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCT
EST: gi|351042433|gb|FQ442900.1|FQ442900
EST:     TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATG                         GCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCT
genomic: TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATGgtaattagtt ... atgatctcagGCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCT
EST: gi|351037271|gb|FQ457104.1|FQ457104
EST:     TCATTTATTTAAGTGATAATGTTGANNNNNNNNAAACATATTTCCCTATG                         GCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCT
genomic: TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATGgtaattagtt ... atgatctcagGCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCT
EST: gi|351032228|gb|FQ460485.1|FQ460485
EST:     TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATG                         GCTGGTTCTGGTTTTTGTCGCTGTGGGTGGGAAGTCTGTTAGAGG
genomic: TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATGgtaattagtt ... atgatctcagGCTGGTTCTGGTTTTTGTCGCTGTGG-TGGGAAGTCTGTTAGAGG
EST: gi|351049572|gb|FQ429194.1|FQ429194
EST:     TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATG                         GCTGGTTCTGGTTTTTGTTGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCT
genomic: TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATGgtaattagtt ... atgatctcagGCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCT
EST: gi|351052197|gb|FQ450767.1|FQ450767
EST:     TCATTTATNTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATG                         GCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTA
genomic: TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATGgtaattagtt ... atgatctcagGCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTA
EST: gi|351055664|gb|FQ452129.1|FQ452129
EST:     TCATTTATTTAAGTGATAGTGTTGAGGGGGGAGAAACATATTTCCCTATG                         GCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCT
genomic: TCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATGgtaattagtt ... atgatctcagGCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatttgtttaacttcttatcacatttagttattttaatttatgaatgatctcagGCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCTGTGGCACCAGTTAAAGGAAATGCAGTGCTTTTTTGGAGCATG
                                ttttaat  putative branch site (score: 3)
       tttaacttcttatcac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctcctcaattacaaatctaaagtttttattttattgtttgtgtttcatttgtttaacttcttatcacatttagttattttaatttatgaatgatctcagGCTGGTTCTGGTTTTTGTCGCTGTGGTGGGAAGTCTGTTAGAGGGTTGTCTGTGGCACCAGTTAAAGGAAATGCAGTGCTTTTTTGGAGCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
-ctcctca
- - - - - -acaaatc