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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcaaaaataattataattttatgaccataggattgaccatgtattggttattattaagattatttgaagcccaattttcttcatgttaaagGTTGATGGGCTGATTCGACTCATGGAAGGAGAGAACACTGGGCCAATCAACATTGGAAACCCAG

Basic information

species Vitis vinifera
transcript Vv06s0004g04390.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA12G06980.1 (Glycine max), 3'ss of exon 10
--gtatgcaaaaataattataattttatg-accataggattgac-catgtattggttattattaagattatttgaagcccaattttcttcatgttaaagGTTGATGGGCTGATTCGACTCATGGAAGGAGAGAACACTGGGCCAATCAACATTGGAAACCCAG
   |||   | | |  ||    ||||  |     |    ||||  || ||| | | | | ||| |   |  |   |       ||      | |||  ||||||||| || || || || |||||||| || |||||||| |||||||||||||| |||||||
gtatatattatacttgtttctcttttgagtgttgttatcttgattcaagtactaggtgtgattgactatgatcatatatacgcttgaaatttatta--gGTTGATGGACTTATACGTCTAATGGAAGGGGAAAACACTGGTCCAATCAACATTGGGAACCCAG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 10
gtatgcaaaaataattataattttatgaccataggat-tgaccatgtattggttattat-taagattatttgaagcccaattttcttcatgttaaagGTTGATGGGCTGATTCGACTCATGGAAGGAGAGAACACTGGGCCAATCAACATTGGAAACCCAG
    | | | || ||     |||  |     |    | | | | ||  |    || ||     ||||   | |      |  ||    || |   |||||||||| || || || || |||||||| || |||||||| |||||||||||||| |||||||
----gtatatatgatacatgtttcttatttgtgatttattatcttgattcaagtactaggcgtgattgactaagattatacatttgaaatctattagGTTGATGGACTTATACGTCTAATGGAAGGGGAAAACACTGGTCCAATCAACATTGGGAACCCAG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 10
gtatgcaaaaataattataattttatgaccataggattgaccatgtattg-gttattattaagattatttgaagcccaattttcttcat-gttaaagGTTGATGGGCTGATTCGACTCATGGAAGGAGAGAACACTGGGCCAATCAACATTGGAAACCCAG
                     | |||  |  | | ||      |  |||| |||| | |||  |||   | ||||  | | |  || || || | |||||||||| || || || ||||||||||||    ||||||||||||||||| ||||||| ||||
------------------gtatatatctcatttgcatctttgtttcattgagttactgttagtatttggt-aagctgattatgttttattgtgatagGTTGATGGACTTATCCGTCTCATGGAAGGATCCGACACTGGGCCAATCAACCTTGGAAATCCAG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA15G04500.1 (Glycine max), 3'ss of exon 11
gtatgcaaaaataattataattt-tatgaccataggattgaccatgtattggttattattaagattatttgaagcccaattttcttcatgttaaagGTTGATGGGCTGATTCGACTCATGGAAGGAGAGAACACTGGGCCAATCAACATTGGAAACCCAG
    | |||  |    ||||| | | |  |  ||   |    | || || | | | | | |  || | || | |    ||||     ||||   |||||||||| || || || ||||||||||||   ||||| || ||||||||| ||||||||||||
----gtaaatgtc-ccataatctatgtatctttaaattactacctgaatagctgaatgtgattatgaatttatgat--atttatgagatgtcttagGTTGATGGCCTTATCCGTCTCATGGAAGGATCAAACACCGGACCAATCAACCTTGGAAACCCAG

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|71885522|gb|DT034577.1|DT034577
EST:     TTCAGGCTCCTGGAACACAGACTCGCAGTTTCTGCTATGTCTCTGACATG                         GTTGATGGGCTGATTCGACTCATGGAAGGAGAGAACACTGGGCCAATCAAC
genomic: TTCAGGCTCCTGGAACACAGACTCGCAGTTTCTGCTATGTCTCTGACATGgtatgcaaaa ... catgttaaagGTTGATGGGCTGATTCGACTCATGGAAGGAGAGAACACTGGGCCAATCAAC
EST: gi|33407209|gb|CF212836.1|CF212836
EST:     TTCAGGCTCCTGGAACACAGACTCGCAGTTTCTGCTATGTCTCTGACATG                         GTTGATGGGCTGATTCGACTCATGGAAGGAGAGAACACTGGGCCAATCAAC
genomic: TTCAGGCTCCTGGAACACAGACTCGCAGTTTCTGCTATGTCTCTGACATGgtatgcaaaa ... catgttaaagGTTGATGGGCTGATTCGACTCATGGAAGGAGAGAACACTGGGCCAATCAAC
EST: gi|71888765|gb|DT037820.1|DT037820
EST:     TTCAGGCTCCTGGAACACAGACTCGCAGTTTCTGCTATGTCTCTGACATG                         GTTGATGGGCTGATTCGACTCATGGAAGGAGAGAACACTGGGCCAATCAAC
genomic: TTCAGGCTCCTGGAACACAGACTCGCAGTTTCTGCTATGTCTCTGACATGgtatgcaaaa ... catgttaaagGTTGATGGGCTGATTCGACTCATGGAAGGAGAGAACACTGGGCCAATCAAC
EST: gi|30297461|gb|CB974255.1|CB974255
EST:     TTCAGGCTCCTGGAACACAGACTCGCAGTTTCTGCTATGTCTCTGACATG                         GATGATGANCTGATTCGTCTCAT
genomic: TTCAGGCTCCTGGAACACAGACTCGCAGTTTCTGCTATGTCTCTGACATGgtatgcaaaa ... catgttaaagGTTGATGGGCTGATTCGACTCAT
EST: gi|33407983|gb|CF213610.1|CF213610
EST:     TTCAGGCTCCTGGAACACAGACTCGCAGTTTCTGCTATGTCTCTGACATG                         ATTGATGGATTGATTCGACTCATGGAAGGAGAGAACACTGATCCAATCAAC
genomic: TTCAGGCTCCTGGAACACAGACTCGCAGTTTCTGCTATGTCTCTGACATGgtatgcaaaa ... catgttaaagGTTGATGGGCTGATTCGACTCATGGAAGGAGAGAACACTGGGCCAATCAAC
EST: gi|56408375|gb|CX016627.1|CX016627
EST:     TTCAGGCTCCTGGAACACAGACTCGCAGTTTCTGCTATGTCTCTGACATG                         GTTGATGGGCTGATTCGTCTCATGGAAGGAGAGAACACTGGGCCAATCAAC
genomic: TTCAGGCTCCTGGAACACAGACTCGCAGTTTCTGCTATGTCTCTGACATGgtatgcaaaa ... catgttaaagGTTGATGGGCTGATTCGACTCATGGAAGGAGAGAACACTGGGCCAATCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatgtattggttattattaagattatttgaagcccaattttcttcatgttaaagGTTGATGGGCTGATTCGACTCATGGAAGGAGAGAACACTGGGCCAATCAACATTGGAAACCCAG
                                      ttttcttcat  CT-rich tract
     tattggttattattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcaaaaataattataattttatgaccataggattgaccatgtattggttattattaagattatttgaagcccaattttcttcatgttaaagGTTGATGGGCTGATTCGACTCATGGAAGGAGAGAACACTGGGCCAATCAACATTGGAAACCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA