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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagtctttgggtcaatgcatattttaatatttgtcttagtcgttgatagttaatgtgtttgctcattggtcctgtaatgtaaattaattttgattgcagGTTTGACAGGAAACTGAAGAACACATACGATCATCTTCTTTTCAGCAG

Basic information

species Vitis vinifera
transcript Vv09s0002g00100.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os03g08570.1 (Oryza sativa), 3'ss of exon 10
-ttagtctttgggtcaatgcatattttaatatttgtcttagtcgttgat-agttaatgtgtttgctcattggtcctgta---atgtaaattaattttga--ttgcagGTTTGACAGGAAACTGAAGAACACATACGATCATCTTCTTTTCAGCAG
 || ||   | |    ||     ||  ||        ||| || |     ||||  ||  | | || ||   || | |    || |   ||  |||  |  || ||||||||| || ||||||||||||||||| || || ||||||||||||||
gttggttggttgaattatttg-gttccaagtcggaaattactcatcatcgagtttgtggttctccttatgactcatattagtatttctgttggtttgaacatttcagGTTTGATAGAAAACTGAAGAACACATATGACCACCTTCTTTTCAGCAG

upper sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 10
-----------------ttagtctttgggtcaatgcatattttaata--tttgtcttagtcg---ttgatagttaatgtgtttgctcattggtcctgtaatgtaaattaattttgattgc---agGTTTGACAGGAAACTGAAGAACACATACGATCATCTTCTTTTCAGCAG
                 || |  | ||      || ||    | ||    ||||||   |     ||| | ||  |    |||    |    | ||| ||  |    |  |||||| | |   ||||||||||| |||||||| |||||||| || || ||||||||||||||
gttagttgattgaaatatttggttctgaactg-tgaattgcctgattcccttgtctggattatgcttgttcgtcgagacatttctgaagctttgctgaaaatttctgttgttttgaatacctcagGTTTGACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAG

upper sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA11G36810.1 (Glycine max), 3'ss of exon 9
ttagtc-tttgggtcaatgcatattttaatatttgtcttagtcgttgatagttaatgtgtttgctcat-tggtcctgtaatgtaaattaattttgattgcagGTTTGACAGGAAACTGAAGAACACATACGATCATCTTCTTTTCAGCAG
|  ||          ||   |  || |||| |||||       | | ||| |||   | |   ||  | ||||    || | || ||  || | | ||||||||||||||| ||||||||||||||||| ||||| ||||| || |||||
tgggtaacaccaacaaaaataatttgtaatgtttgtggataatgattata-ttataatctccactgttgtggtgacatactatatatgcatgt-gtttgcagGTTTGACAGAAAACTGAAGAACACATATGATCACCTTCTCTTTAGCAG

upper sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA18G00720.2 (Glycine max), 3'ss of exon 5
ttagtctttgggtcaatgcatattt-taatatttgtcttagtcgttgatagttaatgtgtttgctcat-tggtcctgtaatgtaaattaattttgattgcagGTTTGACAGGAAACTGAAGAACACATACGATCATCTTCTTTTCAGCAG
    |        ||| |   |||| |||| |||||       | | ||| ||| | | |   ||  | || |    || | || ||  ||     ||||||||||||||| ||||||||||||||||| ||||| ||||| || |||||
-ggataacgccaacaaagttaatttgtaatgtttgtggataatgattata-ttattatctccactggtgtgatgacatactatatatgcatcgcatttgcagGTTTGACAGAAAACTGAAGAACACATATGATCACCTTCTCTTTAGCAG

upper sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: EFJ23885 (Selaginella moellendorffii), 3'ss of exon 10
ttagtctttgggtcaatgcatattttaatatttgtcttagtcgttgatagttaatgtgtttgctcattggtcctgtaatgtaaattaattttgat---tgcagGTTTGACAGGAAACTGAAGAACACATACGATCATCTTCTTTTCAGCAG
                                                   ||||| ||||| | || ||||   ||     | | | | ||| |   ||||||||||||||||| || || ||||| ||||| |||||| | ||||||||
--------------------------------------------------gtaatgcgtttgat-atcggtctgatacgtccagtaactattggtatttgcagGTTTGACAGGAAGCTAAAAAACACTTACGACCATCTTTTATTCAGCAG

upper sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: EFJ10018 (Selaginella moellendorffii), 3'ss of exon 9
ttagtctttgggtcaatgcatattttaatatttgtcttagtcgttgatagttaatgtgtttgctcattggtcctgta-atgta--aattaattttgattgcagGTTTGACAGGAAACTGAAGAACACATACGATCATCTTCTTTTCAGCAG
                                                   ||||| ||||| | || ||||   ||  || |  || || |  |  |||||||||||||||||| || || ||||| ||||| |||||| | ||||||||
--------------------------------------------------gtaatgcgtttgat-atcggtctgatacgtgcagtaactattggtatttgcagGTTTGACAGGAAGCTAAAAAACACTTACGACCATCTTTTATTCAGCAG

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|110392879|gb|EC957437.1|EC957437
EST:     AGGAGATTGGATAAATTAGTTGGAGTTCCAGTGATCAATGTTCATATATG                         GTTTGACAGGAAACTGAAGAACACATACGATCATCTTCTTTTCAGCAG
genomic: AGGAGATTGGATAAATTAGTTGGAGTTCCAGTGATCAATGTTCATATATGgttagttcta ... ttgattgcagGTTTGACAGGAAACTGAAGAACACATACGATCATCTTCTTTTCAGCAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatagttaatgtgtttgctcattggtcctgtaatgtaaattaattttgattgcagGTTTGACAGGAAACTGAAGAACACATACGATCATCTTCTTTTCAGCAG
                            tgtaatgtaaattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagtctttgggtcaatgcatattttaatatttgtcttagtcgttgatagttaatgtgtttgctcattggtcctgtaatgtaaattaattttgattgcagGTTTGACAGGAAACTGAAGAACACATACGATCATCTTCTTTTCAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - -caatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaattaa