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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtttattaattaaattgcaatgcatgttgtctctttttgtcggcattggaatgatgaggttatgatgcaacatttattcattacacagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGA

Basic information

species Vitis vinifera
transcript Vv17s0000g09500.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 9
gtacgtttattaattaaattgcaatgcatgttgtctctttt-tgtcggcattggaatgatgaggttatgatgcaacatttattcattacacagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGA
    || | ||  |     ||||||   || | | | || | |  |  ||   | | |||    ||  | | | | |  ||       | ||||||||||||||||||||||| ||||| ||  ||||||| ||||| |||||||| ||||| || |||||  ||||    |||||||| || || | |||
----gtatgttgttggg--tgcaatatttggtttgtattctatcacaacaacagcaggattt--ttgagttacgaaagctac------cgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA17G13440.1 (Glycine max), 3'ss of exon 7
gtacgttta-ttaattaaattgcaatgcatgttgtctctttttgtcggcattggaatgatgaggttatgatgcaacatttattcattacacagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGA
||| ||||   |   | || | |  |  |       | ||| |       || || |    |    || ||     |   ||| ||   |||||| | ||| |||||||||||||| || ||| ||||||| ||||||||||||||||||||  | |||||| | || |||| |||| |||||||||| ||
gtatgtttggctctctcaaatcctgtataaaaaacatatttatccatctcttagatt--ctattccataatttgtga---atttatattacagGGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA05G02740.1 (Glycine max), 3'ss of exon 8
gtacgtttattaatt---aaattgcaatgcatgttgtctctttttgtcggcattggaatgatgaggttatgatgcaacatttattcattacacagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGA
||| ||||     ||   |||     || ||       | | |   ||  |||   |  |||    || | ||    |||  |||  |   |||||| ||||| ||||||||||||||||| ||| | ||||| ||||| ||||||||||||||  | ||| || | || |||  |||| |||||||||| ||
gtatgtttggctctttcaaaacctttatacaaagcacatttatccatct-catatcatagattgtattct-ataattcatgaatttgtattacagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTTGCAATGATGGAAAGGGTACTTGGTTCATTACCACAGACCATGATGAAGAGAGTCGA

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 8
gtacgtttattaattaaattgcaatgcatgttg-tctctttttgtcggcattggaatgatgaggttatgatgcaacatttattcattacacagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGA
||| ||||     |     | |  |  | |||  | |  |   ||     |||     || || ||||||       | ||||       ||||| ||||| ||||||||||||||||| ||| | ||||| || ||||||||||| |||||| | |||||  | || ||||| ||| | |||||||| ||
gtaagtttggctctctggatacttttgaggttaatattatccagtttttgttgtttaaatcagcttatga----gtttctatt------gcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATGGAGAGGGTGCTTGGTCCTATACCACAGCAGATGTTAAAGAGAGTTGA

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 8
gtacgtttattaattaaattgcaatgcatgttgtctctttttgtcggcattggaatgatgaggttatgatgcaacatttattcattacacagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGA
||| ||||     |     | |  |  | |   | |  |   ||     |||     || || |||||      | | ||||       ||||| ||||| ||||||||||||||||| ||| | ||||| || || |||||||| |||||| | |||||  | || ||||| ||| | |||||||| ||
gtaagtttggctctctggatactttttaggcaattttatccagttttgtttgtttaaatcagcttatgg----gcttctatt------gcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCTATGATGGAGAGGGTGCTTGGTCCTATACCACAGCAGATGTTAAAGAGAGTTGA

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S132_58V6.1 (Physcomitrella patens), 3'ss of exon 9
------------------------------------------------------------------------gtacgtttattaatt--aaattgcaatgcatgttgtctctttttgtc----ggcattggaat-gatgaggttatgatgcaacattta-----ttcattaca-cagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGA
                                                                          |   || | ||||  | |      |  ||||  |   ||||  |     |   ||| ||   |||    | |  | ||    |||     ||   ||   ||||| || ||||||||||||||||| |||||| |||||||  | || ||||||||| | || || |||||  | ||    |||||| | ||||| | |||
gtatgggattcctatcgccttcctttctcttttatattcctctattatccagtaattccctatactttctcttcaaacttgtaaatttgagaaaatctttgatgtcatagtttttcatgcgaagatgttgaaaccaatgtaaatgtttttcagtggttacagtatttgctatggcagGGTGATGCATTGTTTCAGACTCACGAGAATTTGGAGCATTTGGCTATGATGGAACGAGTCTTAGGTCCTATTCCTGTACACATGATCAAGAGGGCAGA

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: EFJ20929 (Selaginella moellendorffii), 3'ss of exon 6
gtacgtttattaattaaattgcaatgcatgttgtctctttttgtcggcattggaatgatgaggtta--tgatgcaacatttattcattaca--cagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGA
                                              | |    ||     | ||    | ||   | |||| ||   | |   ||||||||  |||||||||||||||| || ||||| |||||||| || |||||||||||  |  | |||||  | ||    | |||  |  | |  |||||
----------------------------------------------gtaagaaaactgcaaagtccattaatctcatatttcttggctgcttccagGGAGATCCATTGTTTCAGACTCACGAAAATCTCGAGCACCTGGCAATGATGGAAAGAATTCTCGGTCCCATTCCCAGACGCATAATCGATAACGTAGA

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: EFJ32324 (Selaginella moellendorffii), 3'ss of exon 8
gtacgtttattaattaaattgcaatgcatgttgtctctttttgtcggcattggaatgatgaggtta--tgatgcaacatttattcattaca--cagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGA
                                              | |    ||    || ||    | ||   | |||| ||   | |   ||||||||  || ||||||||||||| || ||||| |||||||| || |||||||||||  |  | |||||  |  |    | |||  |  | |  |||||
----------------------------------------------gtaagaaaactgcgaagtccattaatctcatatttcttggctgcttccagGGAGATCCACTGTTTCAGACTCACGAAAATCTCGAGCACCTGGCAATGATGGAAAGAATTCTCGGTCCCATTTCCAGACGCATAATCGATAACGTAGA

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: EFJ20930 (Selaginella moellendorffii), 3'ss of exon 7
gtacgtttattaattaaattgcaatgcatgttgtctctttttgtcggcattggaatgatga--ggttatgatgcaacatttattcattaca--cagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGA
                                         |      | || || |   |  | ||   ||   | |||| ||   | |   ||||||||  || ||||||||||||| || ||||| ||||||||||| |||||||||||  |  | |||||  | ||    | |||  |  | |  |||||
----------------------------------------gtaagaaaactgcaaagtccattgattccaatcttatatttcttggctgcttccagGGAGATCCACTGTTTCAGACTCACGAAAATCTCGAGCACCTTGCAATGATGGAAAGAATTCTCGGTCCCATTCCCAGACGCATAATCGATAACGTAGA

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|30322713|gb|CD005975.1|CD005975
EST:     ATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGA
genomic: ATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACGgtacgtttat ... cattacacagGGAGAAGCATTGTTTCAGACTCATGA
EST: gi|30133828|gb|CB919167.1|CB919167
EST:     GATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAGAATCTGGAGCACCTTGCCATGATG
genomic: GATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACGgtacgtttat ... cattacacagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATG
EST: gi|222357016|gb|GH717878.1|GH717878
EST:     ATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAGAATCTGGAGTACCTTGCCATGATG
genomic: ATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACGgtacgtttat ... cattacacagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATG
EST: gi|110373955|gb|EC938383.1|EC938383
EST:     ATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAGAATCTGGAGCACCTTGCCATGATG
genomic: ATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACGgtacgtttat ... cattacacagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATG
EST: gi|71886247|gb|DT035302.1|DT035302
EST:     ATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAGAATCTGGAGCACCTTGCCATGATG
genomic: ATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACGgtacgtttat ... cattacacagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATG
EST: gi|110362754|gb|EC926306.1|EC926306
EST:     ATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAGAATCTGGAGCACCTTGCCATGATG
genomic: ATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACGgtacgtttat ... cattacacagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATG
EST: gi|71889805|gb|DT038860.1|DT038860
EST:     ATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAGAATCTGGAGCACCTTGCCATGATG
genomic: ATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACGgtacgtttat ... cattacacagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATG
EST: gi|32272087|gb|CD721246.1|CD721246
EST:     ATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAGAATCTGGAGCACCTTGCCATGATG
genomic: ATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACGgtacgtttat ... cattacacagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATG
EST: gi|32268109|gb|CD717268.1|CD717268
EST:     ATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAGAATCTGGAGCACCTTGCCATGATG
genomic: ATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACGgtacgtttat ... cattacacagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATG
EST: gi|30255726|gb|CB971858.1|CB971858
EST:     ATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAGAATCTGGAGCACCTTGCCATGATG
genomic: ATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACGgtacgtttat ... cattacacagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATG
EST: gi|30324825|gb|CD008087.1|CD008087
EST:     ATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAGAATCTGGAGCACCTTGCCATGATG
genomic: ATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACGgtacgtttat ... cattacacagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATG
EST: gi|32268970|gb|CD718129.1|CD718129
EST:     ATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAGAATCTGGAGCACCTTGCCATGATG
genomic: ATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACGgtacgtttat ... cattacacagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATG
EST: gi|32248754|gb|CD714573.1|CD714573
EST:     ATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACG                         GGAGAAGCATTGTTTCAGACCCATGAGAATCTGGAGCACCTTGCCATGATG
genomic: ATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACGgtacgtttat ... cattacacagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgtcggcattggaatgatgaggttatgatgcaacatttattcattacacagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGA
                                       tttattc  CT-rich tract
                                   aacatttattcatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtttattaattaaattgcaatgcatgttgtctctttttgtcggcattggaatgatgaggttatgatgcaacatttattcattacacagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA