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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcatggatcttgattcttataaacgattaattactgaaatttaatcttattctggaaagcttattttgcaactgatatattagtgaagcttgat...

Basic information

species Vitis vinifera
transcript Vv08s0007g01980.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 5'ss of exon 3
CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcatggatcttgattcttataaacgat-taattactgaaatttaatcttattctggaaagcttattttgcaactgata-tattagtgaagcttgat
|||||||||| || ||||| ||||||||||| || ||||||||  ||||||| ||| | ||||| |||| ||| ||| || |||| | | ||| | |     | |||||  |  | |  ||  |||| ||  ||  |   || || |  || |||||   |   || | ||  | ||  |   |
CCAAGGAGCATGTTGTTGGCTGGTACAGCACCGGTCCAAAACTCAGGGAGAACGACTTGGATATACACGCACTATTCAATAAgtatg-tgatgtaccgaagct-ttatatcctgtattgttcatgaagttatattcttgactagatatgttgttttggtgcaagtaatctttattaaattgtct

upper sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 3
CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcatggatcttgattcttataaacgattaattactgaaatttaatcttattctgga-aagcttattttgcaactgatatattagtgaagcttgat--
|||||||||| || ||||| ||||||||||| || ||||||||  ||||||||||| | ||| | || | | ||||| |   ||  |    || | ||  |     |   | |     |||  |   ||   |   | |||  | |       |  || |  || | ||  || ||  |  |   
CCAAGGAGCATGTTGTTGGCTGGTACAGCACTGGCCCAAAACTAAGGGAGAATGACTTGGATGTCCATGCATTGTTCAACAGgtgtg---gtgaacctgcaagtgaagttatgtcctcttatggttgttcttttaaactcttaatacaacccctgagctatagacaaatatgtaaatttccaaac

upper sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: EFJ23777 (Selaginella moellendorffii), 5'ss of exon 3
CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcatggatcttgattcttataaacgattaattactgaaatttaatcttattctggaaagcttattttgcaactgatatattagtgaagcttgat
| ||||||||||| ||||||||||||||||| || || ||||| || ||||| || || || |||||||  || ||     ||| ||       |  ||| ||||      | |||  |       |||  |||||  ||        || | |     ||  | ||  ||           
CGAAGGAGCACGTTGTTGGATGGTACAGCACTGGTCCCAAACTACGTGAGAACGATCTTGACATTCACGAGCTCTTTAGGAAgtgag------aaatttgtttct------ctatttttcttctggattctatcttgctc------atttgtgtgattgct--tctaccag-----------

upper sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: EFJ21414 (Selaginella moellendorffii), 5'ss of exon 3
CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcatggatcttgattcttataaacgattaattactgaaatttaatcttattctggaaagcttattttgcaactgatatattagtgaagcttgat
| ||||||||||| ||||||||||||||||| || || ||||| || ||||| || || || |||||||  || ||     ||| ||       || ||| ||||         ||  || |||   |||   || |||   |  |     | |  ||                        
CGAAGGAGCACGTTGTTGGATGGTACAGCACTGGTCCCAAACTACGTGAGAACGATCTTGACATTCACGAGCTCTTTAGGAAgtgag-----aaattttgtttctctcttcttctttttttctg---tttg--ctcatttgtgtgattacgtctaccag-----------------------

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|71862429|gb|DT011484.1|DT011484
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCA
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCA
EST: gi|161713904|gb|FC062870.1|FC062870
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|71861116|gb|DT010171.1|DT010171
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATT
EST: gi|110689439|gb|EE065663.1|EE065663
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|30125091|gb|CB910430.1|CB910430
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|110697690|gb|EE074900.1|EE074900
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|33406800|gb|CF212427.1|CF212427
EST:     AGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: AGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|37188068|gb|CF607419.1|CF607419
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|30297109|gb|CB973903.1|CB973903
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|37188648|gb|CF607997.1|CF607997
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTC
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTC
EST: gi|33409710|gb|CF215337.1|CF215337
EST:     GACCAAAACTGGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GACCAAAACT-GCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|294965591|gb|GW837190.1|GW837190
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|71864815|gb|DT013870.1|DT013870
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|294967321|gb|GW836675.1|GW836675
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|110713466|gb|EE089412.1|EE089412
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|110711679|gb|EE088432.1|EE088432
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|71859938|gb|DT008993.1|DT008993
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|110687327|gb|EE064641.1|EE064641
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|37186349|gb|CF605702.1|CF605702
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAA
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAA
EST: gi|161712650|gb|FC062222.1|FC062222
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|110718297|gb|EE094970.1|EE094970
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|30321841|gb|CD005103.1|CD005103
EST:     GGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCGTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|71864932|gb|DT013987.1|DT013987
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|29783602|gb|CB349901.2|CB349901
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|18459292|gb|BM437570.1|BM437570
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|110732758|gb|EE108326.1|EE108326
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|110690336|gb|EE067344.1|EE067344
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|33406603|gb|CF212230.1|CF212230
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|110396200|gb|EC961881.1|EC961881
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|110401013|gb|EC967604.1|EC967604
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|161721407|gb|FC070435.1|FC070435
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
EST: gi|110712994|gb|EE088527.1|EE088527
EST:     GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGA                         CTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT
genomic: GGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcat ... ggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAAGGAGCACGTGGTTGGATGGTACAGCACAGGACCAAAACTGCGGGAGAATGACCTAGATATTCACGGACTGTTCCATGAgtaagctcatggatcttgattcttataaacgattaattactgaaatttaatcttattctggaaagcttattttgcaactgatatattagtgaagcttgat

- - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggaaag