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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcatctttaacaggaacaccatgatataataaatgataatgatttggacagttggtcgtgattgatgtatatcacttcagatactacttcgtaatttcttgtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGATGACTACATATCATTTGTTGGCCTCCTAGCAGATCCACGCTATTGTG

Basic information

species Vitis vinifera
transcript Vv04s0008g00650.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g00650.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G10520.1 (Glycine max), 3'ss of exon 4
gtgagcatctttaacaggaacaccatgatataataaatgataatgatttggacagttggtcgtgattgatgtatatcacttcagatactacttcgtaatttcttgtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGATGACTACATATCATTTGTTGGCCTCCTAGCAGATCCACGCTATTGTG
     |||  ||    ||||  |  | | ||  |  ||  |||   |||  |      ||| | ||  |||| | ||  || |    ||| | | || |   |  |   |  ||||||| ||||| || ||||||||||| |||||||| || ||||||   ||||||||||| ||||||||||||||||| ||||||||||| |||||||
----tcatgattccatggaattc--ttacatt-tgcatattaaatgtttatat-----gtcttcatccatgtgt-tctgttgattggctaat-catattccttgtttggttcagATTGCTTATTCACTTATAGAGGAGCAAGAAGGACGAAAGAGATTGCGAGATGACTACATTTCATTTGTTGGCCTCCTTGCAGATCCACGTTATTGTG

upper sequence: Vv04s0008g00650.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G34990.3 (Glycine max), 3'ss of exon 4
gtgagcatctttaacaggaacaccatgatataataaatgataatgatttggacagttggtcgtgattgatgtatatcacttcagatactacttcgtaat--ttcttgtgca-tgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGATGACTACATATCATTTGTTGGCCTCCTAGCAGATCCACGCTATTGTG
              ||   |   | ||   |   | || | |||  |||| ||   |  || |  |||   | | |   ||     |  ||||  | ||  |||||||    |  ||||||| ||||| || ||||||||||| |||||||| || ||||||   ||||||||||| ||||||||||||||||| ||||||||||| |||||||
--------------catagaattcttgcatttgcatatta-aatcttttgtacgtct--tcatccttgtgttctgttgattggttaatcacttaatcatacttcttgtttggttcagATTGCTTATTCACTTATAGAGGAGCAAGAAGGACGAAAGAGATTGCGAGATGACTACATTTCATTTGTTGGCCTCCTTGCAGATCCACGTTATTGTG

upper sequence: Vv04s0008g00650.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G10520.3 (Glycine max), 3'ss of exon 4
gtgagcatctttaacaggaacaccatgatataataaatgataatgatttggacagttggtcgtgattgatgtatatcacttcagatactacttcgtaatttcttgtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGATGACTACATATCATTTGTTGGCCTCCTAGCAGATCCACGCTATTGTG
     |||  ||    ||||  |  | | ||  |  ||  |||   |||  |      ||| | ||  |||| | ||  || |    ||| | | || |   |  |   |  ||||||| ||||| || ||||||||||| |||||||| || ||||||   ||||||||||| ||||||||||||||||| ||||||||||| ||||   
----tcatgattccatggaattc--ttacatt-tgcatattaaatgtttatat-----gtcttcatccatgtgt-tctgttgattggctaat-catattccttgtttggttcagATTGCTTATTCACTTATAGAGGAGCAAGAAGGACGAAAGAGATTGCGAGATGACTACATTTCATTTGTTGGCCTCCTTGCAGATCCACGTTATT---

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|156737847|gb|EV241968.1|EV241968
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|71863241|gb|DT012296.1|DT012296
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAAGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|37183469|gb|CF602823.1|CF602823
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAG
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAG
EST: gi|71865061|gb|DT014116.1|DT014116
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|161720394|gb|FC070186.1|FC070186
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAAGAAAGACAGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|110722833|gb|EE099455.1|EE099455
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|30129707|gb|CB915046.1|CB915046
EST:     TTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
genomic: TTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|71861590|gb|DT010645.1|DT010645
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAG
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAG
EST: gi|161721247|gb|FC070753.1|FC070753
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|71857680|gb|DT006735.1|DT006735
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|71858100|gb|DT007155.1|DT007155
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAAT
EST: gi|161717589|gb|FC066263.1|FC066263
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|161714427|gb|FC063853.1|FC063853
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|71883347|gb|DT032402.1|DT032402
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|71864703|gb|DT013758.1|DT013758
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAAGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|110365546|gb|EC928709.1|EC928709
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|71859768|gb|DT008823.1|DT008823
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|161717170|gb|FC066568.1|FC066568
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|110722784|gb|EE099350.1|EE099350
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|71861002|gb|DT010057.1|DT010057
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAAGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|110385784|gb|EC950339.1|EC950339
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|110724849|gb|EE101037.1|EE101037
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|161715652|gb|FC066797.1|FC066797
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|71885642|gb|DT034697.1|DT034697
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|71881323|gb|DT030378.1|DT030378
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|110720108|gb|EE095742.1|EE095742
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCACGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|161706212|gb|FC054970.1|FC054970
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAA
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAA
EST: gi|34542987|gb|CF511219.1|CF511219
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|161719650|gb|FC067994.1|FC067994
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|161721651|gb|FC069781.1|FC069781
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|33409202|gb|CF214829.1|CF214829
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
EST: gi|110367167|gb|EC931093.1|EC931093
EST:     CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAA                         ATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT
genomic: CATTGTATTTTCAATTTGGCATCAAGCTGCACAATGTTGTGGATACCCAAgtgagcatct ... gtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtgattgatgtatatcacttcagatactacttcgtaatttcttgtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGATGACTACATATCATTTGTTGGCCTCCTAGCAGATCCACGCTATTGTG
    gattgat  putative branch site (score: 4)
                                       tttcttgt  putative PPT
                                    taatttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcatctttaacaggaacaccatgatataataaatgataatgatttggacagttggtcgtgattgatgtatatcacttcagatactacttcgtaatttcttgtgcatgtagATTGCCTATTCTCTAATAGAGGAGCAGGAAGGACGGAAAAGATTGGTGGATGACTACATATCATTTGTTGGCCTCCTAGCAGATCCACGCTATTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT