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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctctttcatgagatgtcttgttgaaaacaccatctttcagataaggcaaaagtcgtctgctaacttataatctcattgggaattacttataaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCAGATGTTGATGTTAGGTTTTTTGCAAGCCAAGCACTACAGGCAAGTGATC

Basic information

species Vitis vinifera
transcript Vv17s0000g03870.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 12
cctctttcatgagatgtcttgttgaaaacaccatctttcagataaggcaaaagtcgtctgctaacttataatctcattgggaattac---ttataaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCAGATGTTGATGTTAGGTTTTTTGCAAGCCAAGCACTACAGGCAAGTGATC
    |   |||| |||  ||| |   |     | |  |    |    | |||  | ||   |   |||  ||||| |    |||||    ||  | |||| |||| || || |  || ||||||||||||||||||||||| |||||||| ||||||||||||||||||||||| ||    |||||||||||  |  ||||||
--aatgatatgaaatgcattgctattacagaaaaccgttgagtctctccaaatgcatc-attcttttaatatctcttaactaattatcttttgaacaatgaagGTTGTTGAGAGTACCATTCGTCCCTGTTTGGTTGAGCTCAGTGAGGATCCAGATGTTGATGTTAGGTTTTTCGCCTCACAAGCACTACAATCTTGTGATC

upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 11
cctctttcatgagatgtcttg----ttga--aaacaccatc---tttcagataaggcaaaagtcgtctgctaacttataatctcattgggaattacttataaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCAGATGTTGATGTTAGGTTTTTTGCAAGCCAAGCACTACAGGCAAGTGATC
    |   |||| |||  |||    ||||   || || ||    | ||    || |||  | || | |  || ||  ||| || |||    ||   ||  | |||| |||| || || |  || || ||||||||| |||||||||| |||||||| ||||||||||||||||||||||| ||    |||||||||||  | |||||||
----tgatatgaaatgcattgcaatttgacagaaaactattgagtctctccaaatgcatcattcttttaatatctcttaa-ctaatt----atcgtttgaataatgaagGTTGTTGAGAGTACCATCCGTCCCTGTCTGGTTGAGCTCAGTGAGGATCCAGATGTTGATGTTAGGTTTTTCGCCTCACAAGCACTACAATCTAGTGATC
















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|71877536|gb|DT026591.1|DT026591
EST:     TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|349825185|gb|FQ415732.1|FQ415732
EST:     TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACAATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|352769560|gb|FQ468488.1|FQ468488
EST:     TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|352776768|gb|FQ472655.1|FQ472655
EST:     TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|27584295|gb|CB006990.1|CB006990
EST:     TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|352763870|gb|FQ465320.1|FQ465320
EST:     TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|110414406|gb|EC980237.1|EC980237
EST:     TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|71880317|gb|DT029372.1|DT029372
EST:     TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|30134721|gb|CB920059.1|CB920059
EST:     TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|352787200|gb|FQ477820.1|FQ477820
EST:     TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACAATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|22012824|gb|BQ797858.1|BQ797858
EST:     TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACAATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|110427969|gb|EC994426.1|EC994426
EST:     GTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: GTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|33404973|gb|CF210600.1|CF210600
EST:     TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|32246186|gb|CD712005.1|CD712005
EST:     TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|110691608|gb|EE069902.1|EE069902
EST:     TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|110399866|gb|EC966397.1|EC966397
EST:     TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|33405058|gb|CF210685.1|CF210685
EST:     TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|110429193|gb|EC995682.1|EC995682
EST:     TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|22012767|gb|BQ797801.1|BQ797801
EST:     TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|110697249|gb|EE074074.1|EE074074
EST:     TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|351031302|gb|FQ445327.1|FQ445327
EST:     TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACAATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|110428387|gb|EC994857.1|EC994857
EST:     TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|110413858|gb|EC979672.1|EC979672
EST:     GCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: GCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|30300336|gb|CB977130.1|CB977130
EST:     TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|110388878|gb|EC953676.1|EC953676
EST:     TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|110411876|gb|EC977604.1|EC977604
EST:     TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
EST: gi|110420001|gb|EC986261.1|EC986261
EST:     TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCT                         GTGGTAGACAAGACAATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA
genomic: TCAATGTGGCTAAGGTGTTGCAGTCACTTACTCCTATAGTGGACCAGTCTgtaagtaacc ... taaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcaaaagtcgtctgctaacttataatctcattgggaattacttataaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCAGATGTTGATGTTAGGTTTTTTGCAAGCCAAGCACTACAGGCAAGTGATC
             tgctaac  putative branch site (score: 1)
                                    aattacttataaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctctttcatgagatgtcttgttgaaaacaccatctttcagataaggcaaaagtcgtctgctaacttataatctcattgggaattacttataaaatgcagGTGGTAGACAAGACGATTCGTCCCTGTTTGGTTGAGCTGAGTGAGGACCCAGATGTTGATGTTAGGTTTTTTGCAAGCCAAGCACTACAGGCAAGTGATC

- - - -catgaga
- - - - - - - tgtcttg
- - - - - - - - - - -ttgaaaa
- - - - - - - - - - - - - - caccatc
- - - - - - - - - - - - - - - - - - - - - - -ggcaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - cgtctgc