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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgaaattttgcttttaaaacatagtcctttttatgaaatataaaggcaattgctttaaaaacttatcattcatattctcttattctttacaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGTTCAAAGTTTGCAGAG

Basic information

species Vitis vinifera
transcript Vv00s0211g00120.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 9
tatgaaattttgcttttaaaacatagtcctttttatgaaatataaaggcaattgctttaaaaacttatcattcatattctcttattctttacaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGTTCAAAGTTTGCAGAG
        |   |   | |  |||  |  ||  ||| |    | |     |||| |||      |||| | || | |   ||| |  |||| |  | ||||| |||||| ||||||||| |||||| |||||||||||| ||  ||||||| | || |||||  ||
-----gtctgctccacttattcatgttgtttaatattatcctttattcatattg-tttgcctttttatgagtc-tctcagcttttattttatattt-cagGCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG

upper sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 10
tatgaaattttgcttttaaaacatagtcctttttatg-aaatataaaggcaattgc-tttaaaaacttatcattcatattctcttattctttacaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGTTCAAAGTTTGCAGAG
||||   | |   | |   ||  ||    | | |||  | ||||| |   |  |   | || | |  ||| ||  ||||     |  ||||    ||||||||| |||||| | ||||| | ||| ||||||||||||||||||   ||  | |  || |||||| ||
tatgtgctctgcatatattaatttatatatatatatatatatatatatatatatatatatatatatatat-atatatatataact-ctcttggtgaatgcagGCCACTACTCCCGAATATAGAGCATATCAAGAGCAAGTTCTCAGCAACAGCTTTAAATTTGCACAG
















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|33407197|gb|CF212824.1|CF212824
EST:     GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|349827018|gb|FQ419109.1|FQ419109
EST:     GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|32270628|gb|CD719787.1|CD719787
EST:     GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|29785535|gb|CB342622.2|CB342622
EST:     GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|110361521|gb|EC925002.1|EC925002
EST:     GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|352763948|gb|FQ465398.1|FQ465398
EST:     ATTGCTGGCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: ATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|110379633|gb|EC944843.1|EC944843
EST:     GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|29784993|gb|CB341601.2|CB341601
EST:     GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|27755145|gb|CB035900.1|CB035900
EST:     GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|27578509|gb|CB001204.1|CB001204
EST:     GCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: GCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|32250249|gb|CD716068.1|CD716068
EST:     GCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: GCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|351030429|gb|FQ432367.1|FQ432367
EST:     GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|352781813|gb|FQ469111.1|FQ469111
EST:     TCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: TCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|352780984|gb|FQ466297.1|FQ466297
EST:     CTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: CTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|294966171|gb|GW839394.1|GW839394
EST:     GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTA
genomic: GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTA
EST: gi|30133417|gb|CB918756.1|CB918756
EST:     GCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: GCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|110361068|gb|EC924521.1|EC924521
EST:     GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|351016424|gb|FQ423851.1|FQ423851
EST:     GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|110373188|gb|EC937406.1|EC937406
EST:     GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|352777748|gb|FQ466801.1|FQ466801
EST:     TGCATTGAAACAG                         GGTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: TGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|110363609|gb|EC927210.1|EC927210
EST:     GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|110413717|gb|EC979522.1|EC979522
EST:     GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|351029249|gb|FQ435449.1|FQ435449
EST:     GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|32246995|gb|CD712814.1|CD712814
EST:     CCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: CCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|29785493|gb|CB342547.2|CB342547
EST:     GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|37184833|gb|CF604187.1|CF604187
EST:     GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAA
genomic: GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAA
EST: gi|351053957|gb|FQ441723.1|FQ441723
EST:     GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|29785469|gb|CB342488.2|CB342488
EST:     AATTGCTGGCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: AATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|30299931|gb|CB976725.1|CB976725
EST:     GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
EST: gi|351013925|gb|FQ434077.1|FQ434077
EST:     GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAG                         GCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT
genomic: GTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctc ... acaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggcaattgctttaaaaacttatcattcatattctcttattctttacaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGTTCAAAGTTTGCAGAG
                               ttctcttattctttac  CT-rich tract
          tttaaaaacttatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgaaattttgcttttaaaacatagtcctttttatgaaatataaaggcaattgctttaaaaacttatcattcatattctcttattctttacaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGTTCAAAGTTTGCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - -aaaacat
- - - - - - - - - - - - - - - - - - -aaatata
- - - - - - - - - - - - - - - - - - - - - - - - caattgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcattca