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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggattacttggtgttggatttgtttttgatgattgttgccccctacaggaaggaaaaaaatggaatttcctcatttggctgtcttttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCATCAGGGACACACAAGAGAATTACTGTGATCACTCAAGGTGCAGATCCTG

Basic information

species Vitis vinifera
transcript Vv13s0019g04480.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04480.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA10G06580.1 (Glycine max), 3'ss of exon 10
gtagggattacttggtgttggatttgtttttgatgattgttgccccctacaggaaggaaaaaaatggaattt---cctcatttggctgtcttttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCATCAGGGACACACAAGAGAATTACTGTGATCACTCAAGGTGCAGATCCTG
   |  || | |   |    ||| ||      | | |||  |                ||    || | |||    ||  | |   |||| | | ||| ||||||||||| ||||| || || ||  |||| || ||||||| ||||||||||||||  | ||| || || |||||||| ||||| ||||||||||||||||
---gtaatcattaattaacagatctg-----aaggcttgcagttttggtttaagttttaatttgtgtattttgactcttttcttattgtcctat-tgaacagACTGATAATGTTGAAGAAATAGCTTTAAAGATTTCTCAATTGCCAAAAGCATCAGAAAAACATAAAAGGATTACTGTTATCACCCAAGGTGCAGATCCTG

upper sequence: Vv13s0019g04480.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA19G36630.1 (Glycine max), 3'ss of exon 10
gtagggattacttggtgttggatttgttt-ttgatgattgttgccccctacaggaaggaaaaaaatggaatttcctcatttggctgtcttttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCATCAGGGACACACAAGAGAATTACTGTGATCACTCAAGGTGCAGATCCTG
||| |  ||      |||   ||||||    |     || | |      |    ||      | ||    |  || |      |   || || |    |||||||||| || |||||||| ||  |||| || || ||||||||||| |||||||| |||||||| || || || || ||||| || ||||| |||||| 
gtaagccttgt---atgtcaaatttgtaggcttgcagttttggttttgaatgttaaccccttacatcttttgacccccccccccc-cctgttttttctagACTGATAATGTCGAGGAGATAGCTGTAAAGATTTCCCAATGGCCAAAGGCATCAGGAACACACAAAAGGATAACAGTTATCACACAGGGTGCGGATCCTA
















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|266635514|gb|GT568891.1|GT568891
EST:     TTGGG-ATGAANCGGAGGCAAGAACCTTTTCCAGGGTTCATGGCCGGGAG                         ACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCAAAAAGCA
genomic: TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
EST: gi|110418987|gb|EC985176.1|EC985176
EST:     TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAG                         ACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
genomic: TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
EST: gi|110687648|gb|EE065296.1|EE065296
EST:     TTGGGAATGAAACGGAAACAAGAACCTTTTCCAGGGTTCATGGCTGGGAG                         ACTGATAACGTTGAGGAGATTGCAATAAAAAT
genomic: TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAAT
EST: gi|351023138|gb|FQ432521.1|FQ432521
EST:     TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAG                         ACTGATAACGTTGA
genomic: TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGA
EST: gi|351038074|gb|FQ460816.1|FQ460816
EST:     TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAG                         ACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGGCCAAAA-C
genomic: TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGG-CCAAAAGC
EST: gi|352794243|gb|FQ479485.1|FQ479485
EST:     TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGNAG                         ACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCC
genomic: TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCC
EST: gi|352786944|gb|FQ475977.1|FQ475977
EST:     TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAG                         ACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
genomic: TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
EST: gi|349824265|gb|FQ417652.1|FQ417652
EST:     TTGGGAATGAAACGGAAGCAAGAACCTTTGCCAAGGTTCATGGCTGGGAG                         ACTGATAATGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
genomic: TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
EST: gi|352794240|gb|FQ479482.1|FQ479482
EST:     TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAG                         ACTGATAACGTTGAGGAGATTGCAATAAAA
genomic: TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAA
EST: gi|110391898|gb|EC956929.1|EC956929
EST:     TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAG                         ACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
genomic: TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
EST: gi|18459290|gb|BM437568.1|BM437568
EST:     CAAGAACCTTTTCCAGGGTTCATGGCTGGGAG                         ACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
genomic: CAAGAACCTTTTCCAGGGTTCATGGCTGGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
EST: gi|110708040|gb|EE085129.1|EE085129
EST:     GGGAAATGAA-CGGAAGCAAGAACCTTTGCCAAGGTTCATGGCTTGGGAA                         ACTGATAATGTTGAG
genomic: GGGAA-TGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCT-GGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGAG
EST: gi|110399344|gb|EC965847.1|EC965847
EST:     TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAG                         ACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
genomic: TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
EST: gi|30302319|gb|CB979113.1|CB979113
EST:     TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAG                         ACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
genomic: TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
EST: gi|27581929|gb|CB004624.1|CB004624
EST:     TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAG                         ACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
genomic: TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
EST: gi|351026422|gb|FQ428434.1|FQ428434
EST:     TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAG                         ACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
genomic: TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
EST: gi|110689258|gb|EE065335.1|EE065335
EST:     TTGGGAATGAAACGGAAGCAAGAACCTTTGCCAAGGTTCATGGCTGGGAG                         ACTGATTATGTTGANGAGGAT-GCAATAAAAATATCTCAATGGCCACAAGC
genomic: TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGAGGAG-ATTGCAATAAAAATATCTCAATGGCCAAAAGC
EST: gi|352790621|gb|FQ475379.1|FQ475379
EST:     TTCATGGCTGGGAG                         ACTGATAACGGTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
genomic: TTCATGGCTGGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
EST: gi|83275808|gb|DV939816.1|DV939816
EST:     TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAG                         ACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
genomic: TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
EST: gi|351038237|gb|FQ460929.1|FQ460929
EST:     TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAG                         ACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
genomic: TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
EST: gi|110685346|gb|EE063661.1|EE063661
EST:     TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAG                         ACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCCAAAGCA
genomic: TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
EST: gi|110685881|gb|EE062990.1|EE062990
EST:     TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAG                         ACTGATAACGTTGAAGAGATTGCAATAAAA-TATCTCA
genomic: TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCA
EST: gi|110715240|gb|EE093065.1|EE093065
EST:     TTGGGAATGAAACG-AAGCAAGAACCTTTGCCAAGGTTCATGGCTGGGAG                         ACTGATAATGTTGAAGAAGATTGCAATAAAA-TATCTCAATGGCCAAAAGC
genomic: TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGAGGA-GATTGCAATAAAAATATCTCAATGGCCAAAAGC
EST: gi|110698283|gb|EE075646.1|EE075646
EST:     TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAG                         ACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
genomic: TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
EST: gi|22013186|gb|BQ798220.1|BQ798220
EST:     TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAG                         ACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
genomic: TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
EST: gi|32245795|gb|CD711614.1|CD711614
EST:     TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAG                         ACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA
genomic: TTGGGAATGAAACGGAAGCAAGAACCTTTTCCAGGGTTCATGGCTGGGAGgtagggatta ... ttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctacaggaaggaaaaaaatggaatttcctcatttggctgtcttttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCATCAGGGACACACAAGAGAATTACTGTGATCACTCAAGGTGCAGATCCTG
                                      ctgtctttt  CT-rich tract
             aaaaaaatggaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagggattacttggtgttggatttgtttttgatgattgttgccccctacaggaaggaaaaaaatggaatttcctcatttggctgtcttttgtgatcagACTGATAACGTTGAGGAGATTGCAATAAAAATATCTCAATGGCCAAAAGCATCAGGGACACACAAGAGAATTACTGTGATCACTCAAGGTGCAGATCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT