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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTCAGAGATAAGCGGACAGGAAAAACCAGGGGCTTTGGGTTTGTTAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACGgtatcacttctaatagatcttttacatggttctatcgtcttccacatttacagatttgcttcttgggcagtatgcataacatcaatgtaattggtgcagc...

Basic information

species Vitis vinifera
transcript Vv09s0018g01710.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0018g01710.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os08g45240.4 (Oryza sativa), 5'ss of exon 3
GTTGTCAGAGATAAGCGGACAGGAAAAACCAGGGGCTTTGGGTTTGTTAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACGgtatcacttctaatagatcttttacatggttctatcgtcttccacatttacagatttgcttcttgggcagtatgcataacatcaatgtaattggtgcagc
|||||  |||||||| | || || ||||| |  || | ||| ||||| |||||||| |||||| | |||||||| | |||| ||||||||||||| ||| | |  |  |    |  | ||  ||  | ||  | |  | ||  ||      | | || ||     | ||    | |||  | || |           
GTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGCTTTTCAAACCCTACTGACCTTGCTGGAGCAATTAAAGAAATGAATGgtttgaagt--acccaacttgttcaat--tactgccattgttcagcttcgtttttgtactgctaccttattacttttgacactattgcag----------

upper sequence: Vv09s0018g01710.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA20G36570.1 (Glycine max), 5'ss of exon 4
GTTGTCAGAGATAAGCGGACAGGAAAAACCAGGGGCTTTGGGTTTGTTAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACGgt--atcacttctaatagatcttttacatg-gttctatcgtcttccacatttacagat-ttgcttcttgggcagta-tgcataacatcaatgtaattggtgcagc
||||||||||| |||||||| || ||||| |  || | ||| ||||| |||||| |||| ||||| |||||||| || || |||||||||||||| |||   ||| |||  || |  || |    |  ||  ||   | |      |  | | || |||  | ||  || ||| |   |   |    | | | | ||     
GTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGCTTTGCCAATCCTTCTGACCTTGCTGCTGCTCTTAAAGAAATGAATGgttagtcagttcagatgggcctctcttttaagtattactctgtaatgtctaaatacatattgactattacgctgtaatatctgttactcttctgactagt-----

upper sequence: Vv09s0018g01710.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA10G30900.2 (Glycine max), 5'ss of exon 4
GTTGTCAGAGATAAGCGGACAGGAAAAACCAGGGGCTTTGGGTTTGTTAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACGgt--atcacttctaataga----tcttttacatggttctatcgtcttccacatttacagatttgcttcttgggcagtatgcataacatcaatgtaattggtgcagc
||||||||||| |||||||| || ||||| |  || | ||| ||||| |||||| |||| ||||| |||||||| |  || |||||||||||||| |||   ||| |||  || |     |||||||  |  | || | ||  |    |  |||| |||  ||  |        ||   |   |    | | | | ||     
GTTGTCAGAGACAAGCGGACTGGTAAAACAAAAGGTTATGGATTTGTGAGCTTTGCCAATCCTTCTGACCTTGCTGGTGCTCTTAAAGAAATGAATGgttagtcagttcagatgggcctctcttttaagtattactct-gtaatgtctaaatacatattgactattactctgcaatatctgttactcttctgactagt-----

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|349827356|gb|FQ421629.1|FQ421629
EST:     TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACG                         GCAAGTATGTTGGAA
genomic: TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACGgtatcacttc ... caattttcagGCAAGTATGTTGGAA
EST: gi|352795514|gb|FQ480102.1|FQ480102
EST:     TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACG                         GCAAGTATGTTG
genomic: TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACGgtatcacttc ... caattttcagGCAAGTATGTTG
EST: gi|351042630|gb|FQ451045.1|FQ451045
EST:     AGCTTTTTCCA-CCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACG                         GCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAA
genomic: AGCTTTT-CCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACGgtatcacttc ... caattttcagGCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAA
EST: gi|351053774|gb|FQ441540.1|FQ441540
EST:     TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACG                         GCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGG
genomic: TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACGgtatcacttc ... caattttcagGCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGG
EST: gi|349828848|gb|FQ419181.1|FQ419181
EST:     TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACG                         GCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGG
genomic: TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACGgtatcacttc ... caattttcagGCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGG
EST: gi|110728709|gb|EE104516.1|EE104516
EST:     TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACG                         GCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGG
genomic: TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACGgtatcacttc ... caattttcagGCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGG
EST: gi|351044071|gb|FQ452744.1|FQ452744
EST:     TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACG                         GCAAGTATGTTGG
genomic: TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACGgtatcacttc ... caattttcagGCAAGTATGTTGG
EST: gi|110365693|gb|EC929076.1|EC929076
EST:     TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACG                         GCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGG
genomic: TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACGgtatcacttc ... caattttcagGCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGG
EST: gi|349808023|gb|FQ402414.1|FQ402414
EST:     TAGCTTTTTCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACG                         GCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCA
genomic: TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACGgtatcacttc ... caattttcagGCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCA
EST: gi|351037484|gb|FQ460683.1|FQ460683
EST:     TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACG                         GCAAGTATGTTGGAAATAGGCCAATCAAACTACGGGAAAAGCAATTGAAAG
genomic: TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACGgtatcacttc ... caattttcagGCAAGTATGTTGGAAATAGGCCAATCAAACTACGG-AAGAGCAATTGGAAG
EST: gi|27583752|gb|CB006447.1|CB006447
EST:     TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACG                         GCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGG
genomic: TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACGgtatcacttc ... caattttcagGCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGG
EST: gi|30137999|gb|CB923337.1|CB923337
EST:     TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAATG                         GCAAATATGTTGGAAATAGGCCAATCNAACTACGGAAGAGCAATTGGAAGG
genomic: TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACGgtatcacttc ... caattttcagGCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGG
EST: gi|351028807|gb|FQ433237.1|FQ433237
EST:     TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACG                         GCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGG
genomic: TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACGgtatcacttc ... caattttcagGCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGG
EST: gi|349819475|gb|FQ413359.1|FQ413359
EST:     TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACG                         GCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCCATTGGAA
genomic: TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACGgtatcacttc ... caattttcagGCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAA
EST: gi|351036139|gb|FQ463984.1|FQ463984
EST:     TAGCTTTTCCAACCCTTCAGACCCTGCAGCAGCACTTAAAGAAATGAACG                         GCAAGTATGTTGGAAATAGGCCAATCAAA
genomic: TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACGgtatcacttc ... caattttcagGCAAGTATGTTGGAAATAGGCCAATCAAA
EST: gi|351036156|gb|FQ464001.1|FQ464001
EST:     AGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAAACG                         GCA-GTATGTTGGAAATAGGCCAATCAAACTACGGAAG
genomic: AGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAA-CGgtatcacttc ... caattttcagGCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAG
EST: gi|33404798|gb|CF210425.1|CF210425
EST:     TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAATG                         GCAAATATGTTGGAAATAGGCCAATCAAACTACGGAAGGGCAATTGGAAGG
genomic: TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACGgtatcacttc ... caattttcagGCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGG
EST: gi|351016422|gb|FQ423849.1|FQ423849
EST:     TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACG                         GCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGG
genomic: TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACGgtatcacttc ... caattttcagGCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGG
EST: gi|351037773|gb|FQ464214.1|FQ464214
EST:     TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACG                         GCAAGTATGTTGGAAATAAGGC-AATCAAACTACGGAAGA
genomic: TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACGgtatcacttc ... caattttcagGCAAGTATGTTGGAAATA-GGCCAATCAAACTACGGAAGA
EST: gi|349824137|gb|FQ417524.1|FQ417524
EST:     TAGCTTTTC-AACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACG                         GCAAGTATGTTGGAAATAGGCCAAATCAA-CTACGGAAGAGCAATTGGAAG
genomic: TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACGgtatcacttc ... caattttcagGCAAGTATGTTGGAAATAGGCCAA-TCAAACTACGGAAGAGCAATTGGAAG
EST: gi|349819739|gb|FQ402676.1|FQ402676
EST:     TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACG                         GCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGG
genomic: TAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACGgtatcacttc ... caattttcagGCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGG
EST: gi|351033445|gb|FQ462096.1|FQ462096
EST:     AGCTTTTCCAACC-TTCAGACCTTGCAGCAGCACTTAAAGAAAATGAACG                         GCAAGTATGTTGGAAATA
genomic: AGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAA-TGAACGgtatcacttc ... caattttcagGCAAGTATGTTGGAAATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGTCAGAGATAAGCGGACAGGAAAAACCAGGGGCTTTGGGTTTGTTAGCTTTTCCAACCCTTCAGACCTTGCAGCAGCACTTAAAGAAATGAACGgtatcacttctaatagatcttttacatggttctatcgtcttccacatttacagatttgcttcttgggcagtatgcataacatcaatgtaattggtgcagc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacatcaa