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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGCGTTAATTGATGACCGGAGAATACATGTGGATTTCAGTCAAAGTGTTTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAGgtaaaagaccactgctgctctgcagagggcatagtaatatggctgttggttgcaacatcataacaacttgtacttagtattgttttattttgtttgtttc...

Basic information

species Vitis vinifera
transcript Vv19s0027g01660.t01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0027g01660.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: LOC_Os06g45910.1 (Oryza sativa), 5'ss of exon 12
AATGCGTTAATTGATGACCGGAGAATACATGTGGATTTCAGTCAAAGTGTTTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAGgtaaaagaccactgctgctctgcagagggcatagtaatatggctgttggttgcaacatcataacaacttg-tacttagtattgttttattttgtttgtttc----
|||   || |||||||| || ||||||||||| || || ||||||||||||||||||||||||   || | ||| |  ||  |     |  |    |||||||         |  | |  ||      | |||  | |   | | |  ||| |    | ||   | ||   | | | |||   || | |||| ||          
AATTGTTTGATTGATGATCGAAGAATACATGTTGACTTTAGTCAAAGTGTTTCAAAACTGTGGGGTCAGTTCAGACAAAGCAAAAGAAATGCAAATAAAGgta-----ttcttatttccatggccttagaatatgattgcagttttcagtttcttttttatttaagctaactgcatggtagctttcttttttcttaaggaaaagc

upper sequence: Vv19s0027g01660.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: LOC_Os06g45900.1 (Oryza sativa), 5'ss of exon 13
AATGCGTTAATTGATGACCGGAGAATACATGTGGATTTCAGTCAAAGTGTTTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAGgtaaaagaccactgctgctctgcagagggcatagtaatatggctgttggttgcaacatcataacaacttgtacttagtattgttttattttgtttgtttc----
|||   || |||||||| || ||||||| ||| || ||||| |||||||||||||||| ||||   || | ||| |  ||  |     |  |    |||||||| | |  | |  ||   |        ||| |   ||| | ||    || || | || |    | ||   || | |      | | |  |   | | |    
AATTGTTTGATTGATGATCGAAGAATACGTGTTGACTTCAGCCAAAGTGTTTCAAAACAGTGGCGTCAGTTCAGACAAAGCAAAAGTAATGCAAATAAAGgtaagata--agtcatgtattcttatttccatggct-tatcgttgc-aattccagcttcttttttatttaagctaactgcaaaatcagtaggggaggtgctcta

upper sequence: Vv19s0027g01660.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA19G00460.1 (Glycine max), 5'ss of exon 12
---AATGCGTTAATTGATGACCGGAGAATACATGTGGATTTCAGTCAAAGTGTTTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAGgtaaaagaccactgctgctctgcagagggcatagtaatatggctgttggttgcaacatcataacaacttgtacttagtattgttttattttgtttgtttc----
   ||||| || |||||||| || || ||||| |||||||| ||||||||||| |||||||||||||| ||||||||||| | |||   ||||| ||| ||||||||  ||  |      || |   ||    |||   || |     |||  |   ||||   ||  |  ||   ||  ||||||    |||        ||    
GATAATGCTTTGATTGATGATCGAAGGATACACGTGGATTTTAGTCAAAGTGTGTCAAAACTGTGGTCACAATACAGGCGGAAAGA---CCAAAAGGGTAAAGgtaag-gataaagatgtctgttaggatttaataactatgtatgacttgagtctcacattggaa--atatgagattc-tattgtgaggtttgtaagacctcggga

upper sequence: Vv19s0027g01660.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA15G28380.1 (Glycine max), 5'ss of exon 12
---AATGCGTTAATTGATGACCGGAGAATACATGTGGATTTCAGTCAAAGTGTTTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAGgtaaaagaccactgctgctctgcagagggcatagtaatatggctgttggttgcaacatcataacaacttgtacttagtattgttttattttgtttgtttc-
   ||||| || |||||||| || || ||||| |||||||| |||||||||||  ||||||||||||| ||||||||||| | ||||||   || ||| ||||||||  ||  |      || |   ||    | ||  |  |     |||  |   ||||   ||  |   |    || | |    ||  |       | |  
GATAATGCTTTGATTGATGATCGAAGGATACACGTGGATTTTAGTCAAAGTGTGGCAAAACTGTGGTCACAATACAGGCGGAAAGATCA---AAAGGGTAAAGgtaag-gataaagatatctattaggatttaagagctaggtatgacttgagtctcacattggaaatatgagattctattgtgaggtttctaaaaccttgtga

upper sequence: Vv19s0027g01660.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: AT1G53720.1 (Arabidopsis thaliana), 5'ss of exon 11
AATGCGTTAATTGATGACCGGAGAATACATGTGGATTTCAGTCAAAGTGTTTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAGgtaaaagaccactgctgc--tctgcagagggcatagtaatatggctgttggttgcaacatcataacaacttgtacttagtattgttttattttgtttgtttc
|||||  | || |||||  |  | |||||||||||||||||||| ||||| || ||||| ||||| || | |||||  | |||   ||||| |||||||||||||       |  |     || |  | || |||        ||| | |     |  |  |    ||    |    |  ||                    
AATGCTCTGATCGATGATAGACGGATACATGTGGATTTCAGTCAGAGTGTGTCCAAACTTTGGTCACAGTTCAGGCAAAAAGACTCCCAAAAGGGCAAAGgtaaatctttttttttttctcctccctatggaataagtgacctgctatagacgaaacaagtaatgaaatccttggcaaacatgaaacag-------------

upper sequence: Vv19s0027g01660.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: PP1S45_218V6.1 (Physcomitrella patens), 5'ss of exon 12
AATGCGTTAATTGATGACCGGAGAATACATGTGGATTTCAGTCAAAGTGTTTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAGgtaaaagaccactgctgctctgcagagggcatagtaatatggctgttggttgcaacatcataacaacttgtacttagtattgttttattttgtttgtttc---------------
      || |||||||| || || |||||||| |||||||| |||||||||||| |  | |||   | ||||   || |           |  ||||   | | | |  ||  |    |      |     | | | ||| ||  ||  |      || |  |  |||||   ||      ||| |||   ||||    |               
------TTGATTGATGATCGAAGGATACATGTTGATTTCAGCCAAAGTGTTTCACATTTATGGAATCGATAC---CGTAAGC----TTGGAAAGGCAGGTGGAGATGGTCAAGgtgagttaaatcattcacttgaactattgcattttctcatgctattaggaagacttggggttgccg--gttgtatgacgttttcacccactaattcatcgaa

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|351013338|gb|FQ425043.1|FQ425043
EST:     TTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAG                         GAACAGGTTGCTTCAAATGTGGTGCAGTCGACCACATTGCCAAGGATTGTA
genomic: TTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAGgtaaaagacc ... ttggctgtagGAACAGGTTGCTTCAAATGTGGTGCAGTCGACCACATTGCCAAGGATTGTA
EST: gi|351056299|gb|FQ454160.1|FQ454160
EST:     TTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAG                         GAACAGGTTGCTTCAAATGTGGTGCAGTCGACCACATTGCCAAGGATTGTA
genomic: TTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAGgtaaaagacc ... ttggctgtagGAACAGGTTGCTTCAAATGTGGTGCAGTCGACCACATTGCCAAGGATTGTA
EST: gi|351019880|gb|FQ439697.1|FQ439697
EST:     TTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAG                         GAACAGGTTGCTTCAAATGTGGTGCAGTCGACCACATTGCCCAGGATTGTA
genomic: TTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAGgtaaaagacc ... ttggctgtagGAACAGGTTGCTTCAAATGTGGTGCAGTCGACCACATTGCCAAGGATTGTA
EST: gi|349829098|gb|FQ419630.1|FQ419630
EST:     TTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAG                         GAACAGGTTGCTTCAAATGTGGTGCAGTCGACAACATTGCCAAGGATTGTA
genomic: TTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAGgtaaaagacc ... ttggctgtagGAACAGGTTGCTTCAAATGTGGTGCAGTCGACCACATTGCCAAGGATTGTA
EST: gi|349828467|gb|FQ417209.1|FQ417209
EST:     TTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAG                         GAACAGGTTGCTTCNAATGTGGTGCAGTCGACCACATTGCCAAGGATTGTA
genomic: TTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAGgtaaaagacc ... ttggctgtagGAACAGGTTGCTTCAAATGTGGTGCAGTCGACCACATTGCCAAGGATTGTA
EST: gi|352786284|gb|FQ478895.1|FQ478895
EST:     TTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAG                         GAACAGGTTGCTTCAAATGTGGTGCAGTCGACCACATTGCCAAGGATTGTA
genomic: TTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAGgtaaaagacc ... ttggctgtagGAACAGGTTGCTTCAAATGTGGTGCAGTCGACCACATTGCCAAGGATTGTA
EST: gi|349824097|gb|FQ417484.1|FQ417484
EST:     TTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAG                         GAACAGGTTGCTTCAAATGTGGTGCAGTCGACCACATTGCCCAGGATTGTA
genomic: TTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAGgtaaaagacc ... ttggctgtagGAACAGGTTGCTTCAAATGTGGTGCAGTCGACCACATTGCCAAGGATTGTA
EST: gi|351014258|gb|FQ434847.1|FQ434847
EST:     TTCAAAACTGTGGTCCCAATACCGGCGCAGAGATCACCAAACGGGCAAAG                         GAACAGGTTGCTTCAAATGTGGTGCAGTCGACCACATTGCCAAGG
genomic: TTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAGgtaaaagacc ... ttggctgtagGAACAGGTTGCTTCAAATGTGGTGCAGTCGACCACATTGCCAAGG
EST: gi|351019573|gb|FQ439390.1|FQ439390
EST:     TTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAG                         GAACAGGTTGCTTCAAATGTGGTGCAGTCGACCAC
genomic: TTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAGgtaaaagacc ... ttggctgtagGAACAGGTTGCTTCAAATGTGGTGCAGTCGACCAC
EST: gi|351030963|gb|FQ438999.1|FQ438999
EST:     TTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAG                         GAACAGGTTGCTTCAAATGTGGTGCAGTCGACCACATTGCCTAGGATTG
genomic: TTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAGgtaaaagacc ... ttggctgtagGAACAGGTTGCTTCAAATGTGGTGCAGTCGACCACATTGCCAAGGATTG
EST: gi|351015056|gb|FQ444345.1|FQ444345
EST:     TTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAG                         GAACAGGTTGCTTCAAATGTGGTGCAGTCGACCACATTGCCAAGGATTGTA
genomic: TTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAGgtaaaagacc ... ttggctgtagGAACAGGTTGCTTCAAATGTGGTGCAGTCGACCACATTGCCAAGGATTGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGCGTTAATTGATGACCGGAGAATACATGTGGATTTCAGTCAAAGTGTTTCAAAACTGTGGTCCCAATACAGGCGCAGAGATCACCAAACGGGCAAAGgtaaaagaccactgctgctctgcagagggcatagtaatatggctgttggttgcaacatcataacaacttgtacttagtattgttttattttgtttgtttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataacaac