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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGAATGCACTTAAAAATCTAGGGCTGAATGTTGTTAAAGCAAATGTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgtggagtagaatttagatgcatttttgcttcaattcccatatctatcaattcttttctttcattccaccttgttactgatatctcccaattt...

Basic information

species Vitis vinifera
transcript Vv09s0018g01780.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0018g01780.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA15G00560.1 (Glycine max), 5'ss of exon 4
ATGAATGCACTTAAAAATCTAGGGCTGAATGTTGTTAAAGCAAATGTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgtggagtagaatttagatgcatttttgcttcaattcccatatctatcaattcttttctttcattccaccttgttactgatatctcccaattt--
||||||||  | |||||  | ||||||||||||||||| |||||||||||| | |||||||| || ||||||||||  ||| ||||||| ||||||||||| | |    ||      ||    | |     || |    |   ||  | | |   |    ||  | |   |  |   | ||||       || |   
ATGAATGCGTTAAAAAACTTGGGGCTGAATGTTGTTAAGGCAAATGTCTTTCTAGATTCTTCTGGCAAGCACAACAAGTTTTCCATCACAAAAGCgtaagtac-tatcatatgtgccagtaataataaaa-ttgatgaactgaattgaactacaataaaattgaactgacctgtaaaagtgattcggatgaactgaa

upper sequence: Vv09s0018g01780.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA13G44740.1 (Glycine max), 5'ss of exon 4
ATGAATGCACTTAAAAATCTAGGGCTGAATGTTGTTAAAGCAAATGTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgtggagtagaatttagatgcatttttgcttcaattcccatatctatcaattcttt-tctttcattccaccttgttactgatat-ctcccaattt-
||||||||  | | |||  | ||||||||||||||||| |||||||| ||| |||||||||| || || |||||||  ||| ||||||| ||||||||||| |     |||   | ||  |   |    |    ||| |      ||||  || |||  |     | || |     |||   | |  ||  |||    
ATGAATGCGTTAAGAAACTTGGGGCTGAATGTTGTTAAGGCAAATGTATTTCTGGATTCTTCTGGCAAACACAACAAGTTTTCCATCACAAAAGCgtaagtactatatgta---tgtacgtatgtgacagtaataatacattgtcctatgtatgcttcattccagaatcaaatcaattaaaaagaggctggcaagaaa

upper sequence: Vv09s0018g01780.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA07G02580.1 (Glycine max), 5'ss of exon 4
ATGAATGCACTTAAAAATCTAGGGCTGAATGTTGTTAAAGCAAATGTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgtggagtagaatttagatgcatttttgcttcaattcccatatctat-caattcttttctttcattccaccttgttactgatatctcccaattt-----
||||||||| | |||||  |||| || ||||||||||| |||||||||||| ||||||| || || ||||||||||  ||  ||||||| |||||||||||  ||    |  | |    ||||||| |   |   | |   ||   | | |   ||  |   ||  |      || |||||||| | | | || |      
ATGAATGCATTAAAAAACTTAGGTCTCAATGTTGTTAAGGCAAATGTCTTTCTGGATTCATCTGGCAAGCACAACAAGTTCTCCATCACAAAAGCgtaagt--gttacatgcatt----atgcattgtgtatgtgactgttatgcatgtgctgctccctgtattggtcttgtgttattactgatgtatgctaaatggtagc

upper sequence: Vv09s0018g01780.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA08G23440.1 (Glycine max), 5'ss of exon 4
ATGAATGCACTTAAAAATCTAGGGCTGAATGTTGTTAAAGCAAATGTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgtggagtagaatttagatg-catttttgcttcaattcccatatctatcaattcttttctttcattccaccttgttac-tgatatctcccaattt
||||||||| | |||||  |||| || ||||||||||| |||||||||||| ||||||| || || ||||||||||  ||  ||||||| |||||||||||       | |  || ||  |  |  || ||| |   || |    | |||   |  | |  | | | |      || ||  || || ||   |||  
ATGAATGCATTAAAAAACTTAGGTCTCAATGTTGTTAAGGCAAATGTCTTTCTGGATTCATCTGGCAAGCACAACAAGTTCTCCATCACAAAAGCgtaagtgttacatgcattatgtatgtaactgttatgcatgtgttgctccctgtattggtcttgtgttattactgatgtatgctaaatggtagctaaaaat--

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|29784297|gb|CB344831.2|CB344831
EST:     GTCTTTTTGGA-TCTTCGGGAAAGCACAACACATTTGCCATCTCCAAAGC                         TGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
EST: gi|349823556|gb|FQ414966.1|FQ414966
EST:     GTCTTTTTGGATTCTTCAGGAAAGCACAACACATTTGCCATCACCAAAGC                         TGATACTGGTAGAAAAGTTGAGGATCCCGAGTTGCTTGAGGCAATTCGTTT
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
EST: gi|28965852|gb|CB344885.1|CB344885
EST:     GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGC                         TGATACTGGTAGAAAAGGTGAGGATCCTGAGTTGCTTGAGGCAATTCGATT
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
EST: gi|32271352|gb|CD720511.1|CD720511
EST:     GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGC                         TGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
EST: gi|110375956|gb|EC940987.1|EC940987
EST:     GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGC                         TGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
EST: gi|110386695|gb|EC951311.1|EC951311
EST:     GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGC                         TGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
EST: gi|111125066|gb|EE253677.1|EE253677
EST:     GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGC                         TGATACTGGTAGAAAAGTTGAGGATCCCGAGTTGCTTGAGGCAATTCGTTT
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
EST: gi|351024111|gb|FQ423534.1|FQ423534
EST:     GTCTTTTTGGATTCTTCAGGAAAGCACAACACACTTGCCATCACCAAAGC                         TGATACTGGTAGAAAAGTTGAGGATCCCGAGTTGCTTGAGGCAATTCGTTT
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
EST: gi|351031377|gb|FQ445402.1|FQ445402
EST:     GTCTTTTTGGATTCTTCAGGAAAGCACAACACATTTGCCATCACCAAAGC                         TGAAACTGGTAGAAAAGTTGAGGATCCCGAGTTGCTTGA
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGA
EST: gi|34542620|gb|CF510852.1|CF510852
EST:     GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGC                         TGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
EST: gi|349823504|gb|FQ414914.1|FQ414914
EST:     GTCTTTTTGGATTCTTCAGGAAAGCACAACACATTTGCCATCACCAAAGC                         TGATACTGGTAGAAAAGTTGAGGATCCCGAGTTGCTTGAGGCAATTCGTTT
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
EST: gi|110372559|gb|EC936737.1|EC936737
EST:     GTCTTTTTGGATTCTTCAGGAAAGCACAACACATTTGCCATCACCAAAGC                         TGATACTGGTAGAAAAGTTGAGGATCCCGAGTTGCTTGAGGCAATTCGTTT
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
EST: gi|32248427|gb|CD714246.1|CD714246
EST:     GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGC                         TGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
EST: gi|110387079|gb|EC951719.1|EC951719
EST:     GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGC                         TGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
EST: gi|351015119|gb|FQ444408.1|FQ444408
EST:     GTCTTTTTGGATTCTTCAGGAAAGCACAACACATTTGCCATCACCAAAGC                         TGATACTGGTAGAAAAGTTGAGGATCCCGAGTTGCTTGAGGCAATTCGTTT
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
EST: gi|351022170|gb|FQ438755.1|FQ438755
EST:     GTCTTTTTGGATTCTTCAGGAAAGCACAACACATTTGCCATCACCAAAGC                         TGATACTGGGTAGAAAAGTTTGAGGATCCCGAGTTGCTTGAGGGCA-TTCG
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGG-TAGAAAAGTT-GAGGATCCTGAGTTGCTTGAGG-CAATTCG
EST: gi|110390868|gb|EC955807.1|EC955807
EST:     GTCTTTTTGGATTCTTCAGGAAAGCACAACACATTTGCCATCACCAAAGC                         TGATACTGGTAGAAAAGTTGAGGATCCCGAGTTGCTTGAGGCAATTCGTTT
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
EST: gi|29784413|gb|CB345109.2|CB345109
EST:     GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGC                         TGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
EST: gi|32268834|gb|CD717993.1|CD717993
EST:     GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGC                         TGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
EST: gi|110385943|gb|EC950505.1|EC950505
EST:     GTCTTTTTGGATTCTTCAGGAAAGCACAACACATTTGCCATCACCAAAGC                         TGATACTGGTAGAAAAGTTGAGGATCCCGAGTTGCTTGAGGCAATTCGTTT
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
EST: gi|110413183|gb|EC978960.1|EC978960
EST:     GTCTTTTTGGATTCTTCAGGAAAGCACAACACATTTGCCATCACCAAAGC                         TGATACTGGTAGAAAAGTTGAGGATCCCGAGTTGCTTGAGGCAATTCGTTT
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
EST: gi|29784391|gb|CB345050.2|CB345050
EST:     GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGC                         TGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
EST: gi|32269676|gb|CD718835.1|CD718835
EST:     GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGC                         TGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
EST: gi|110372429|gb|EC936593.1|EC936593
EST:     GTCTTTTTGGATTCTTCAGGAAAGCACAACACATTTGCCATCACCAAAGC                         TGATACTGGTAGAAAAGTTGAGGATCCCGAGTTGCTTGAGGCAATTCGTTT
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
EST: gi|110383897|gb|EC948302.1|EC948302
EST:     GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGC                         TGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT
EST: gi|110687744|gb|EE065504.1|EE065504
EST:     GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGC                         TGATACTGGTAGAAAAGTTGAAGATCCTGAGTTTGCT-GANNGCA-TTCGT
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTT-GCTTGAG-GCAATTCGT
EST: gi|29785638|gb|CB342854.2|CB342854
EST:     GTCTTTTTGGATTCTTCAGGAAAGCACAACACATTTGCCATCACCAAAGC                         TGATACTGGTAGAAAAGTTGAGGATCCCGAGTTGCTTGAGGCAATTCGTTT
genomic: GTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgt ... ttgtttgcagTGATACTGGTAGAAAAGTTGAGGATCCTGAGTTGCTTGAGGCAATTCGTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGAATGCACTTAAAAATCTAGGGCTGAATGTTGTTAAAGCAAATGTCTTTTTGGATTCTTCGGGAAAGCACAACACATTTGCCATCACCAAAGCgtaagtccgtggagtagaatttagatgcatttttgcttcaattcccatatctatcaattcttttctttcattccaccttgttactgatatctcccaattt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagtagaa