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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAAGGAATCATTGTTGCAAAGATGCCTAGAGGTGGAGCAAACAGCTAAAGAACAAGCAACAGATAACGCAATTCTAGACCAGCTTCACAAGgtaatcttttttgttctgaaagagaggcactcagatttgatatatctcatgggtttcagttagtttttcccccttaataaagctttatgccactttttcc...

Basic information

species Vitis vinifera
transcript Vv19s0090g01210.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0090g01210.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: LOC_Os06g20320.1 (Oryza sativa), 5'ss of exon 9
-GTCAAGGAATCATTGTTGCAAAGATGCCTAGAGGTGGAGCAAACAGCTAAAGAACAAGCAACAGATAACGCAATTCTAGACCAGCTTCACAAGgtaatcttttttgttctgaaagag------aggcactcagatttgatatatctcatgggtttcagttagtttttcccccttaataaagctttatgccactttttcc--------------------------------------------
  || || |  |||| |||||||||||   ||| |||||| ||||||| | |||||||||||||||||| ||||| || || ||||||   |||||| |||| ||  | || ||  ||      ||  |   ||   |||  ||    ||   | |   | |   ||    |  |  | ||  ||| ||| || || |||                                            
GTTCGAGAACGCATT-TTGCAAAGATGTAAAGAAGTGGAGAAAACAGCAATAGAACAAGCAACAGATAATGCAATCCTTGATCAGCTTGGAAAGgtagtcttcttactcctaaataaggccttaagttatgaagtcctgacttaggggatcattgtacatcatgcttctttctgttgtcaatttttttgc-accttctccaacatcctgtagtcttgctctaaattttcacttggtttgtatag

upper sequence: Vv19s0090g01210.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA02G46430.1 (Glycine max), 5'ss of exon 9
GTCAAGGAATCATTGTTGCAAAGATGCCTAGAGGTGGAGCAAACAGCTAAAGAACAAGCAACAGATAACGCAATTCTAGACCAGCTTCACAAGgtaatcttttttgttctgaaagagaggcactcagatttgatatatctcatgggtttcagttagtttttcccccttaataaagctttatgccactttttcc--
||||| || | |||||| || | |||||||||||||||||||||||||| |||||||||||| ||||| || ||  |||| ||| ||   ||||||| | ||    |    |     |  || |  || |    || |      |   |  | ||   |       ||| ||    ||| ||  |    |     
GTCAAAGACTTATTGTTACAGAAATGCCTAGAGGTGGAGCAAACAGCTAGAGAACAAGCAACTGATAATGCTATCTTAGATCAGATTTCTAAGgtaa-cattacaatatgcatgcttatacattgtgaataatgatgtgcttctgacat-ggatacactagagttattattattattttctggtaggcatataat

upper sequence: Vv19s0090g01210.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA14G02220.1 (Glycine max), 5'ss of exon 9
GTCAAGGAATCATTGTTGCAAAGATGCCTAGAGGTGGAGCAAACAGCTAAAGAACAAGCAACAGATAACGCAATTCTAGACCAGCTTCACAAGgtaatcttttttgttctgaaagagaggcactcagatttgatatatctcatgggtttcagttagtttttcccccttaataaagctt---tatgccactttttcc----
||||| || |  ||||| || | ||||| |||||||||||||||||||| ||||||||| || ||||| || ||  |||| ||| ||   |||||||  ||   |      ||  ||  | | | |||||   | | |||||||  | | | ||||  | | ||     | |    ||   |||||    || | |    
GTCAAAGACTTGTTGTTACAGAAATGCCAAGAGGTGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAGGTTTCTAAGgtaacattacatt-----aagtagctgtatt-agattgattttgtctcatgt-tctaaattagaatataccttgccacatgttttcaatatgcatgcttatacattg

upper sequence: Vv19s0090g01210.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA14G02220.2 (Glycine max), 5'ss of exon 9
GTCAAGGAATCATTGTTGCAAAGATGCCTAGAGGTGGAGCAAACAGCTAAAGAACAAGCAACAGATAACGCAATTCTAGACCAGCTTCACAAGgtaatcttttttgttctgaaagagaggcactcagatttgatatatctcatgggtttcagttagtttttcccccttaataaagctttatgccactttttcc
||||| || |  ||||| || | ||||| |||||||||||||||||||| ||||||||| || ||||| || ||  |||| ||| ||   |||||||  ||   |      ||  ||  | | | |||||   | | |||||||  | | | ||||  | | ||     | |    || |     | |  |  
GTCAAAGACTTGTTGTTACAGAAATGCCAAGAGGTGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAGgtttctaaggtaacattacatt-----aagtagctgtatt-agattgattttgtctcatgt-tctaaattagaatataccttgccacatgttttcaatatgcatgct--

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|351048256|gb|FQ442226.1|FQ442226
EST:     CAGCTAAAGAACAAGCAACAGATAGCGCAATTCTAGACCAGCTTCACAAG                         ATGATTGAAGTAGATATTCCTCAATCCTTGTTTGAGGAACAGGGCAGGCAG
genomic: CAGCTAAAGAACAAGCAACAGATAACGCAATTCTAGACCAGCTTCACAAGgtaatctttt ... tcattttcagATGATTGAAGTAGATATTCCTCAATCCTTGTTTGAGGAACAGGGCAGGCAG
EST: gi|254915760|gb|GR905191.1|GR905191
EST:     CAGCTAAAGAACAAGCAACAGATAACGCAATTCTAGACCAGCTTCACAAG                         ATGATTGAAGTAGATATTCCTCAATCCTTGTTTGAGGAACAGGGCAGGCAG
genomic: CAGCTAAAGAACAAGCAACAGATAACGCAATTCTAGACCAGCTTCACAAGgtaatctttt ... tcattttcagATGATTGAAGTAGATATTCCTCAATCCTTGTTTGAGGAACAGGGCAGGCAG
EST: gi|71868474|gb|DT017529.1|DT017529
EST:     CAGCTAAAGAACAAGCAACAGATAACGCAATTCTAGACCAGCTTCACAAG                         ATGATTGAAGTAGATATTCCTCAATCCTTGTTTGAGGAACAGGGCAGGCAG
genomic: CAGCTAAAGAACAAGCAACAGATAACGCAATTCTAGACCAGCTTCACAAGgtaatctttt ... tcattttcagATGATTGAAGTAGATATTCCTCAATCCTTGTTTGAGGAACAGGGCAGGCAG
EST: gi|351056173|gb|FQ453635.1|FQ453635
EST:     CAGCTAAAGAACAAGCAACAGATAACGCAATTCTAGACCAGCTTCACAAG                         ATGATTGAAGTAGATATTCCTCAATCCTTGTTTGAGGAACAGGGCAGGCAG
genomic: CAGCTAAAGAACAAGCAACAGATAACGCAATTCTAGACCAGCTTCACAAGgtaatctttt ... tcattttcagATGATTGAAGTAGATATTCCTCAATCCTTGTTTGAGGAACAGGGCAGGCAG
EST: gi|351040007|gb|FQ425093.1|FQ425093
EST:     CAGCTAAAGAACAAGCAACAGATAACGCAATTCTAGACCAGCTTCACAAG                         ATGATTGAAGTAGATATTCCTCAATCCTTGTTTGAGGAACAGGGCAGGCAG
genomic: CAGCTAAAGAACAAGCAACAGATAACGCAATTCTAGACCAGCTTCACAAGgtaatctttt ... tcattttcagATGATTGAAGTAGATATTCCTCAATCCTTGTTTGAGGAACAGGGCAGGCAG
EST: gi|254915870|gb|GR905301.1|GR905301
EST:     CAGCTAAAGAACAAGCAACAGATAACGCAATTCTAGACCAGCTTCACAAG                         ATGATTGAAGTAGATATTCCTCAATCCTTGTTTGAGGAACAGGGCAGGCAG
genomic: CAGCTAAAGAACAAGCAACAGATAACGCAATTCTAGACCAGCTTCACAAGgtaatctttt ... tcattttcagATGATTGAAGTAGATATTCCTCAATCCTTGTTTGAGGAACAGGGCAGGCAG
EST: gi|30320634|gb|CD003896.1|CD003896
EST:     CAGCTAAAGAACAAGCAACAGATAACGCAATTCTAGACCAGCTTCACAAG                         ATGATTGAAGTAGATATTCCTCAATCCTTGTTTGAGGAACAGGGCAGGCAG
genomic: CAGCTAAAGAACAAGCAACAGATAACGCAATTCTAGACCAGCTTCACAAGgtaatctttt ... tcattttcagATGATTGAAGTAGATATTCCTCAATCCTTGTTTGAGGAACAGGGCAGGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAAGGAATCATTGTTGCAAAGATGCCTAGAGGTGGAGCAAACAGCTAAAGAACAAGCAACAGATAACGCAATTCTAGACCAGCTTCACAAGgtaatcttttttgttctgaaagagaggcactcagatttgatatatctcatgggtttcagttagtttttcccccttaataaagctttatgccactttttcc

- - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaagag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccccct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aataaag