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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTGGTGAAACTGTTGGTTACCAGATTCGCCTGGAAGCAAAGCGCTCTGCTCAAACACGTTTGCTATTTTGCACCACTGGAGTACTACTTCGGCAGCTGgtaatatattttttgtacctgttatttttcattggtaaaagtttcactcttatatttttgttcttcagtctttatgtctgtatcttagcgtttttagaac...

Basic information

species Vitis vinifera
transcript Vv08s0032g01230.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0032g01230.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G399212_T01 (Zea mays), 5'ss of exon 8
TCTTGGTGAAACTGTTGGTTACCAGATTCGCCTGGAAGCAAAGCGCTCTGCTCAAACACGTTTGCTATTTTGCACCACTGGAGTACTACTTCGGCAGCTGgtaatatattttttgtacctgttatttttcattggtaaaagtttcactcttatattt-ttgttcttcagtctttatgtctgtatcttagcgtttttagaac----
 || || ||  ||||||| |||||||||||||| ||| |||| || ||||| |||||||| ||||| || ||||| ||||||||  | ||| |    ||||||   |   ||       | |   | |||||   |  |  | ||      | |||| ||| |    || ||||    |||   |  || ||  |  |       
ACTCGGCGAGGCTGTTGGATACCAGATTCGCCTTGAATCAAAACGGTCTGCACAAACACGGTTGCTGTTCTGCACTACTGGAGTTTTGCTTAGAAGACTGgta---tgccttagaatattttgcatattcatatattgagatgtcttgaccacatttcttggtgagaagcctttcca-ctgagccaaag-gtcctgggtttgaca

upper sequence: Vv08s0032g01230.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA02G35240.1 (Glycine max), 5'ss of exon 8
TCTTGGTGAAACTGTTGGTTACCAGATTCGCCTGGAAGCAAAGCGCTCTGCTCAAACACGTTTGCTATTTTGCACCACTGGAGTACTACTTCGGCAGCTGgtaatata----ttttttgtacctgttatttttcattggtaaaagtttcactcttatatttttgttcttcagtctttatgtctgtatcttagcgtttttagaac
|||||| ||| | ||||| ||||| || || || ||| |||| || |||||  |||||||  | || || ||||||||||| ||| ||||||||||| |||||||||     |  | |  | ||   | | | || |  |  |  || || |    | | |   ||  |   | |||  |||| | |  ||  |    |     
TCTTGGGGAAGCAGTTGGATACCAAATCCGTCTTGAATCAAAACGTTCTGCAGAAACACGCCTTCTTTTCTGCACCACTGGTGTATTACTTCGGCAGTTGgtaatattagattcctctcaaactaaaagtctccagttttttagattccagttcc-tgtctaaatttgtttatgtttcagtctttcttctattgccactca---

upper sequence: Vv08s0032g01230.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA10G10180.1 (Glycine max), 5'ss of exon 6
TCTTGGTGAAACTGTTGGTTACCAGATTCGCCTGGAAGCAAAGCGCTCTGCTCAAACACGTTTGCTATTTTGCACCACTGGAGTACTACTTCGGCAGCTGgtaatata----ttttttgtacctgttatttttcattggtaaaagtttcactcttatatttttgttcttcagtctttatgtctgtatcttagcgtttttagaac
||| || ||| | ||||| ||||| || || || ||| |||| || |||||  |||||||  | || || ||||||||||| ||| ||||||||||| |||||||||     |  | |  | |||  | | | |  |  |  |   | || |    | | |    |  |   | |||  |||| | |  ||  |    |     
TCTCGGAGAAGCAGTTGGATACCAAATCCGTCTTGAATCAAAACGTTCTGCAGAAACACGCCTTCTTTTCTGCACCACTGGTGTATTACTTCGGCAGTTGgtaatattagattcctctcaaactgaaagtctcctgttttttagactccagttcc-tgtctaaacttgtttatgtttcggtctttcttctattgccactca---

upper sequence: Vv08s0032g01230.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT2G35920.1 (Arabidopsis thaliana), 5'ss of exon 6
TCTTGGTGAAACTGTTGGTTACCAGATTCGCCTGGAAGCAAAGCGCTCTGCTCAAACACGTTTGCTATTTTGCACCACTGGAGTACTACTTCGGCAGCTGgta--atatattttttgtacctgtta-tttttcattggtaaaagtttcactcttatatttttgttcttcagtctttatgtctgtatcttagcgtttttagaac--
  |||||||| |||| ||||| |||||||| || ||| ||||||| |||| ||||||||| |||||||||||||| ||||| ||  |||| |||| |||||||  ||| |  | || |||   | |  |  ||||       ||||  | | | |||||||     |     ||||           | |    ||  |   |  
CATTGGTGAATCTGTGGGTTATCAGATTCGTCTAGAATCAAAGCGTTCTGATCAAACACGATTGCTATTTTGCACTACTGGTGTTTTACTCCGGCGGCTGgtaagatacaactattctactactcaactactcatcacatgtagttgaagtatgatattttaagcttctttactttgaaatgtcgaatcaattgttgaaatgcag

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|352773708|gb|FQ472490.1|FQ472490
EST:     CTCAAACACGTTTGCTATTTTGCACCACTGGAGTACTACTTCGGCAGCTG                         GTTCAGGACCCAGATCTAACTGGTGTAAGCCATTTGCTAGTGGATGAAATT
genomic: CTCAAACACGTTTGCTATTTTGCACCACTGGAGTACTACTTCGGCAGCTGgtaatatatt ... ttaaatacagGTTCAGGACCCAGATCTAACTGGTGTAAGCCATTTGCTAGTGGATGAAATT
EST: gi|352778146|gb|FQ468808.1|FQ468808
EST:     CTCAAACACGTTTGCTATTTTGCACCACTGGAGTACTACTTCGGCAGCTG                         GTTCAGGACCCAGATCTAACTGGTGTAAGCCATTTGCTAGTGGATGAAATT
genomic: CTCAAACACGTTTGCTATTTTGCACCACTGGAGTACTACTTCGGCAGCTGgtaatatatt ... ttaaatacagGTTCAGGACCCAGATCTAACTGGTGTAAGCCATTTGCTAGTGGATGAAATT
EST: gi|352764590|gb|FQ472947.1|FQ472947
EST:     CTCAAACACGTTTGCTATTTTGCACCACTGGAGTACTACTTCGGCAGCTG                         GTTCAGGACCCAGATCTAACTGGTGTAAGCCATTTGCTAGTGGATGAAATT
genomic: CTCAAACACGTTTGCTATTTTGCACCACTGGAGTACTACTTCGGCAGCTGgtaatatatt ... ttaaatacagGTTCAGGACCCAGATCTAACTGGTGTAAGCCATTTGCTAGTGGATGAAATT
EST: gi|352773574|gb|FQ472356.1|FQ472356
EST:     CTCAAACACGTTTGCTATTTTGCACCACTGGAGTACTACTTCGGCAGCTG                         GTTCAGGACCCAGATCTAACTGGTGTAAGCCATTTGCTAGTGGATGAAATT
genomic: CTCAAACACGTTTGCTATTTTGCACCACTGGAGTACTACTTCGGCAGCTGgtaatatatt ... ttaaatacagGTTCAGGACCCAGATCTAACTGGTGTAAGCCATTTGCTAGTGGATGAAATT
EST: gi|352768279|gb|FQ469454.1|FQ469454
EST:     CTCAAACACGTTTGCTATTTTGCACCACTGGAGTACTACTTCGGCAGCTG                         GTTCAGGACCCAGATCTAACTGGTGTAAGCCATTTGCTAGTGGATGAAATT
genomic: CTCAAACACGTTTGCTATTTTGCACCACTGGAGTACTACTTCGGCAGCTGgtaatatatt ... ttaaatacagGTTCAGGACCCAGATCTAACTGGTGTAAGCCATTTGCTAGTGGATGAAATT
EST: gi|352782101|gb|FQ470003.1|FQ470003
EST:     CTCAAACACGTTTGCTATTTTGCACCACTGGAGTACTACTTCGGCAGCTG                         GTTCAGGACCCAGATCTAACTGGTGTAAGCCATTTGCTAGTGGATGAAATT
genomic: CTCAAACACGTTTGCTATTTTGCACCACTGGAGTACTACTTCGGCAGCTGgtaatatatt ... ttaaatacagGTTCAGGACCCAGATCTAACTGGTGTAAGCCATTTGCTAGTGGATGAAATT
EST: gi|352763797|gb|FQ473500.1|FQ473500
EST:     CTCAAACACGTTTGCTATTTTGCACCACTGGAGTACTACTTCGGCAGCTG                         GTTCAGGACCCAGATCTAACTGGTGTAAGCCATTTGCTAGTGGATGAAATT
genomic: CTCAAACACGTTTGCTATTTTGCACCACTGGAGTACTACTTCGGCAGCTGgtaatatatt ... ttaaatacagGTTCAGGACCCAGATCTAACTGGTGTAAGCCATTTGCTAGTGGATGAAATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTGGTGAAACTGTTGGTTACCAGATTCGCCTGGAAGCAAAGCGCTCTGCTCAAACACGTTTGCTATTTTGCACCACTGGAGTACTACTTCGGCAGCTGgtaatatattttttgtacctgttatttttcattggtaaaagtttcactcttatatttttgttcttcagtctttatgtctgtatcttagcgtttttagaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtaaaa