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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttataactagtctaacttattccaattcatggatgatacatgatgattaaattatagatttttttgctaactgcttaatccactccctaaattttcatgcagTTGTCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCAGA

Basic information

species Vitis vinifera
transcript Vv18s0001g06010.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g06010.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os01g66240.1 (Oryza sativa), 3'ss of exon 7
-gtaagttataactagtctaacttattccaattcatggatgatacatgatgattaaattatagatttttttgctaactgcttaatccactccctaaattttcatgcagTTGTCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCAGA
  |    | |  |   | |  |   || | || |||  ||| ||  ||||  ||| ||| || ||  |    | | |  |  | |||  || |  | |||   |||||| |   |||||||||| ||||||||||||||||| |||||||| || ||||| 
gttttcctgtttcctttgtctccccttaccatacatttatggta--tgat--ttagattgtaaataatcc-acgagcatcccagtcc--tcacggattttctttgcagTGGCTCTGAGCATGGTAGAACAAGCTGCAAAACCGCTTGCACGTCCTGTCAGG

upper sequence: Vv18s0001g06010.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G007160_T02 (Zea mays), 3'ss of exon 7
gtaagttataactagtctaacttattccaattcatggatgatacatgatgattaaattatagatttttttgctaactgcttaatccactccctaaattttcatgcagTTGTCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCAGA
    ||| | | || | ||  |  || |  ||     ||| ||        ||| |  | |  |  ||    |   |  |    |       | |  |||   ||||| | |||||| ||||| ||||||||||||||||| ||||| || || || |||
----gtttttattaatatatgtctttaccgttttgaaatgttatgct----ttacaacaaaagtaattaaaatggatattggtactcacatatgagcttt---gcagTGGCCTTGAGTATGGTAGAACAAGCTGCAAAACCACTTGCTCGTCCTGTTAGA

upper sequence: Vv18s0001g06010.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G01670.1 (Glycine max), 3'ss of exon 7
gtaagttataactagtctaacttattccaattcatggatgatacatgatgattaaattatagatttttttgc-taactgctt--aatccactccctaaattttcatgcagTTGTCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCAGA
                            | ||  || ||| || | | | |||    | ||  | ||||    || ||  ||    |    |   |  |||||  | ||||||| |||||||||||||| ||||||||||| || ||||| || ||||| |||
-------------------------gttagttattgaatgttataagtttatttttatgtacctattttcatgtagctatttttggttactttgttccatttt--ttcagTTGTTTTGAGCATGGTGGACCAAGCTGCAAAGCCACTTGCTCGGCCAGTGAGA

upper sequence: Vv18s0001g06010.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA01G44190.1 (Glycine max), 3'ss of exon 7
gtaagttataactagtctaacttattccaattcatggatgatacatgatgattaaattatagatttttttgctaact-gcttaatccactccctaaattttcatgcagTTGTCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCAGA
                            | |   || ||| |  | | | |||   ||||     ||| |   |  | ||    || | |  |    ||||  | ||||||| ||||||||||| || ||||||||||| |||||||| || ||||| |||
-------------------------gttagtcactgaatgttttaagttcattt--ttatgtgcctttctttaagttagccatttctatttacattgtttttcttcagTTGTTTTGAGCATGGTAGACCAAGCTGCAAAGCCTCTTGCTCGGCCAGTGAGA

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|30295766|gb|CB972560.1|CB972560
EST:     GCTTAGAATAACACCTCGAGTTCTAGTTGGTCACAGCTTTGGAGGAAAAG                         TTGTCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCA
genomic: GCTTAGAATAACACCTCGAGTTCTAGTTGGTCACAGCTTTGGAGGAAAAGgtaagttata ... tttcatgcagTTGTCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCA
EST: gi|352776833|gb|FQ472720.1|FQ472720
EST:     GCTTAGAATAACACCTCGAGTTCTAGTTGGTCACAGCTTTGGAGGAAAAG                         TTGTCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCA
genomic: GCTTAGAATAACACCTCGAGTTCTAGTTGGTCACAGCTTTGGAGGAAAAGgtaagttata ... tttcatgcagTTGTCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCA
EST: gi|352773576|gb|FQ472358.1|FQ472358
EST:     GCTTAGAATAACACCTCGAGTTCTAGTTGGTCACAGCTTTGGAGGAAAAG                         TTGTCTTGAGCATGGTGGAACAAGCTGCNAAACCTCTTGCACGACCAGTCA
genomic: GCTTAGAATAACACCTCGAGTTCTAGTTGGTCACAGCTTTGGAGGAAAAGgtaagttata ... tttcatgcagTTGTCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCA
EST: gi|352769737|gb|FQ468665.1|FQ468665
EST:     GCTTAGAATAACACCTCGAGTTCTAGTTGGTCACAGCTTTGGAGGAAA-G                         TTGTCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCA
genomic: GCTTAGAATAACACCTCGAGTTCTAGTTGGTCACAGCTTTGGAGGAAAAGgtaagttata ... tttcatgcagTTGTCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCA
EST: gi|352768560|gb|FQ467516.1|FQ467516
EST:     GCTTAGAATAACACCTTGAGTTCTAGTTGGTCACAGCTTTGGAGGAAAAG                         TTGTCTTGAGCATGGTGGAACAAACTGCAAAACCTCTTGCACGACCAGTCA
genomic: GCTTAGAATAACACCTCGAGTTCTAGTTGGTCACAGCTTTGGAGGAAAAGgtaagttata ... tttcatgcagTTGTCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCA
EST: gi|352781488|gb|FQ468332.1|FQ468332
EST:     GCTTAGAATAACACCTCGAGTTCTAGTTGGTCACAGCTTTGGAGGAAAAG                         TTGTCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCA
genomic: GCTTAGAATAACACCTCGAGTTCTAGTTGGTCACAGCTTTGGAGGAAAAGgtaagttata ... tttcatgcagTTGTCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCA
EST: gi|352781638|gb|FQ468936.1|FQ468936
EST:     CTTAGAATAACACCTCGAGTTCTAGTTGGTCACAGCTTTGGAGGAAAAAG                         T-GTCTTGAGCATGGTGGA
genomic: CTTAGAATAACACCTCGAGTTCTAGTTGGTCACAGCTTTGGAGGAAAA-Ggtaagttata ... tttcatgcagTTGTCTTGAGCATGGTGGA
EST: gi|352776761|gb|FQ472648.1|FQ472648
EST:     GCTTAGAATAACACCTCGAGTTCTAGTTGGTCACAGCTTTGGAGGAAAAG                         TTGTCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCA
genomic: GCTTAGAATAACACCTCGAGTTCTAGTTGGTCACAGCTTTGGAGGAAAAGgtaagttata ... tttcatgcagTTGTCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaattatagatttttttgctaactgcttaatccactccctaaattttcatgcagTTGTCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCAGA
                                            ttttcat  CT-rich tract
     tatagattttttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttataactagtctaacttattccaattcatggatgatacatgatgattaaattatagatttttttgctaactgcttaatccactccctaaattttcatgcagTTGTCTTGAGCATGGTGGAACAAGCTGCAAAACCTCTTGCACGACCAGTCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC