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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTGgtaacatttcatcctcttcattgaattgcacccccttttgttaggcaccttcgaacagactttctaattgcctattaaaaaaaaaaacctgtgttgaaac...

Basic information

species Vitis vinifera
transcript Vv11s0016g02890.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g02890.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G051288_T01 (Zea mays), 5'ss of exon 4
AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTGgtaacatttcatcctcttcattgaattgcacccccttttgttaggcaccttcgaacagactttctaattgcctattaaaaaaaaaaacctgtgttgaaac
 |||||||||    ||  | ||||| ||||||||||||||||||||| ||||| | ||||| ||||||||  | ||||| ||||||  ||               ||| ||||     | | |||  ||| ||  | ||  |   ||   ||  | |||     | ||  | ||||||| |  
GGAATGCATCACAAGGCGGTACTACATATGTTCATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTGgtaggat---------------gaactgcatt---tgtagtt--gcaactcagtacgcatgctcctgtt--caatttcctgataatccttgtgttgcag-

upper sequence: Vv11s0016g02890.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA05G36020.1 (Glycine max), 5'ss of exon 4
AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTGgtaacatttcatcctcttcattgaattgcacccccttttgttaggcaccttcgaacagactttctaattgcctattaaaaaaaaaaacctgtgttgaaac
|||||||| ||| ||||| ||||||||||||||| ||||||||||| || || ||||| ||||| ||||||||||| ||| ||||||    | ||| |  | | ||| ||| |||  | ||    ||||  |   |  | || | | |   |  |  |  |          ||          
AGAATGCAACTTGCGGTAAAACTACTTATGTTCACTGTAAAGCTGGTCGGGGGAGGAGTACAACAATTGTGCTTTGTTATCTGgtaagtgattatctttatgactgagttgtaccatcattga--aggcttcaaggtgctgaatgttttccttgcggtctacttgtgttttctag--------

upper sequence: Vv11s0016g02890.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA08G03600.1 (Glycine max), 5'ss of exon 5
AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTGgtaacatttcatcctcttcattgaattgcacccccttt---tgttaggcaccttcgaacagactttctaattgcctattaaaaaaaaaaacctgtgttgaaac
|||||||| ||| ||| | ||||||||||||||| ||||||||||| || || ||||| ||||| ||||||||||| ||| ||||||    | ||| |  | ||||| |||   |  | ||    | | |        |||     |   || ||   | ||  |                     
AGAATGCAACTTGCGGCAAAACTACTTATGTTCACTGTAAAGCTGGGCGGGGGAGGAGTACAACAATTGTGCTTTGTTATATGgtaattgatgatctttatgattgagttgtggcatcattgaaggcttgaaggtgctgaatgttttccatacttatgtttttcag--------------------

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|156735982|gb|EV240103.1|EV240103
EST:     ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTG                         GTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT
genomic: ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTGgtaacatttc ... aattttgcagGTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT
EST: gi|351032518|gb|FQ458883.1|FQ458883
EST:     ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTG                         GTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT
genomic: ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTGgtaacatttc ... aattttgcagGTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT
EST: gi|351034943|gb|FQ458300.1|FQ458300
EST:     ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTG                         GTTGAGTATAAG
genomic: ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTGgtaacatttc ... aattttgcagGTTGAGTATAAG
EST: gi|349809160|gb|FQ398901.1|FQ398901
EST:     ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTG                         GTTGAGTATAAGCACATGACACCTGCTGCTGCC
genomic: ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTGgtaacatttc ... aattttgcagGTTGAGTATAAGCACATGACACCTGCTGCTGCC
EST: gi|351039844|gb|FQ464882.1|FQ464882
EST:     ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTG                         GTTGAGTATTAGCACATGACACCTGCTGCTG
genomic: ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTGgtaacatttc ... aattttgcagGTTGAGTATAAGCACATGACACCTGCTGCTG
EST: gi|110379170|gb|EC944349.1|EC944349
EST:     ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTG                         GTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT
genomic: ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTGgtaacatttc ... aattttgcagGTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT
EST: gi|351044066|gb|FQ452739.1|FQ452739
EST:     ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTG                         GTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT
genomic: ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTGgtaacatttc ... aattttgcagGTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT
EST: gi|83274947|gb|DV939043.1|DV939043
EST:     GAAGGAGCACAACTATTGTGCTTTGCTATTTG                         GTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT
genomic: GAAGGAGCACAACTATTGTGCTTTGCTATTTGgtaacatttc ... aattttgcagGTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT
EST: gi|110388085|gb|EC952801.1|EC952801
EST:     ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTG                         GTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT
genomic: ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTGgtaacatttc ... aattttgcagGTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT
EST: gi|351037982|gb|FQ465220.1|FQ465220
EST:     ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTG                         GTTGAGTATAAGCACATGACACCTGCTGCTGCCCGGGAA
genomic: ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTGgtaacatttc ... aattttgcagGTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAA
EST: gi|351052950|gb|FQ453937.1|FQ453937
EST:     ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTG                         GTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT
genomic: ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTGgtaacatttc ... aattttgcagGTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT
EST: gi|349819705|gb|FQ402642.1|FQ402642
EST:     ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTG                         GTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT
genomic: ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTGgtaacatttc ... aattttgcagGTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT
EST: gi|351038655|gb|FQ464521.1|FQ464521
EST:     ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATGGTGCTTTGCTATTTG                         GTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT
genomic: ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTGgtaacatttc ... aattttgcagGTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT
EST: gi|351056738|gb|FQ443365.1|FQ443365
EST:     ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTG                         GTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTC
genomic: ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTGgtaacatttc ... aattttgcagGTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTC
EST: gi|71856681|gb|DT005736.1|DT005736
EST:     ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTG                         GTTGAGTATAAGCACATGACACCTGCT
genomic: ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTGgtaacatttc ... aattttgcagGTTGAGTATAAGCACATGACACCTGCT
EST: gi|351041750|gb|FQ455960.1|FQ455960
EST:     ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTG                         GTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT
genomic: ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTGgtaacatttc ... aattttgcagGTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT
EST: gi|351041720|gb|FQ455930.1|FQ455930
EST:     ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTG                         GTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT
genomic: ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTGgtaacatttc ... aattttgcagGTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT
EST: gi|351038816|gb|FQ464682.1|FQ464682
EST:     TTGTAAAGCTGGACGAGGAAGGAGCANCA-CTATTGTGCTTTGCTATTTG                         GTTGAGTATAAGC
genomic: TTGTAAAGCTGGACGAGGAAGGAGCA-CAACTATTGTGCTTTGCTATTTGgtaacatttc ... aattttgcagGTTGAGTATAAGC
EST: gi|110729962|gb|EE106494.1|EE106494
EST:     ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTG                         GTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT
genomic: ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTGgtaacatttc ... aattttgcagGTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT
EST: gi|110689256|gb|EE065319.1|EE065319
EST:     ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTG                         GTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT
genomic: ATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTGgtaacatttc ... aattttgcagGTTGAGTATAAGCACATGACACCTGCTGCTGCCCTGGAATATGTTCGTTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTGgtaacatttcatcctcttcattgaattgcacccccttttgttaggcaccttcgaacagactttctaattgcctattaaaaaaaaaaacctgtgttgaaac

- - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcctcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaacaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa