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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTTGCTGTTAGCAACAAACATACATATATGTTCTCAGCTGGTGATGACAAACAAGTTAAATGCTGGGACCTTGAACAGAATAAGgttagaaccttttttaaactcaccgctgaatcctgtactacaagtgactaaattcatatgctatatatttttctttgttcag

Basic information

species Vitis vinifera
transcript Vv05s0077g02310.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g02310.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: LOC_Os03g21990.1 (Oryza sativa), 5'ss of exon 10
GCCTTGCTGTTAGCAACAAACATACATATATGTTCTCAGCTGGTGATGACAAACAAGTTAAATGCTGGGACCTTGAACAGAATAAGgttagaaccttttttaa-actcaccgctgaatcctgtactacaagtgactaaattcatatgctatatatttttctttgttcag
| |||||||| ||| |    || |||||| | || || |||||||||||||||||||| || || ||||| |||||||| || ||||||||    |  ||  |     |  || | || | |  |     |  | ||   | | ||  | | | ||||  ||| || ||
GGCTTGCTGTGAGCCAACGGCACACATATTTATTTTCTGCTGGTGATGACAAACAAGTAAAGTGTTGGGATCTTGAACAAAACAAGgttagcttatagttcgatgtagattgcagtatacagggcatattggcattatcgtaacattttgtttcttttcattt-ttaag

upper sequence: Vv05s0077g02310.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM2G017089_T02 (Zea mays), 5'ss of exon 8
GCCTTGCTGTTAGCAACAAACATACATATATGTTCTCAGCTGGTGATGACAAACAAGTTAAATGCTGGGACCTTGAACAGAATAAGgttagaaccttttttaaactcaccgctgaatcctgtactacaagt-gactaaa-ttcatatgctatatattt-ttctttgttcag-
| |||||||| ||| |    || || ||| | || || |||||||||||||||||||| ||||| ||||| |||||||| || ||||||||    |  |||||       | || ||  ||     ||  | ||||    || | ||   || | | | |||| |||| |  
GACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAGgttagt-tttactttaagtat---ggtgtattttgggtggcattttgacttctcttgacatctgatctgtatattctatgttaaag

upper sequence: Vv05s0077g02310.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: AT4G15900.1 (Arabidopsis thaliana), 5'ss of exon 9
GCCTTGCTGTTAGCAACAAACATACATATATGTTCTCAGCTGGTGATGACAAACAAGTTAAATGCTGGGACCTTGAACAGAATAAGgttagaaccttttttaaactcaccgctgaatcctgtactacaagtgactaaattcatatgctatatatttttctttgttcag
|||| ||||| |||||   |||||| ||||||||||| |||||||||||||| ||||| ||||||||||||||||| ||||||||||||| |||  | ||    |||  |  |     ||| | | |   |  ||||     |   ||    ||||||  ||    ||
GCCTCGCTGTAAGCAATCGACATACCTATATGTTCTCTGCTGGTGATGACAAGCAAGTCAAATGCTGGGACCTTGAGCAGAATAAGgttacaactctatt----ctcttcatta---tctggatttctcatatctaa-----tgctcttggaatttttgatttgatag

upper sequence: Vv05s0077g02310.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: AT3G16650.1 (Arabidopsis thaliana), 5'ss of exon 9
GCCTTGCTGTTAGCAACAAACATACATATATGTTCTCAGCTGGTGATGACAAACAAGTTAAATGCTGGGACCTTGAACAGAATAAGgttagaacctt-------ttttaaactcaccgctgaatc--ctgtactacaagtga-ctaaa---ttcatatgctatat-------atttttctttgttcag
|||| ||||| ||||| | |||||| |||||||| || |||||||||||||| ||||| ||||||||||||||||| ||||||||||||  |||           ||| | |||| |  |  ||    |   || |   ||| || ||   ||||| | | || |       |||| |||||| |   
GCCTCGCTGTAAGCAATAGACATACCTATATGTTTTCTGCTGGTGATGACAAGCAAGTCAAATGCTGGGACCTTGAGCAGAATAAGgtttaaactcgatgatggatttcatctcatctgtatattaattactcttctcctgatctgaacttttcatgtccaatgtctttggaatttgtctttgatag-

upper sequence: Vv05s0077g02310.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: PP1S402_49V6.1 (Physcomitrella patens), 5'ss of exon 8
GCCTTGCTGTTAGCAACAAACATACATATATGTTCTCAGCTGGTGATGACAAACAAGTTAAATGCTGGGACCTTGAACAGAATAAGgttag----aaccttttttaaactcaccgct----gaatcctgtactac-------aagtgacta--aattcatatgctatatatttttctttgttcag-------------------------------
||||||| || |||  |   ||| | ||| | ||||||||||||||||||||||| || ||||| ||||| |||||| | ||||||||  |      | |||   |  ||    | |    | ||||   | ||        | ||| |||  ||| ||| | |||||| | ||| |  | | ||                               
GCCTTGCAGTGAGCGCCCGGCATCCTTATTTATTCTCAGCTGGTGATGACAAACAGGTCAAATGTTGGGATCTTGAATACAATAAGgtgtgtccaggcttttacgacgcttgttggttgtagcatccgtaattagttcatgaatgtgtctatgaatccatgtactatatgtatttatc-gctgaggatctttgctctggtgtattggtttgtgcag

upper sequence: Vv05s0077g02310.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: PP1S169_73V6.2 (Physcomitrella patens), 5'ss of exon 8
GCCTTGCTGTTAGCAACAAACATACATATATGTTCTCAGCTGGTGATGACAAACAAGTTAAATGCTGGGACCTTGAACAGAATAAGgttag----aaccttttttaaactcaccgctgaat--cctgtactacaa---gtgactaaattcatatgctatatatttttctttg-ttcag-----------------------
| || || || ||      |||| | || ||||| |||||||||||||| || ||||| ||||||||||| |||||  | || |||||  |      |   |||||| |  |    ||  |  ||| ||||       | | |  |  |||| |   || |  ||||||  |  ||                         
GTCTCGCAGTGAGTGCTCGACATCCTTACATGTTTTCAGCTGGTGATGATAAGCAAGTCAAATGCTGGGATCTTGAGTACAACAAGgtgtgttctggctccttttaagcatattaatgcgtagcctttacttggctctgagtcagaggtcatttcaaatgtcattttctgagactctactctgggatatgggtttgctcag

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|110416775|gb|EC982779.1|EC982779
EST:     CAGCTGGTGATGACAAACAAGTTAAATGCTGGGACCTTGAACAGAATAAG                         GTTATTCGGTCTTATCATGGTCATCTGAGTGGGGTTTATTGTTTGGCACTT
genomic: CAGCTGGTGATGACAAACAAGTTAAATGCTGGGACCTTGAACAGAATAAGgttagaacct ... ctttgttcagGTTATTCGGTCTTATCATGGTCATCTGAGTGGGGTTTATTGTTTGGCACTT
EST: gi|77578499|gb|DV218043.1|DV218043
EST:     CAGCTGGTGATGACAAACAAGTTAAATGCTGGGACCTTGAACAGAATAAG                         GTTATTCGGTCTTATCATGGTCATCTGAGTGGGGTTTATTGTTTGGCACTT
genomic: CAGCTGGTGATGACAAACAAGTTAAATGCTGGGACCTTGAACAGAATAAGgttagaacct ... ctttgttcagGTTATTCGGTCTTATCATGGTCATCTGAGTGGGGTTTATTGTTTGGCACTT
EST: gi|349818063|gb|FQ408838.1|FQ408838
EST:     CAGCTGGTGATGACAAACAAGTTAAATGCTGGGACCTTGAACAGAATAAG                         GTTATTCGGTCTTATCATGGTCATCTGAGTGGGGTTTATTGTTTGGCACTT
genomic: CAGCTGGTGATGACAAACAAGTTAAATGCTGGGACCTTGAACAGAATAAGgttagaacct ... ctttgttcagGTTATTCGGTCTTATCATGGTCATCTGAGTGGGGTTTATTGTTTGGCACTT
EST: gi|110724126|gb|EE099691.1|EE099691
EST:     CAGCTGGTGATGACAAACAAGTTAAATGCTGGGACCTTGAACAGAATAAG                         GTTATTCGGTCTTATCATGGTCATCTGAGTGGGGTTTATTGTTTGGCACTT
genomic: CAGCTGGTGATGACAAACAAGTTAAATGCTGGGACCTTGAACAGAATAAGgttagaacct ... ctttgttcagGTTATTCGGTCTTATCATGGTCATCTGAGTGGGGTTTATTGTTTGGCACTT
EST: gi|110688178|gb|EE066434.1|EE066434
EST:     CAGCTGGTGATGACAA-CAAGTTAAATGCTGGGACCTTGAACAGAATAAA                         GTTATTCGGTCTTATCATGGTCATCTG
genomic: CAGCTGGTGATGACAAACAAGTTAAATGCTGGGACCTTGAACAGAATAAGgttagaacct ... ctttgttcagGTTATTCGGTCTTATCATGGTCATCTG
EST: gi|161707291|gb|FC057696.1|FC057696
EST:     GACAAACAAGTTAAATGCTGGGACCTTGAACAGAATAAG                         GTTATTCGGTCTTATCATGGTCATCTGAGTGGGGTTTATTGTTTGGCACTT
genomic: GACAAACAAGTTAAATGCTGGGACCTTGAACAGAATAAGgttagaacct ... ctttgttcagGTTATTCGGTCTTATCATGGTCATCTGAGTGGGGTTTATTGTTTGGCACTT
EST: gi|110728878|gb|EE104832.1|EE104832
EST:     CAGCTGGTGATGACAAACAAGTTAAATGCTGGGACCTTGAAAAGAATAAA                         GTTATTCNGTCTTATCATGGTCATCTGAGTGGGGGTTTATTGTTTGGCACT
genomic: CAGCTGGTGATGACAAACAAGTTAAATGCTGGGACCTTGAACAGAATAAGgttagaacct ... ctttgttcagGTTATTCGGTCTTATCATGGTCATCTGAGTGGGG-TTTATTGTTTGGCACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTTGCTGTTAGCAACAAACATACATATATGTTCTCAGCTGGTGATGACAAACAAGTTAAATGCTGGGACCTTGAACAGAATAAGgttagaaccttttttaaactcaccgctgaatcctgtactacaagtgactaaattcatatgctatatatttttctttgttcag

- - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG