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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAGAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCGgtgaggaaaactaaccttcagatttatagaaactggaatttagaacttacacattttctttgttgatagtccaccttggccagaccaacaatgaaactag...

Basic information

species Vitis vinifera
transcript Vv18s0089g01240.t01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0089g01240.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: LOC_Os02g35630.1 (Oryza sativa), 5'ss of exon 10
ACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAGAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCGgtgag-----gaaaactaaccttcagatttatagaaa----ctggaatttagaacttacacattttctttgttgatagtccaccttggccagaccaacaatgaaactag--------------------
 |||||||||||||| ||||| ||||| |||||||| ||||||||||||||  | |||||  |  | | ||||   ||||||||||||||  | ||||| || ||      ||  |  |  || | |||| | | ||    |     ||||      |  ||| |      |   |       ||  |  | |||   |||  |  |                      
GCGGCAAGATTCTTCTATTGGCTTTGGGGCACCTGTCCGTGCTAACATGAGGGCAGGTGGCATCTCAAGTGCTCAAGTGACATCATCCTTGTTGGAATCAgtaagcaccaaaattccgagtttaacattttttggaaatctcctttgtttaaggagaatgcatgtgtgaattcagtgaaattactgtgtaaaaccttaaatctaggtgtttaaactgttcatttcttag

upper sequence: Vv18s0089g01240.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA10G32040.1 (Glycine max), 5'ss of exon 8
ACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAGAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCGgtgaggaaaactaaccttcagatttatagaaactggaatttagaacttacacattttctttgttgatagtccaccttggccagaccaac--aatgaaactag
||| |||||||||||||||||||||||||||||||| ||| | || |||||| |||||||  | || |||||||  || |||||||| ||||| || |||||||| |      |   | |   | |   |||||    | |    ||| |       |||  | | |||   || |||  ||    |||  ||| ||    |
ACGACAAGATTCTTCAATTGGTTTTGGAGCACCTGTCCGTTCCAATATGAGAGCTGGTGGAATTACAAATGCTGCAGTCACATCATCTTTACTTGAGTCGgtgagaattcactatgattat-ctgactaaaacttttttattccccttcctgtaaaacttgataggtagat-actttgagcaattaaacctaataaattgtg

upper sequence: Vv18s0089g01240.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA20G35600.1 (Glycine max), 5'ss of exon 10
ACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAGAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCGgtgaggaa-aactaaccttcagatttatagaaactggaatttagaacttacacattttctttgttgatagtccaccttggccagaccaac--aatgaaactag
||| |||||||||||||||||||||||| |||| || ||| | || ||||||||||||||  | || |||||||  || |||||||| ||||| || |||||||| |  |||||   ||  |  | |   |||||    | |    ||| |       ||   | | |||   || |||  ||    |||  ||| || |  |
ACGACAAGATTCTTCAATTGGTTTTGGATCACCAGTCCGTTCCAATATGAGAACTGGTGGAGTTACAAATGCTGCAGTCACATCATCTTTACTTGAGTCGgtgagaattaactatgatt--gtctgactaaaacttttttattctccttcctgtaaaactagataggtagat-actttgtgcaattaaacctaataaatcatg

upper sequence: Vv18s0089g01240.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA16G33080.1 (Glycine max), 5'ss of exon 11
ACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAGAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCGgtgaggaaaactaaccttcagatttatagaaactggaatttagaacttacacattttctttgttgatagtccaccttggccagaccaacaatgaaactag
||| ||||||||||| ||||||||||||||||| |||||||| || |||||| |||||||  ||||  || |||  || |||||||| ||||| || || |||||               ||  |||  |        |||   | ||  |    |   | | |    |   ||  |   |     ||   || || || 
ACGACAAGATTCTTCTATTGGTTTTGGAGCACCAGTTCGTGCCAATATGAGAGCTGGTGGAATAACAGATTCTGCAGTAACATCATCTTTACTTGAGTCAgtgagtgttgtctcttacatgaaatattaatctcctttttttataattgtaaggctagatagatagatggatactgtaagccattgaagcttgtaaataa

upper sequence: Vv18s0089g01240.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA09G28260.1 (Glycine max), 5'ss of exon 11
ACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAGAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCGgtgaggaaaactaaccttcagatttatagaaactggaatttagaacttacacattttctttgttgatagtccacct---tggccagaccaacaatgaaactag-----------
||| ||||||||||| |||||||||||||| || |||||||| || |||||| ||| |||  ||||  || |||  || |||||||| ||||| || || |||||      |  |  | |   ||||     ||| ||| |  | ||    | ||||  |  |||  || |||  |   | |  |||   | | || ||  |            
ACGACAAGATTCTTCTATTGGTTTTGGAGCCCCAGTTCGTGCAAATATGAGAGCTGTTGGAATAACAGATTCTGCAGTAACATCATCTTTACTTGAGTCAgtgagtg---ttggctctta---ttat-----ctgaaatattaatctc---cttttttataattgtaaggccagatagatagatagatggatactgtaagcaattgaagattgt

upper sequence: Vv18s0089g01240.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: AT1G33360.1 (Arabidopsis thaliana), 5'ss of exon 10
ACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAGAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCGgtgaggaaaactaaccttcagatttatagaaactggaatttagaacttacacattttctttgttgatagtccaccttggccagaccaacaatgaaactag
||| ||||| || ||||||||||||||||| ||||||||||| ||||||   ||  ||||  | |||| || ||   | || ||||| || ||||||||||| |   | ||||      || ||| |  |  || |  |  | |  |  ||   || ||     || |    |  || |  |  ||  |    |    ||
ACGACAAGACTCATCAATTGGTTTTGGAGCTCCTGTTCGTGCCAACATGGCTACCAGTGGAGTGACCAGTGGTGCAATAACTTCATCTTTGCTAGAATCGgtaa---acacta---catagttttgttaagcctagtgtaaacacttctca---ttcctggaaagagatcttagttttggaatgccggctgc-atttcag

upper sequence: Vv18s0089g01240.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: PP1S171_84V6.1 (Physcomitrella patens), 5'ss of exon 10
ACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAGAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCGgtgaggaaaactaaccttcagatttatagaa-actggaatttagaacttacacattttctttgttgatagtccaccttggccagaccaacaatgaaactag
    |||||||| |||||||| |||||| ||||||||||||| |  |||||         | ||||| |  |||   | || || || || ||||||  |||     | | |   |   | | |  |     ||||  || |   ||||||| |||  | |  |   | |  |   |     ||          |  ||  
GAAACAAGATTCGTCAATTGGATTTGGATCACCTGTTCGTGCCAGTATGAGGGGGAACAAGCTAACCGACTCTGCCATTACTTCTTCTTTGCTAGAAATGgtacaagacattctgcagaacactgttgttttactgtcatgtgccacttaca-attcccgtactgcctggagcttgtgcatgaggttcttgtatatgcttt

upper sequence: Vv18s0089g01240.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: PP1S98_222V6.1 (Physcomitrella patens), 5'ss of exon 11
ACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAGAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCGgtgaggaaaac---taaccttcagatttatagaaactggaatttagaacttacacattttctttgttgatagtccaccttggccagaccaacaatgaaactag
   ||||||||| ||||||||||||||||||||||||||||| || ||| ||          | | | | || |   | || ||||| || || ||  ||||     | |    |||   |   | |  |      || |||||  || ||| |  |    |||         ||  |     |   |      | |  |   
GAAGCAAGATTCATCAATTGGTTTTGGAGCACCTGTTCGTGCCAATATGCGAGGAAACAAACTGATCGACGCCGCCATTACTTCATCTTTGCTTGAGACGgtacctcacatctttaataatagtactcttttcctttgtaattt--aatttaaaagtggcttttaaattggacccgtccccctcgagcattttttcatgcct-

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|26257016|gb|CA808079.1|CA808079
EST:     GGACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCG                         GTTGAAAGTAGTGATCTTATTGCATATGGCCTCATACCAGAGTTTATTGGA
genomic: GAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCGgtgaggaaaa ... gcattttcagGTTGAAAGTAGTGATCTTATTGCATATGGCCTCATACCAGAGTTTATTGGA
EST: gi|71862340|gb|DT011395.1|DT011395
EST:     GAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCG                         GTTGAAAGTAGTGATCTTATTGCATATGGCCTCATACCAGAGTTTATTGGA
genomic: GAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCGgtgaggaaaa ... gcattttcagGTTGAAAGTAGTGATCTTATTGCATATGGCCTCATACCAGAGTTTATTGGA
EST: gi|110698280|gb|EE075629.1|EE075629
EST:     GAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCG                         GTTGAAAGTAGTGATCTTATTGCATATGGCCTCATACCAGAGTTTATTGGA
genomic: GAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCGgtgaggaaaa ... gcattttcagGTTGAAAGTAGTGATCTTATTGCATATGGCCTCATACCAGAGTTTATTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAGAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCGgtgaggaaaactaaccttcagatttatagaaactggaatttagaacttacacattttctttgttgatagtccaccttggccagaccaacaatgaaactag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgaaa