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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTTATTGATCAGGCTTTAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCGgtatgcacaatcaggttctaaaattttaattgctcaaaaaattgatataccattttgaggataacgtgcagcaaatataaaaattgcttgtgttcggaaa...

Basic information

species Vitis vinifera
transcript Vv17s0000g09910.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g09910.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA06G18320.1 (Glycine max), 5'ss of exon 5
ACTTATTGATCAGGCTTTAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCGgtatgcacaatcaggttctaaaattttaattgctcaaaaaattgatataccattttgaggataacgtgca-gcaaatataaaaattgcttgtgttcggaaa------
  |||| || |||||||| |   | || ||| | ||||| || ||||||||||||||||||||||||||||||| ||||||   |||    |  |||| || |||  | |  | |   | ||   ||| ||   ||   |  ||       |       |||  ||        
GATTATCGACCAGGCTTTTGCTCAAGGAGTCCAAGTTGCAGTTTGCAGCACTTCCAATGAGAAGGCGgtatgcataatcag---cta----tccaattccttaaatgaatcttttctgacttaagggaaaattggctcactgatccttgtttcatgatagtttagagtttcaat

upper sequence: Vv17s0000g09910.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA04G36600.1 (Glycine max), 5'ss of exon 4
ACTTATTGATCAGGCTTTAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCGgtatgcacaatcaggttctaaaattttaattgctcaaaaaattgatataccattttgaggataac--gtgcagcaa-----atataaaaattgcttgtgttcggaaa
  |||| ||||||||||| |   | || ||| | ||||| || |||||||||||||| |||||||||||||||| ||||||        | |  |||| || |||  | |  | |   |  |   ||| ||   |  ||   |      | | | | | | | | |||   |  
GATTATCGATCAGGCTTTTGCTCAAGGAGTCCAAGTTGCAGTTTGCAGCACTTCCAACGAGAAGGCGgtatgcataatcagc-------aatccaattccttaaatgaatcttttctgacataagggaaaattggctcactgatccttgtttcatagtagttggagtttcaatt

upper sequence: Vv17s0000g09910.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT3G48420.1 (Arabidopsis thaliana), 5'ss of exon 4
ACTTATTGATCAGGCTTTAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCGgtatgcacaatcaggttctaaaattttaattgctcaaaa---aattgatatacc-----attttgag----gataacgtgcagcaaatataaaaat-tgcttgtgt-tcggaaa-------------------------------------------------------------------------------
  |  ||||||| ||||||   || || ||||| || ||||| ||||| ||||| |||||||||||||||||  |||||||||||||  | || | || |   | |    |   ||||| |     || |||      ||| |  |   | ||| |  |  |   ||   ||  |||  ||                                                                               
GTTGGTTGATCAAGCTTTAACAAACGGAGTCAAAGTAGCTGTGTGCAGTACTTCAAATGAGAAGGCGgtatgatcaatcaggttctactacttcagtttcctgagaccataaccatatatctcaaaatcttgtatcctgatgagttttcgtaaacaagactacgcgcagctgcatcgttaacatgaatatgcgagcatcgtcttagcttagaagaactgtataatcggaaatacttttctcatttcttgcctgatttcag

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|351049437|gb|FQ450038.1|FQ450038
EST:     TAGGGAAAGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAAGCG                         GACTCTGCGATAGTTTCATGCTTGCTGGGGCCTAAACGAGCAGAAAAAATC
genomic: TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCGgtatgcacaa ... aatatcccagGTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATC
EST: gi|110357588|gb|EC921779.1|EC921779
EST:     TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCG                         GTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATC
genomic: TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCGgtatgcacaa ... aatatcccagGTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATC
EST: gi|351046213|gb|FQ442591.1|FQ442591
EST:     TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCG                         GACTCTGCGATAGTTTCATGCTTGCTGGGGCCTAAACGAGCAGAAAAAATC
genomic: TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCGgtatgcacaa ... aatatcccagGTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATC
EST: gi|351046860|gb|FQ454470.1|FQ454470
EST:     TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCG                         GACTCTGCGATAGTTTCATGCTTGCTGGGGCCTAAACGAGCAGAAAAAATC
genomic: TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCGgtatgcacaa ... aatatcccagGTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATC
EST: gi|110376295|gb|EC941348.1|EC941348
EST:     TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCG                         GTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATC
genomic: TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCGgtatgcacaa ... aatatcccagGTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATC
EST: gi|351048691|gb|FQ448965.1|FQ448965
EST:     TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCG                         GACTCTGCGATAGTTTCATGCTTGCTGGGGCCTAAACGAGCAGAAAAAATC
genomic: TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCGgtatgcacaa ... aatatcccagGTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATC
EST: gi|351053962|gb|FQ441728.1|FQ441728
EST:     TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCG                         GACTCTGCGATAGTTTCATGCTTGCTGGGGCCTAAACGAGCAGAAAAAATC
genomic: TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCGgtatgcacaa ... aatatcccagGTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATC
EST: gi|110383854|gb|EC948256.1|EC948256
EST:     GCAGCACTTCCAATGAGAAGGCG                         GTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATC
genomic: GCAGCACTTCCAATGAGAAGGCGgtatgcacaa ... aatatcccagGTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATC
EST: gi|110376164|gb|EC941208.1|EC941208
EST:     TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCG                         GTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATC
genomic: TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCGgtatgcacaa ... aatatcccagGTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATC
EST: gi|18459790|gb|BM438068.1|BM438068
EST:     TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCG                         GTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATC
genomic: TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCGgtatgcacaa ... aatatcccagGTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATC
EST: gi|110361698|gb|EC925191.1|EC925191
EST:     TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCG                         GTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATC
genomic: TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCGgtatgcacaa ... aatatcccagGTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATC
EST: gi|351031800|gb|FQ460057.1|FQ460057
EST:     TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCG                         GACTCTGCGATAGTTTCATGCTTGCTGGGGCCTAAACGAGCAGAAAAAATC
genomic: TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCGgtatgcacaa ... aatatcccagGTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATC
EST: gi|351039737|gb|FQ464775.1|FQ464775
EST:     TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCG                         GACTCTGCGATAGTTTCATGCTTGCTGGGGC-TAAACGAGCAGAAAAAATC
genomic: TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCGgtatgcacaa ... aatatcccagGTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATC
EST: gi|351054042|gb|FQ441808.1|FQ441808
EST:     TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCG                         GACTCTGCGATAGTTTCATGCTTGCTGGGGCCTAAACGAGCAGAAAAAATC
genomic: TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCGgtatgcacaa ... aatatcccagGTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATC
EST: gi|351031985|gb|FQ460242.1|FQ460242
EST:     TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCG                         GACTCTGCGATAGTTTCATGCTTGCTGGGGCCTAAACGAGCAGAAAAAATC
genomic: TAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCGgtatgcacaa ... aatatcccagGTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTTATTGATCAGGCTTTAGGGAAGGGGGTCAATGTTGCTGTCTGCAGCACTTCCAATGAGAAGGCGgtatgcacaatcaggttctaaaattttaattgctcaaaaaattgatataccattttgaggataacgtgcagcaaatataaaaattgcttgtgttcggaaa

- - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataaaaa