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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATTGGCTCGGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCGgtgagtaaagatttgatcataacctactaatatccttagtatagcttccatatggaagttctgggatatgcatgcagttgctgaaaataatccaacacat...

Basic information

species Vitis vinifera
transcript Vv14s0060g00830.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g00830.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os01g22870.1 (Oryza sativa), 5'ss of exon 4
TCATTGGCTCGGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCGgtgagtaaagatttgatcataacctactaatatccttagtat--agcttccatatggaagttctgggatatgcatgcagttgctgaaaataatccaacacat-
||  | ||| |||||||||||||||| |||||||| ||||||||||| || ||| |  | || ||| |   | |   ||  |      |   |  ||||| |  ||  ||| |||   | |      |  | ||| |||||  |  |   ||  ||       
TCTCTTGCTAGGATGAACAAGAAGGACTCATGGCTGTTCTGGTGGACTCTGTACTTGACTgtaagtgatattct--ccactatgattcagcgtttttagtttctagtatccgtatatgaatatatacaatttcattcagtttatatatg-aacacattgggaa

upper sequence: Vv14s0060g00830.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os05g06700.2 (Oryza sativa), 5'ss of exon 4
TCATTGGCTCGGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCGgtgagtaaagatttgatcataacctactaatatccttagtatagcttccatatgga-agttctgggatatgcatgcagttgctgaaaataatccaacacat
 |  | |||||||||||||| ||||| || ||||| ||||||||||| |||||| |  | || ||| |    ||     | |   | |  |      | ||||   |  |  |||| || | |     ||| |         || | ||    ||  ||  
GCTCTTGCTCGGATGAACAAAAAGGACTCGTGGCTGTTCTGGTGGACTCTTTACTTGACTgtaagtgatctattatctgttaaagagtgtttaatggaatatattatgtagctggatagatatattgcatgtaaagcaagtttgtagatttagcagaacc-

upper sequence: Vv14s0060g00830.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G048117_T01 (Zea mays), 5'ss of exon 4
TCATTGGCTCGGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCGgtgagtaaagatttgatcataacctactaatatccttagtatagcttccatatggaagttctgggatatgcat-gcagttgctgaaaataatccaacacat--------
||  | ||||||||||||||||||||||||||||| ||||||||||| |||||| |  | |||||| ||  ||   | ||||      ||| || |  || |||       || ||  |  | ||||  |  |     |  |||| | || |  |  |||         
TCTCTCGCTCGGATGAACAAGAAGGATTCATGGCTGTTCTGGTGGACTCTTTACTTGACTgtgagtgaattttctgttataatg----aatgtcat-ggtgtagacg----atagacatcgttggatcggtgtcatgatgtctgagattacttgattacaagttgctgt

upper sequence: Vv14s0060g00830.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA10G28620.1 (Glycine max), 5'ss of exon 4
TCATTGGCTCGGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCGgtgagtaaagat--ttgatcataacctac--taatatccttagtatagcttccatatgga-agttctgggatatgcatgcagttgctgaaaataatccaacacat
||||||||||||||||||||||||||||||||||| |||||||||||||| |||||| |||| ||  |  ||  ||||| |   | | |  | | || |    | |  |||  ||    | ||   |   || |  |||  |||| |  ||   |||||  |   
TCATTGGCTCGGATGAACAAGAAGGATTCATGGCTTTTCTGGTGGACCCTGTACCTTACGgtaagatagtatgattgattactgcatgcaatgacattccagttttctcttggatccttacagagttacaatctaaatgtggttgttctaag--atccagta---

upper sequence: Vv14s0060g00830.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA20G22720.1 (Glycine max), 5'ss of exon 4
TCATTGGCTCGGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCGgtgagtaaagat--ttgatcataacctactaatatccttagtatagcttccatatggaagttctgggatatgcatgcagttgctgaaaataatccaacacat-----
|||||||||||||||||||||||||| |||||||| |||||||||||||| || ||| | || ||  || ||  ||||  |   | | ||  |  | ||  | |    ||| ||  ||  | | |  | |   |||  |||| ||  |   |||||  | ||     
TCATTGGCTCGGATGAACAAGAAGGACTCATGGCTTTTCTGGTGGACCCTGTATCTTACAgtaagataatatgattgactactgcatgctg-tgacattcctctttgatccttacagagttacagtcaaa---atgtggttgttgtcag--atccagta-atagggg

upper sequence: Vv14s0060g00830.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT1G09330.1 (Arabidopsis thaliana), 5'ss of exon 4
TCATTGGCTCGGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCGgtgagtaaagatttgatcataacctactaatatccttagtatagcttccatatggaagttctgggatatgcatgcagttgctgaaaataatccaacacat--
|| |||||||||||||||||||| || |||||||| ||||||||||| ||||||||||| || ||||     |   | | |    | |   | | | ||  ||  | |   |      |||      ||   || |  |   |   || |      | |   
TCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTTTACCTTGCAgtaagtatttcatatctaacacttcagttgcagcataagc-taattacttaaaacccattcacaatcat-tgtggaactttagtggatgactaggaataaga

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|110686994|gb|EE064014.1|EE064014
EST:     GGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCG                         GCAGTTGTATGGATCTTGCTCGGGATATTCTCTCTCATAAGGTTTCAAGCT
genomic: GGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCGgtgagtaaag ... tattttgtagGCGGTTGTATGGATCTTGCTCGGGATATTCTCTCTCGTAAGGTTTCAAGCT
EST: gi|30126361|gb|CB911700.1|CB911700
EST:     GGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCG                         GCGGTTGTATGGATCTTGCTCGGGATATTCTCTCTCGTAAGGTTTCAAGCT
genomic: GGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCGgtgagtaaag ... tattttgtagGCGGTTGTATGGATCTTGCTCGGGATATTCTCTCTCGTAAGGTTTCAAGCT
EST: gi|30126427|gb|CB911766.1|CB911766
EST:     GGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCG                         GCGGTTGTATGGATCTTGCTCGGGATATTCTCTCTCGTAAGGTTTCAAGCT
genomic: GGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCGgtgagtaaag ... tattttgtagGCGGTTGTATGGATCTTGCTCGGGATATTCTCTCTCGTAAGGTTTCAAGCT
EST: gi|110723141|gb|EE100115.1|EE100115
EST:     GGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCG                         GCGGTTGTATGGATCTTGCTCGGGATATTCTCTCTCGTAAGGTTTCAAGCT
genomic: GGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCGgtgagtaaag ... tattttgtagGCGGTTGTATGGATCTTGCTCGGGATATTCTCTCTCGTAAGGTTTCAAGCT
EST: gi|294964678|gb|GW838481.1|GW838481
EST:     GGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCG                         GCAGTTGTATGGATCTTGCTCGGGATATTCTCTCTCGTAAGGTTTCAAGCT
genomic: GGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCGgtgagtaaag ... tattttgtagGCGGTTGTATGGATCTTGCTCGGGATATTCTCTCTCGTAAGGTTTCAAGCT
EST: gi|71874522|gb|DT023577.1|DT023577
EST:     GGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCG                         GCAGTTGTATGGATCTTGCTCGGGATATTCTCTCTCATAAGGTTTCAAGCT
genomic: GGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCGgtgagtaaag ... tattttgtagGCGGTTGTATGGATCTTGCTCGGGATATTCTCTCTCGTAAGGTTTCAAGCT
EST: gi|110730513|gb|EE107677.1|EE107677
EST:     GGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCG                         GCAGTTGTATGGATCTTGCTCGGGATATTCTCTCTCGTAAGGTTTCAAGCT
genomic: GGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCGgtgagtaaag ... tattttgtagGCGGTTGTATGGATCTTGCTCGGGATATTCTCTCTCGTAAGGTTTCAAGCT
EST: gi|349817728|gb|FQ407717.1|FQ407717
EST:     GGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCG                         GCAGTTGTATGGATCTTGCTCGGGATATTCTCTCTCATAAGGTTTCAAGCT
genomic: GGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCGgtgagtaaag ... tattttgtagGCGGTTGTATGGATCTTGCTCGGGATATTCTCTCTCGTAAGGTTTCAAGCT
EST: gi|71876447|gb|DT025502.1|DT025502
EST:     GGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCG                         GCAGTTGTATGGATCTTGCTCGGGATATTCTCTCTCATAAGGTTTCAAGCT
genomic: GGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCGgtgagtaaag ... tattttgtagGCGGTTGTATGGATCTTGCTCGGGATATTCTCTCTCGTAAGGTTTCAAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATTGGCTCGGATGAACAAGAAGGATTCATGGCTATTCTGGTGGACCCTTTACCTTGCGgtgagtaaagatttgatcataacctactaatatccttagtatagcttccatatggaagttctgggatatgcatgcagttgctgaaaataatccaacacat

- - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa