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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCTTACTGCTTCTTTATATGAGTGAAGAAGATGCATTCTGGTTGATGGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAATGGAAGGATTATATTTGgtaaactttctttcttcagataaaaatttttggtaatctttattttttgactttcgaggaattttgatctcactctagaagatgagaagcttaacttgtc...

Basic information

species Vitis vinifera
transcript Vv14s0083g00540.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os08g31840.2 (Oryza sativa), 5'ss of exon 5
TGGCTTACTGCTTCTTTATATGAGTGAAGAAGATGCATTCTGGTTGATGGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAATGGAAGGATTATATTTGgtaaactttctttcttcagataaaaatttttggtaatctttattttttg-actttcgaggaattttgatctcactctagaagatgagaagcttaacttgtc----------
|||||| || ||||||||||||||||||||||||||||| |||||  | ||||| || || || |||||||||||||| ||||||||||| || |||  |||||          | ||  | ||    |||||  |  |   ||   ||   |||| |  |||| | ||    || |||||  | | |     |||||             
TGGCTTGCTACTTCTTTATATGAGTGAAGAAGATGCATTTTGGTTATTAGTTGCTTTGCTGAAGGGAGCTGTTCATGCGCCAATGGAAGGTTTGTATCAGgtaa----------tgcaattgaattcctttggccacataatttccctgtggtttcaataaattataatgattctttagaac-tcaaacttccaacttccgatgaaagagt

upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G047223_T02 (Zea mays), 5'ss of exon 5
TGGCTTACTGCTTCTTTATATGAGTGAAGAAGATGCATTCTGGTTGATGGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAATGGAAGGATTATATTTGgtaaactttctttcttcag------ataaaaatttttggtaatctttattttttgactttcgaggaattttgatctcactctagaagatgagaagcttaacttgtc
|||  | |||||||||||||||||||| || ||||||||||||||  | || || || || || |||||||| ||||| ||||||||||| || |||  |||||    | ||   | ||      ||    ||||   || ||  ||   |    |  ||   |   | || ||           |  |||      |||      
TGGGCTGCTGCTTCTTTATATGAGTGAGGAGGATGCATTCTGGTTATTAGTCGCGTTGCTAAAGGGAGCTGTCCATGCACCAATGGAAGGCTTGTATCAGgtaatggctattatcttaggattgcattgggatttccagttataattcgatggctatattatggctgtctttattgtctatccttatctgacgtatataa------

upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA19G05360.1 (Glycine max), 5'ss of exon 5
TGGCTTACTGCTTCTTTATATGAGTGAAGAAGATGCATTCTGGTTGATGGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAATGGAAGGATTATATTTGgtaa--actttctttcttcagataaa-------aatttttggtaatctttat------tttttgactttcgaggaat-tttgatctcactctagaagatgagaagcttaacttgtc--------------------------------------------------------------------------------
 ||  |  ||||||||||||||||||| || |||||||| |||||| |||| ||||| || |||||||| ||||||||||||||||| || || ||| ||||||  | ||| ||||   |  | |         ||| ||| |  | |  ||      |   || |||       ||   | | |  | ||||  ||    |||    |  |  |                                                                                 
GGGGCTTTTGCTTCTTTATATGAGTGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAATGGAGGGCTTGTATCTGgtaactattttgtttcactaatttatttgttttgattattgatggtgtcaatgtattatccctgccttatattagatacataaacatattctatgaggaatgaactggatatcattaaattgcatgtttcttgttaatattatatactctttgatgataataactctcttagcaaaataactgtatttgactgcag

upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA13G07090.1 (Glycine max), 5'ss of exon 4
TGGCTTACTGCTTCTTTATATGAGTGAAGAAGATGCATTCTGGTTGATGGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAATGGAAGGATTATATTTGgtaa--actttctttcttcagataaa-------aatttttggtaatctttattttttgactttcgaggaattttgat-ctcactctagaagatgagaagcttaacttgtc---------------------------------------------------------------------------------
 ||  |  |||||||||||||||| || || |||||||| |||||| |||| ||||| || |||||||| ||||||||||||||||| || || ||| |||||   | ||| |||| |    | |         ||| ||| |  | |  || | ||  | ||     |  |  ||| |  | ||||  ||   |||| ||  |  |||                                                                                  
GGGACTTTTGCTTCTTTATATGAGCGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAATGGAGGGCTTGTATCTGgtagctattttgtttcatgcatttatttgtttcgattattgatggtgtcaatgtattatccttgccttatataagatacatattctatgaggaaagaa-ctggatatgtattaaattgctcgtttcttgttaatattatatactatttgatgataataactctcagcaaaattactgttttttgactgcag

upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT3G02460.1 (Arabidopsis thaliana), 5'ss of exon 5
TGGCTTACTGCTTCTTTATATGAGTGAAGAAGATGCATTCTGGTTGATGGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAATGGAAGGATTATATTTGgtaaactttctttcttcagataaaaatttttggtaatctttattttttgactttcgaggaattttgatctcactctagaagatgagaagcttaacttgtc-
 || ||  ||||||| |||||||| ||||||||||| ||||||||  | |||||||||||||||||||||||||||||||||||||||||| | |||   || |   || ||  ||   | || | |    |  ||| ||   |  |||| |       ||     || |    |  ||    |||    | | |  ||  
CGGTTTGTTGCTTCTCTATATGAGCGAAGAAGATGCCTTCTGGTTATTAGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAATGGAAGGACTGTATCATgtgagtctt-ttaattattagaagattgcaagaaaatgttgtatagttgaatgaaacaaaaagagtattttctgcgtgagttagagtttgtgaccacgttt

upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT5G15930.1 (Arabidopsis thaliana), 5'ss of exon 5
TGGCTTACTGCTTCTTTATATGAGTGAAGAAGATGCATTCTGGTTGATGGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAATGGAAGGATTATATTTGgtaaactttctttcttcagataaaaatttttggtaatctttattttttgactttcgaggaattttgatctcac--tctagaagatgagaagcttaacttgtc--
 || ||  |||||||||||||||| ||||||||||||||||||||  | ||||||||||| ||||||||||| ||  | ||||| |||||||| |||  ||| |   ||  |||||    || ||  |   | ||  || |   ||   ||||||       |||| |  | |    | ||  |||| |        |||    
CGGTTTGTTGCTTCTTTATATGAGCGAAGAAGATGCATTCTGGTTATTAGTTGCATTACTCAAAGGAGCTGTCCACTCCCCAATAGAAGGATTGTATCAGgtgagactttcttcttactctagaagataccgatatgctattagttgctactttcct----ctttggttacgcgagtttgataatgatagagccgctttgattg

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|161719620|gb|FC067048.1|FC067048
EST:     TTGCATTACTTAAAGGAGCTGTTCATGCTCCAATGGAAGGATTATATTTG                         GTGGGCTTGCCTCTGGTACAGCAATACCTTTTTCAGTTTGAAAACTTGGTG
genomic: TTGCATTACTTAAAGGAGCTGTTCATGCTCCAATGGAAGGATTATATTTGgtaaactttc ... tgtggagtagGTGGGCTTGCCTCTGGTACAGCAATACCTTTTTCAGTTTGAAAACTTGGTG
EST: gi|349829177|gb|FQ419687.1|FQ419687
EST:     TTGCATTACTTAAAGGAGCTGTTCATGCTCCAATGGAAGGATTATATTTG                         GTGGGCTTGCCTCTGGTACAGCAATACCTTTTTCAGTTTGAAAACTTGGTG
genomic: TTGCATTACTTAAAGGAGCTGTTCATGCTCCAATGGAAGGATTATATTTGgtaaactttc ... tgtggagtagGTGGGCTTGCCTCTGGTACAGCAATACCTTTTTCAGTTTGAAAACTTGGTG
EST: gi|351012823|gb|FQ430386.1|FQ430386
EST:     TTGCATTACTTAAAGGAGCTGTTCATACTCCAATGGAAGGATTATATTTG                         GTGGGCTTGCCTCTGGTACAGCAATACCTTTTTCAGTTTGAAAACTTGGTG
genomic: TTGCATTACTTAAAGGAGCTGTTCATGCTCCAATGGAAGGATTATATTTGgtaaactttc ... tgtggagtagGTGGGCTTGCCTCTGGTACAGCAATACCTTTTTCAGTTTGAAAACTTGGTG
EST: gi|349827061|gb|FQ421334.1|FQ421334
EST:     TTGCATTACTTAAAGGAGCTGTTCATGCTCCAATGGAAGGATTATATTTG                         GTGGGCTTGCCTCTGGTACAGCAATACCTTTTTCAGTTTGAAAACTTGGTG
genomic: TTGCATTACTTAAAGGAGCTGTTCATGCTCCAATGGAAGGATTATATTTGgtaaactttc ... tgtggagtagGTGGGCTTGCCTCTGGTACAGCAATACCTTTTTCAGTTTGAAAACTTGGTG
EST: gi|349829128|gb|FQ419660.1|FQ419660
EST:     TTGCATTACTTAAAGGAGCTGTTCATGCTCCAATGGAAGGATTATATTTG                         GTGGGCTTGCCTCTGGTACAGCAATACCTTTTTCAGTTTGAAAACTTGGTG
genomic: TTGCATTACTTAAAGGAGCTGTTCATGCTCCAATGGAAGGATTATATTTGgtaaactttc ... tgtggagtagGTGGGCTTGCCTCTGGTACAGCAATACCTTTTTCAGTTTGAAAACTTGGTG
EST: gi|351038918|gb|FQ457593.1|FQ457593
EST:     TTGCATTACTTAAAGGAGCTGTTCATGCTCCAATGGAAGGGTTATATTTG                         GTGGGCTTGCCTCTGGTACAGCAATACCTTTTTCAGTTTGAAAACTTGGTG
genomic: TTGCATTACTTAAAGGAGCTGTTCATGCTCCAATGGAAGGATTATATTTGgtaaactttc ... tgtggagtagGTGGGCTTGCCTCTGGTACAGCAATACCTTTTTCAGTTTGAAAACTTGGTG
EST: gi|110417184|gb|EC983219.1|EC983219
EST:     TTGCATTACTTAAAGGAGCTGTTCATGCTCCAATGGAAGGATTATATTTG                         GTGGGCTTGCCTCTGGTACAGCAATACCTTTTTCAGTTTGAAAACTTGGTG
genomic: TTGCATTACTTAAAGGAGCTGTTCATGCTCCAATGGAAGGATTATATTTGgtaaactttc ... tgtggagtagGTGGGCTTGCCTCTGGTACAGCAATACCTTTTTCAGTTTGAAAACTTGGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCTTACTGCTTCTTTATATGAGTGAAGAAGATGCATTCTGGTTGATGGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAATGGAAGGATTATATTTGgtaaactttctttcttcagataaaaatttttggtaatctttattttttgactttcgaggaattttgatctcactctagaagatgagaagcttaacttgtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaggaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctcactc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgagaa