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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTAGATTGTTAAAGCAGGAAGGGAAACCACCTGTGTTTCTGAAAGTTGATTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAACgtgtgtcatgttttcaatccctcttaaaatagtcaattaccgtttccattttttactgtctgaaaaacttgttggcttgcctttgacatgatattttggtttacag

Basic information

species Vitis vinifera
transcript Vv18s0001g01940.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g01940.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA16G27570.2 (Glycine max), 5'ss of exon 3
------AGTAGATTGTTAAAGCAGGAAGGGAAACCACCTGTGTTTCTGAAAGTTGATTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAACgtgtgtcatgttttcaatccctcttaaaatagtcaattaccgtttccattttttactgtctgaaaaacttgttggcttgcctttgacatgatattttggtttacag
         |||||||| ||||||| ||||||| | ||||| |||||||||||||||||||| ||||||||||||||||||||||| |  ||  |||||  | |  |  | |||   ||||  ||     | |||   |  |||| || ||   || | |  | ||   |   | | ||    |||                          
TGGTGGGACAGATTGTTGAAGCAGGGAGGGAAATCTCCTGTCTTTCTGAAAGTTGATTGGGATAAATGGGTTGATGAAGATGAGGAGCAAGATAATAAACgttagtgattatcaaaatttc--tctgaacttaaaggtttcattatcgattattttgtctcatttccatattcccttttcagctgcag------------------------

upper sequence: Vv18s0001g01940.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA16G27570.1 (Glycine max), 5'ss of exon 3
------AGTAGATTGTTAAAGCAGGAAGGGAAACCACCTGTGTTTCTGAAAGTTGATTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAACgtgtgtcatgttttcaatccctcttaaaatagtcaattaccgtttccattttttactgtctgaaaaacttgttggcttgcctttgacatgatattttggtttacag
         |||||||| ||||||| ||||||| | ||||| |||||||||||||||||||| ||||||||||||||||||||||| |  ||  |||||  | |  |  | |||   ||||  ||     | |||   |  |||| || ||   || | |  | ||   |   | | ||                                 
TGGTGGGACAGATTGTTGAAGCAGGGAGGGAAATCTCCTGTCTTTCTGAAAGTTGATTGGGATAAATGGGTTGATGAAGATGAGGAGCAAGATAATAAACgttagtgattatcaaaatttc--tctgaacttaaaggtttcattatcgattattttgtctcatttccatattcccttttcag------------------------------

upper sequence: Vv18s0001g01940.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA02G08440.1 (Glycine max), 5'ss of exon 3
------AGTAGATTGTTAAAGCAGGAAGGGAAACCACCTGTGTTTCTGAAAGTTGATTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAACgtgtgtcatgttttcaatccctcttaaaatagtcaattaccgtttccattttttactgtctgaaaaacttgttggcttgcctttgacatgatattttggtttacag
         |||||||| ||||||| ||||||| | || || |||||||||||||||||||| ||||||||||||||||||||||| |   |||||||   |||||||  || || || | |||  || ||||  |  |   || |  |||||||| |||  ||||| |    | | ||  |||  |                         
TGGTGGGACAGATTGTTGAAGCAGGGAGGGAAATCTCCAGTCTTTCTGAAAGTTGATTGGGATAAATGGGTTGATGAAGATGAGGAGC---AAGATAA---TAAACgttagtgattttctaaatttctgttaactt--taggtttcattttccattgttt--tgtctcatttccatattcccttttcag-----------------------

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|110429290|gb|EC995781.1|EC995781
EST:     TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAAC                         TAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
genomic: TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAACgtgtgtcatg ... tggtttacagTAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
EST: gi|351013532|gb|FQ425563.1|FQ425563
EST:     TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAAC                         TAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
genomic: TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAACgtgtgtcatg ... tggtttacagTAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
EST: gi|349825032|gb|FQ415579.1|FQ415579
EST:     TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAAC                         TAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
genomic: TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAACgtgtgtcatg ... tggtttacagTAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
EST: gi|351025087|gb|FQ433504.1|FQ433504
EST:     TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAAC                         TAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
genomic: TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAACgtgtgtcatg ... tggtttacagTAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
EST: gi|349812059|gb|FQ410856.1|FQ410856
EST:     TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAAC                         TAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
genomic: TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAACgtgtgtcatg ... tggtttacagTAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
EST: gi|110690904|gb|EE068398.1|EE068398
EST:     TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAAC                         TAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
genomic: TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAACgtgtgtcatg ... tggtttacagTAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
EST: gi|351049075|gb|FQ431619.1|FQ431619
EST:     TTGGGACAAATGGGTTGATGAAGACGAGGAACCGGAAGATAAAGATAAAC                         TAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
genomic: TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAACgtgtgtcatg ... tggtttacagTAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
EST: gi|27583236|gb|CB005931.1|CB005931
EST:     TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAAC                         TAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
genomic: TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAACgtgtgtcatg ... tggtttacagTAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
EST: gi|351014311|gb|FQ437313.1|FQ437313
EST:     TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAAC                         TAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
genomic: TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAACgtgtgtcatg ... tggtttacagTAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
EST: gi|110729569|gb|EE105653.1|EE105653
EST:     TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAAC                         TAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
genomic: TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAACgtgtgtcatg ... tggtttacagTAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
EST: gi|351049132|gb|FQ449854.1|FQ449854
EST:     TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAAC                         TAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
genomic: TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAACgtgtgtcatg ... tggtttacagTAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
EST: gi|32246080|gb|CD711899.1|CD711899
EST:     TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAAC                         TAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
genomic: TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAACgtgtgtcatg ... tggtttacagTAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
EST: gi|110426354|gb|EC992760.1|EC992760
EST:     TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAAC                         TAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
genomic: TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAACgtgtgtcatg ... tggtttacagTAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
EST: gi|351012422|gb|FQ427023.1|FQ427023
EST:     TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAAC                         TAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
genomic: TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAACgtgtgtcatg ... tggtttacagTAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
EST: gi|33403447|gb|CF209074.1|CF209074
EST:     TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAAC                         TAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
genomic: TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAACgtgtgtcatg ... tggtttacagTAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
EST: gi|351046326|gb|FQ448631.1|FQ448631
EST:     TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAAC                         TAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
genomic: TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAACgtgtgtcatg ... tggtttacagTAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
EST: gi|349825031|gb|FQ415578.1|FQ415578
EST:     TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAAC                         TAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT
genomic: TTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAACgtgtgtcatg ... tggtttacagTAGGAGCTGATATGGACTTTGGCGACTTCGATTTTTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTAGATTGTTAAAGCAGGAAGGGAAACCACCTGTGTTTCTGAAAGTTGATTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAACgtgtgtcatgttttcaatccctcttaaaatagtcaattaccgtttccattttttactgtctgaaaaacttgttggcttgcctttgacatgatattttggtttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA