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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATCAAGATGGAACAACTGATATAACTCGAACTGTTCATTTTGGAAAACCTTCATCACATGAGAAAGCATGCTATACTGCGgtatgtggctcttgttgctttcttttcaggatatcttgtatttatttggcatttgaacacttcttaaccttgttcattcaaaacagaatatggttgtttt...

Basic information

species Vitis vinifera
transcript Vv04s0023g01300.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g01300.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA11G06900.1 (Glycine max), 5'ss of exon 11
TATCAAGATGGAACAACTGATATAACTCGAACTGTTCATTTTGGAAAACCTTCATCACATGAGAAAGCATGCTATACTGCGgtatgtggctcttgttgctttcttttcaggatatcttgtatttatttggcatttgaacacttcttaaccttgttcattcaaaacagaatatggttgtttt
|||| |||||||||||| ||||| || ||||| ||||||||||| ||||||||  | || || ||||| || ||||| || ||||||| || |  || |||| ||| || | ||  | || |  |      | |   |  | | |  || | |||   |        |||||         
TATCTAGATGGAACAACAGATATTACACGAACAGTTCATTTTGGTAAACCTTCGACTCACGAAAAAGCGTGTTATACAGCAgtatgtgcctttcttttctttttttacaagttaattagtttcaaaactatactatgaatcatatgcacatggtttggtttgctggaaatataaagaaagg

upper sequence: Vv04s0023g01300.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA01G38410.1 (Glycine max), 5'ss of exon 11
TATCAAGATGGAACAACTGATATAACTCGAACTGTTCATTTTGGAAAACCTTCATCACATGAGAAAGCATGCTATACTGCGgtatgtggctcttgttgctttctttt-caggatatcttgtatttatttggcatttgaacacttcttaaccttgttcattcaaaacagaatatggttgtttt
|||| |||||||||||| ||||| || ||||| ||||||||||| ||||||||  | || || ||||| || ||||| || ||||||| || |  ||||| | |||| || | ||  | || |  |      | |   |  | | |  || | |||   |        ||| |         
TATCTAGATGGAACAACAGATATTACACGAACAGTTCATTTTGGTAAACCTTCGACTCACGAAAAAGCGTGTTATACAGCAgtatgtgcctttctttgctcttttttacaagttaattagtttcaaaactatactatgaatcatatacacatggtttggtttgctggaaatgtaaagaaag-

upper sequence: Vv04s0023g01300.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: AT4G36760.1 (Arabidopsis thaliana), 5'ss of exon 10
TATCAAGATGGAACAACTGATATAACTCGAACTGTTCATTTTGGAAAACCTTCATCACATGAGAAAGCATGCTATACTGCGgtatgtggctcttgttgctttcttttcaggatatc----ttgtatttatttggcatttgaacacttcttaaccttgttcattcaaaacagaatatggttgtttt
||||  |||||||||||||||||||| ||||| ||||| ||||||||||||||| | ||||| || | |||||||||||||||||||   | ||| || |  | |||  | ||||     |  ||||||||||| ||  | | | ||  | |   | |   |||||        ||  ||     
TATCTCGATGGAACAACTGATATAACCCGAACGGTTCACTTTGGAAAACCTTCAGCTCATGAAAAGGAATGCTATACTGCGgtatgtacttattgatgataacctttt-gaatattacattcttatttatttggaataagcatatttgctga---tatatgttcaatgtgccgcatccttag---

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|110726497|gb|EE102329.1|EE102329
EST:     CTGTTCATTTTGGAAAACCTTCATCACATGAGAAAGCATGCTATACTGCG                         GTTCTCAAGGGTCATATCAGTCTGGGTAATGCTCGATTTCCTAGTGGAACC
genomic: CTGTTCATTTTGGAAAACCTTCATCACATGAGAAAGCATGCTATACTGCGgtatgtggct ... tttcatgcagGTTCTCAAGGGTCATATCAGTCTGGGTAATGCTCGATTTCCTAGTGGAACC
EST: gi|110694334|gb|EE071348.1|EE071348
EST:     CTGTTCATTTTGGAAAACCTTCGTCACATGAGAAAGCATGCTATACTGCG                         GTTCTCAAGGGTCATATCGGTTTGGGTAATGCTCGATTTCCTAGTGGAACC
genomic: CTGTTCATTTTGGAAAACCTTCATCACATGAGAAAGCATGCTATACTGCGgtatgtggct ... tttcatgcagGTTCTCAAGGGTCATATCAGTCTGGGTAATGCTCGATTTCCTAGTGGAACC
EST: gi|110700420|gb|EE078440.1|EE078440
EST:     CTGTTCATTTTGGAAAACCTTCATCACATGAGAAAGCA-GCTATACTGCG                         GTTCTCAAGGGTCATATCAGTCTGGGTAATGCTCGATTTCCTAGTGGAACC
genomic: CTGTTCATTTTGGAAAACCTTCATCACATGAGAAAGCATGCTATACTGCGgtatgtggct ... tttcatgcagGTTCTCAAGGGTCATATCAGTCTGGGTAATGCTCGATTTCCTAGTGGAACC
EST: gi|30299030|gb|CB975824.1|CB975824
EST:     CTGTTCATTTTGGAAAACCTTCGTCACATGAGAAAGCATGCTATACTGCG                         GTTCTCAAGGGTCATATCGGTTTGGGTAATGCTCGATTTCCTAGTGGAACC
genomic: CTGTTCATTTTGGAAAACCTTCATCACATGAGAAAGCATGCTATACTGCGgtatgtggct ... tttcatgcagGTTCTCAAGGGTCATATCAGTCTGGGTAATGCTCGATTTCCTAGTGGAACC
EST: gi|110712732|gb|EE088034.1|EE088034
EST:     CTGTTCATTTTGGAAAACCTTCATCACATGAGAAAGCATGCTATACTGCG                         GTTCTCAAGGGTCATATCAGTCTGGGTAATGCTCGAATTCCTAGTGGAACC
genomic: CTGTTCATTTTGGAAAACCTTCATCACATGAGAAAGCATGCTATACTGCGgtatgtggct ... tttcatgcagGTTCTCAAGGGTCATATCAGTCTGGGTAATGCTCGATTTCCTAGTGGAACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATCAAGATGGAACAACTGATATAACTCGAACTGTTCATTTTGGAAAACCTTCATCACATGAGAAAGCATGCTATACTGCGgtatgtggctcttgttgctttcttttcaggatatcttgtatttatttggcatttgaacacttcttaaccttgttcattcaaaacagaatatggttgtttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caggata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacagaa