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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTGTTTTCTACTCTGGGAAGGCTCCTAAAGGCATCCGAACAAGCTGGATCATGAACGAGTACCGCTTGCCCCAACAGGAAACCGAGCGCAGCCAAAAGgtaaattatatcaggctaatcatatctttataagggtttctcccccacctgcagatgatgatgatcaggacagtagcagtactgtacatcatctttgatt...

Basic information

species Vitis vinifera
transcript Vv12s0035g02020.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g02020.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G134687_T01 (Zea mays), 5'ss of exon 2
TCTTGTTTTCTACTCTGGGAAGGCTCCTAAAGGCATCCGAACAAGCTGGATCATGAACGAGTACCGCTTGCCCCAACAGGAAACCGAGCGCAGCCAAAAGgtaaattatatcaggctaatcata-tctttataagggtttct---cccccacctgcag-atgatgatgatcaggacagtagcagtactgtacatcatctttgatt----
         |||||| || ||||| ||||| ||| |||| |  |||||||||||||||||||||||| | || | ||     |||||   |   |      |     |  | |||  | |  || | |   |  ||  |        |   ||||     |  |      ||   ||  |  | |  | |   ||    ||| |     
---------CTACTCCGGCAAGGCGCCTAAGGGCGTCCGCAGCAGCTGGATCATGAACGAGTACCGCCTCCCGCCACCACCTACCGACGCCGATCCTTTCATTCCCAAGgtgaggtcagttttaatttgcgtgtggactgtggagttcttgcctgtttcgtcgtcgcttccaattcaaaaaaaatgttttttttcgaaattggtgtgtg

upper sequence: Vv12s0035g02020.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA07G40140.1 (Glycine max), 5'ss of exon 2
TCTTGTTTTCTACTCTGGGAAGGCTCCTAAAGGCATCCGAACAAGCTGGATCATGAACGAGTACCGCTTGCCCCAACAGGAAACCGAGCGCAGCCAAAAGgta---aattatatcaggctaatcatatctttataagggtttctcccccacctgcagatgatgatgatcaggacagtagcagtactgtacatcatctttgatt
 || |||||||| |||||||| |||||||||||||| ||||| || ||||| ||||||||||| |||||||| ||||| ||||| || ||    |||||||||   |  |||||   |     ||||| | | |    | |        | | |     | |        |  |     |  |  | |  |||     |||  
CCTAGTTTTCTATTCTGGGAAAGCTCCTAAAGGCATTCGAACCAGTTGGATTATGAACGAGTATCGCTTGCCGCAACATGAAACTGAACGATATCAAAAGgtacttaggtatatatagtagcacatatgtatgtctctgatatataataatccgtt--cggtttcttctcgttcttcttccatgatatctatctatcatgaa-

upper sequence: Vv12s0035g02020.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA17G00650.1 (Glycine max), 5'ss of exon 2
TCTTGTTTTCTACTCTGGGAAGGCTCCTAAAGGCATCCGAACAAGCTGGATCATGAACGAGTACCGCTTGCCCCAACAGGAAACCGAGCGCAGCCAAAAGgtaaattatatcaggctaatcatatctttataagggtttctcccccacctgcagatgatgatgatcaggacagtagcagtactgtacatcatctttgatt----
 || |||||||| |||||||| |||||||||||||| ||||| || ||||| ||||||||||| |||||||| ||||| ||||| || ||    |||||||||   ||  |    | |  |||| |          |  | |       ||    | ||  | |      |     |       |   || ||  ||||     
CCTAGTTTTCTATTCTGGGAAAGCTCCTAAAGGCATACGAACCAGTTGGATTATGAACGAGTATCGCTTGCCGCAACATGAAACTGAACGATATCAAAAGgta--ctagctagtacca--cataccacataccacataccacatatgtatgtgctttatatttaattaagcttcttctccttcttctttcttccatgataaatc

upper sequence: Vv12s0035g02020.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT2G02450.1 (Arabidopsis thaliana), 5'ss of exon 2
TCTTGTTTTCTACTCTGGGAAGGCTCCTAAAGGCATCCGAACAAGCTGGATCATGAACGAGTACCGCTTGCCCCAACAGGAAACCGAGCGCAGCCAAAAGgtaaattatatcaggctaatcatatctttataagggtttctcccccacctgcagatgatgatgatcaggacagtag-----cagtactgtacatcatctttgatt
 || |||||||||||||| || || ||||||||||  || || || ||||||||||||||||| ||  | || || || |||||||||     ||||||||||   || ||    |||    | | | ||||     |||   |  || |  | || |   |    |||     ||      |  | || |  | |||  |    
CCTAGTTTTCTACTCTGGTAAAGCCCCTAAAGGCACTCGTACTAGTTGGATCATGAACGAGTATCGTCTTCCGCACCATGAAACCGAGAAGTACCAAAAGgta---taaattctactataactctatatatatcctattcatacatacatagatataaccctagctaggtggtgaggcctttaaaattgaaattaatccctag--

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|71857846|gb|DT006901.1|DT006901
EST:     TCATGAACGAGTACCGCTTGCCCCAACAGGAAACCGAGCGCAGCCAAAAG                         GCTGAAATATCGCTTTGTCGCGTGTATA
genomic: TCATGAACGAGTACCGCTTGCCCCAACAGGAAACCGAGCGCAGCCAAAAGgtaaattata ... ttcctctcagGCTGAAATATCGCTTTGTCGCGTGTATA
EST: gi|110386083|gb|EC950656.1|EC950656
EST:     TCATGAACGAGTACCGCTTGCCCCAACAGGAAACCGAGCGCAGCCAAAAG                         GCTGAAATATCGCTTTGTCGCGTGTATAAGAGAGCTGGGGTTGAAGACCAC
genomic: TCATGAACGAGTACCGCTTGCCCCAACAGGAAACCGAGCGCAGCCAAAAGgtaaattata ... ttcctctcagGCTGAAATATCGCTTTGTCGCGTGTATAAGAGAGCTGGGGTTGAAGACCAC
EST: gi|349823684|gb|FQ415094.1|FQ415094
EST:     TCATGAACGAGTACCGCTTGCCCCAACAGGAAACCGAGCGCAGCCAAAAG                         GCTGAAATATCGCTTTGTCGCGTGTATAAGAGAGCTGGGGTTGAAGACCAC
genomic: TCATGAACGAGTACCGCTTGCCCCAACAGGAAACCGAGCGCAGCCAAAAGgtaaattata ... ttcctctcagGCTGAAATATCGCTTTGTCGCGTGTATAAGAGAGCTGGGGTTGAAGACCAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTGTTTTCTACTCTGGGAAGGCTCCTAAAGGCATCCGAACAAGCTGGATCATGAACGAGTACCGCTTGCCCCAACAGGAAACCGAGCGCAGCCAAAAGgtaaattatatcaggctaatcatatctttataagggtttctcccccacctgcagatgatgatgatcaggacagtagcagtactgtacatcatctttgatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caggaca