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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCCAGACAGAACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTTTTGGACAGgtaaaatgtgtgaatttcacataaagaataaaataagataaaataaaacaaaaaaaaggacttacaagtccatgttggtgtgaaattcattggtttttccttgttgcag

Basic information

species Vitis vinifera
transcript Vv12s0028g03130.t01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: LOC_Os09g15750.1 (Oryza sativa), 5'ss of exon 13
GCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCCAGACAGAACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTTTTGGACAGgtaaaatgtgtgaatttcacataaagaataaaataagataaaataaaacaaaaaaaaggacttacaagtccatgttggtgtgaaattcattggtttttccttgttgcag
| |||||||||| |    | |  |  | ||| |||| ||||| |||||||| ||||| || || |||||||||||||| || |||||||| ||||| ||||| |  | || ||||||||   || |  |                |    ||  ||||  || | | || | |||||  |                             
GATTGATGGCCGAGGGGCTACAAGCTCCAGTCTTGATTCTGCAAGACAGAATCTGGCGGCAACATTTGTCAATGCATTCGTGAATGCTGGATTTGGCCAGgttagttatgcgaatttcatcaaaggttt--------------ccagggcaagcaaagttctca-atgttcttgttgcag-----------------------------

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: LOC_Os06g48640.3 (Oryza sativa), 5'ss of exon 13
GCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCCAGACAGAACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTTTTGGACAGgtaaaatgtgtgaatttcacataaagaataaaataagataaaataaaacaaaaaaaaggacttacaagtccatgttggtgtgaaattcattggtttttccttgttgcag
| |||||||||| |    | |  |  | ||| |||| || || |||||||| ||||| || || |||||||||||||| || |||||||| ||||| ||||| |  | || ||||||||   ||||  |              |  |    ||  ||||   |  |  | | |||||  |                             
GATTGATGGCCGAGGGGCTACAAGCTCCAGTCTTGATTCCGCAAGACAGAATCTGGCGGCAACATTTGTCAATGCATTCGTGAATGCTGGATTTGGCCAGgttagttatgcgaatttcat-caaaggtt--------------tccagggcaagcaaggttctcaacattcttgttgcag-----------------------------

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA12G13410.1 (Glycine max), 5'ss of exon 13
GCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCCAGACAGAACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTTTTGGACAGgtaaaatgtgtgaatttcacataaagaataaaataagataaaataaaacaaaaaaaaggacttacaagtccat--gttggtgtgaaattcattggtttttccttgttgcag-----
||||||||||||||||||||||||||||||||||||||| || ||||||||||| || || |||||||| |||||||||||||||||||| ||||| |||||| |||||   | ||  | || | ||||    ||   |    | |         || ||  ||    || ||   |   | |   | |  |    ||  | || |    |     
GCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCTTTGGTCAGgtacaatgtt--atttctagattatgaatgttgtatt-tgttgtgattttgggttaatgatctattcttctattcctcaatcttctacttctca-cttcccattatcattgtgcag

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 13
GCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCCAGACAGAACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTTTTGGACAGgtaaaatgtgtgaatttcacataaagaataaaataagataaaataaaacaaaaaaaaggacttacaagtccatgttggtgtgaaattca-ttggtttttccttgttgcag
|||||||||||||||||||||||||||||||||||| || || ||||||||||| || || |||||||| |||||||||||||||||||| ||||| |||||| |||||         |    |    |   ||  | |   ||        ||  |   ||| | | |||    |  | |     ||| ||    ||  | |   ||||
GCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGATTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCTTTGGTCAGgtacaatgttatttaaagattctatatgttgtatttgttgtgattttgggttaatgatctctt-ctattcctcaatcttctacttctcacttcccattatcattgcgcag

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: AT2G20580.1 (Arabidopsis thaliana), 5'ss of exon 11
GCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCCAGACAGAACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTTTTGGACAGgtaaaatgtgtgaatttcacataaagaataaaataagataaaataaaacaaaaaaaaggacttacaagtccatgttggtgtgaaattcattggtttttccttgttgcag
 || || ||| |||||||  | |||||||| || || ||||| ||||||||  |||| ||||| |||||||||||||| ||||||||||||||||| ||||||   | ||   |||  | |||||  |  |  ||    || |     |     ||   | || |   ||   |                                   
ACTCGACGGCAGGGCTAGCTCCGGTGCAAGCGTGGATTCTGCTAGACAGAATTTGGCTGCTACCTTTGTCAATGCATTCGTAAATGCTGGTTTTGGTCAGgtatggt-tgcagattata-ataaaata-gatctagtggaagacgtgtcctcttaatatatttgcttatcgcag-----------------------------------

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: AT4G28470.1 (Arabidopsis thaliana), 5'ss of exon 11
GCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCCAGACAGAACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTTTTGGACAGgtaaaatgtgtgaatttcacataaagaataaaataagataaaataaaacaaaaaaaaggacttacaagtccatgttggtgtgaaattcattggtttttccttgttgcag
|||||||||  |||||||  ||||| ||||||| ||||| || || || || ||  | || |||||||| |||||||||||||||||||| || || ||||||  ||    | || |                     |||  |  |||| || ||     ||  |||      ||         |||||   | ||||||| ||||||
GCTTGATGGTAGGGCTAGCTCTGGTCCAAGTGTGGACTCAGCTAGGCAAAATCTATCTGCGACTTTTGTGAATGCATTTGTAAATGCTGGATTCGGCCAGgtatgattacaggatct---------------------taatgtgcaacataagaagaactttggaagctgccctt---------ttcat--atatttccttattgcag

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: PP1S414_22V6.1 (Physcomitrella patens), 5'ss of exon 13
GCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCCAGACAGAACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTTTTGGACAGgtaaaatgtgtgaatttcacataaagaataaaataagataaaataaaacaaaaaaaaggacttacaagtccatgttggtgtgaaattcattggtttttcc--ttgttgcag--------------------------------------------------------
  | ||||| || || ||||| || || || || ||||||||  | || |||||||| || ||||||||||||| |||||| |||||||| |||||   ||||   ||| ||||| |    |      |    |  | ||   |      ||  |  |    | ||   |    ||  | | ||    |     | || |  ||  ||||                                                         
AGTGGATGGTCGTGCCAGTGCAGGAGCTAGCGTAGACTCTGCTCGTCAAAACCTGGCTGCCACTTTTGTCAATGGATTTGTGAATGCTGGCTTTGGCGTGgtatgctgt-tgaatattttctt-----tgtcttgtgctacttttcgtgcaagcatggtttatgcagtactgcttttatttaaagactaccaagtgttacacttcatgcatggacatcgctgtcatgtacgttttttgtgaattaatcttcttatgtcgtgatgtag

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: EFJ14427 (Selaginella moellendorffii), 5'ss of exon 12
GCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCCAGACAGAACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTTTTGGACAGgtaaa-atgtgtgaatttcacataaagaataaaataagataaaataaaacaaaaaaaaggacttacaagtccatgttggtgtgaaattcattggtttttccttgttgcag
  |||||||  | || ||||| || || |||||||| || || ||||| ||||| ||||| ||||| |||||||| || || || |||||||||||||||||  | |||     ||||     |     |  | ||| || |  |    | |                                                          
AATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCTAGACAAAACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTTTTGGACAGgtggacatgacctgatttt---caggatctgcactaaaattatttctttccag---------------------------------------------------------

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: EFJ26022 (Selaginella moellendorffii), 5'ss of exon 12
GCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCCAGACAGAACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTTTTGGACAGgtaaa-atgtgtgaatttcacataaagaataaaataagataaaataaaacaaaaaaaaggacttacaagtccatgttggtgtgaaattcattggtttttccttgttgcag
  |||||||  | || ||||| || || |||||||| || || ||||| ||||| ||||| ||||| |||||||| || || || ||||||||||||||||| || |||     ||||     |     |  | ||| || |  |    | |                                                          
AATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCTAGACAAAACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTTTTGGACAGgtgaacatgaactgatttt---caggatgtgcactaaaattatttctttccag---------------------------------------------------------

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|30304134|gb|CB980928.1|CB980928
EST:     ACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTTTTGGACAG                         GACAAGCTAATGACAGTGGCTTCAGAAGCTTCCAGTGGTGGTTCTTCAGGA
genomic: ACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTTTTGGACAGgtaaaatgtg ... cttgttgcagGACAAGCTAATGACAGTGGCTTCAGAAGCTTCCAGTGGTGGTTCTTCAGGA
EST: gi|71864029|gb|DT013084.1|DT013084
EST:     ACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTTTTGGACAG                         GACAAGCTAATGACAGTGGCTTCAGAAGCTTCCAGTGGTGGTTCTTCAGGA
genomic: ACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTTTTGGACAGgtaaaatgtg ... cttgttgcagGACAAGCTAATGACAGTGGCTTCAGAAGCTTCCAGTGGTGGTTCTTCAGGA
EST: gi|30304206|gb|CB981000.1|CB981000
EST:     ACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTTTTGGACAG                         GACAAGCTAATGACAGTGGCTTCAGAAGCTTCCAGTGGTGGTTCTTCAGGA
genomic: ACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTTTTGGACAGgtaaaatgtg ... cttgttgcagGACAAGCTAATGACAGTGGCTTCAGAAGCTTCCAGTGGTGGTTCTTCAGGA
EST: gi|71860625|gb|DT009680.1|DT009680
EST:     ACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTTTTGGACAG                         GACAAGCTAATGACAGTGGCTTCAGAAGCTTCCAGTGGTGGTTCTTCAGGA
genomic: ACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTTTTGGACAGgtaaaatgtg ... cttgttgcagGACAAGCTAATGACAGTGGCTTCAGAAGCTTCCAGTGGTGGTTCTTCAGGA
EST: gi|71863903|gb|DT012958.1|DT012958
EST:     ACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTTTTGGACAG                         GACAAGCTAATGACAGTGGCTTCAGAAGCTTCCAGTGGTGGTTCTTCAGGA
genomic: ACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTTTTGGACAGgtaaaatgtg ... cttgttgcagGACAAGCTAATGACAGTGGCTTCAGAAGCTTCCAGTGGTGGTTCTTCAGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCCAGACAGAACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTTTTGGACAGgtaaaatgtgtgaatttcacataaagaataaaataagataaaataaaacaaaaaaaaggacttacaagtccatgttggtgtgaaattcattggtttttccttgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG