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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACGgtgcgttactgattctaattatgtcattagggcatctataatatttgagcttgtggattcttatgattccatatctattcctattcagatcttaatatag...

Basic information

species Vitis vinifera
transcript Vv14s0171g00490.t01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GRMZM2G130230_T03 (Zea mays), 5'ss of exon 13
GTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACGgtgcgt--tactgattctaattatgtcattagggcat-ctataatatttgag----cttgtggattcttatgattccatatctattcctat---tcagatcttaatatag------------------------------------------
|  | | ||| || |||||||| ||||| |||||||||||||| | ||| ||||| |||||||| || || ||  ||  | ||  |||  | || |   | |   | |  | | ||   | |     | ||    |||||  ||  |  ||        |||   |  | | | ||| |                                            
GCAAGAAGCAAGGAAGAAATGAGTTTGTTATACGCCTCCAACCATCAGAAGCCATGTACATGAAACTAACTgtaagtcctgctagttc--actagggtctaatttcttgttttgatgagtaaaacgtcatgacatttctttggaaactgtacacgccgatatatatggggtttgaatgtgtagcagaatctctaattaatctttgaaaattaaattgatgcag

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA19G24250.1 (Glycine max), 5'ss of exon 13
GTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACGgtgcgttactgattctaattatgtcattagggcatctataatatttgagcttgtggattcttatgattccatatctattcctattcagatctta-atatag----
|| ||| ||||||||||||||| ||||| || ||||| ||||||||||| || || |||||||||||||||||| |  | | ||||||||  |   || |    || ||| ||       |||||     || || |   | || |  |||   || |  | ||| ||  |     
GTAAAAAGCAGGGGAGAAATGAGTTTGTTATCCGCCTACAACCTTTAGAAGCTATGTACATGAAGCTTACGgtgaggcaatcattctaat-gtcctataataagatttattatgcc---acttgtttgacctgattacatctta-cagttctcttttatctgttacattcatttat

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA19G22690.1 (Glycine max), 5'ss of exon 13
GTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACGgtgcgttactgattctaattatgtcattagggcatctat-------aatatttgagcttgtggattcttatgattccatatctattcctattcagatcttaatatag
|||||| ||||||||||||||| ||||| |||||||| ||||||| ||| || || |||||||||||||| ||  ||   | ||||| || ||    ||| |  | || |         | ||||| ||  |    |||     || ||||| |||    ||| |||    | |||  
GTCAAAAGCAGGGGAGAAATGAGTTTGTTATACGCCTGCAACCTTCAGAAGCTATGTACATGAAGCTTACAgtatgtctatcattctgataatacttttatgagaactgttctgccatttgtttgacctgattacctctggaagtttcatatgtatc---attgagaca--agtat--

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA16G06850.3 (Glycine max), 5'ss of exon 13
GTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACGgtgcgttactgattctaattatgtcattagggcatctataatatttgagcttgtggattcttatgattccata----tctattcctattcagatcttaatatag
|| ||| ||||||||||||||| | ||| || ||||| || |||| ||| || ||||||||||||||||||||| |  | | ||||||||  |  ||| | |  ||  || ||       |||||     || || |   | ||    ||| ||     ||  || || || || 
GTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAGCTATTTACATGAAGCTTACGgtgaggcaatcattctaat-gttccatcatgagattgatcatgcc---acttgtttgacctgattacatcctaaagttctcttttatctcttattttcatttat

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|352763752|gb|FQ473455.1|FQ473455
EST:     CGCCTCCAACCCTTATGAGGCCATTTACATGAAGCTTACG                         GTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
genomic: CGCCTCCAACCTTTA-GAGGCCATTTACATGAAGCTTACGgtgcgttact ... tctcatgcagGTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
EST: gi|110716825|gb|EE092144.1|EE092144
EST:     AATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACG                         GTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
genomic: AATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACGgtgcgttact ... tctcatgcagGTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
EST: gi|351015046|gb|FQ444335.1|FQ444335
EST:     AATTTGTAATACGCCTCCAACCTTCAGAGGCCATTTACATGAAGCTTACG                         GTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
genomic: AATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACGgtgcgttact ... tctcatgcagGTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
EST: gi|352773448|gb|FQ472230.1|FQ472230
EST:     AATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACG                         GTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
genomic: AATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACGgtgcgttact ... tctcatgcagGTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
EST: gi|110365367|gb|EC928242.1|EC928242
EST:     AATTTGTAATACGCCTCCAACCTTCAGAGGCCATTTACATGAAGCTTACG                         GTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
genomic: AATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACGgtgcgttact ... tctcatgcagGTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
EST: gi|110715492|gb|EE093605.1|EE093605
EST:     AATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACG                         GTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
genomic: AATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACGgtgcgttact ... tctcatgcagGTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
EST: gi|33405782|gb|CF211409.1|CF211409
EST:     AATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACG                         GTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
genomic: AATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACGgtgcgttact ... tctcatgcagGTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
EST: gi|110361886|gb|EC925389.1|EC925389
EST:     AATTTGTAATACGCCTCCAACCTTCAGAGGCCATTTACATGAAGCTTACG                         GTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
genomic: AATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACGgtgcgttact ... tctcatgcagGTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
EST: gi|110696408|gb|EE072500.1|EE072500
EST:     AATTTGTAATACGCCTCCAACCTTCAGAGGCCATTTACATGAAGCTTACG                         GTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
genomic: AATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACGgtgcgttact ... tctcatgcagGTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
EST: gi|110390234|gb|EC955134.1|EC955134
EST:     AATTTGTAATACGCCTCCAACCTTCAGAGGCCATTTACATGAAGCTTACG                         GTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
genomic: AATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACGgtgcgttact ... tctcatgcagGTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
EST: gi|352763934|gb|FQ465384.1|FQ465384
EST:     AATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACG                         GTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
genomic: AATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACGgtgcgttact ... tctcatgcagGTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
EST: gi|352777620|gb|FQ466673.1|FQ466673
EST:     AATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACTTGAAGCTTACG                         GTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
genomic: AATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACGgtgcgttact ... tctcatgcagGTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
EST: gi|352781379|gb|FQ468223.1|FQ468223
EST:     ATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTTACATGAAGCTTACG                         GTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
genomic: ATTTGTAATACGCCTCCAACCTTTAGAGGCCA-TTTACATGAAGCTTACGgtgcgttact ... tctcatgcagGTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
EST: gi|56409520|gb|CX017772.1|CX017772
EST:     AATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACG                         GTCAAGCAGCCTGGGCTTGAAATGTCAACT
genomic: AATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACGgtgcgttact ... tctcatgcagGTCAAGCAGCCTGGGCTTGAAATGTCAACT
EST: gi|352781474|gb|FQ468318.1|FQ468318
EST:     AATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACG                         GTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
genomic: AATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACGgtgcgttact ... tctcatgcagGTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
EST: gi|110416304|gb|EC982275.1|EC982275
EST:     AATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACG                         GTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
genomic: AATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACGgtgcgttact ... tctcatgcagGTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
EST: gi|110373098|gb|EC937308.1|EC937308
EST:     AATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACG                         GTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG
genomic: AATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACGgtgcgttact ... tctcatgcagGTCAAGCAGCCTGGGCTTGAAATGTCAACTGTACAAAGCGAACTAGACTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACGgtgcgttactgattctaattatgtcattagggcatctataatatttgagcttgtggattcttatgattccatatctattcctattcagatcttaatatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC