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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTGACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAAgtacgaactctgcagaaaatttttaagctatgttacaattgtatttcacataattttggaagtgaattgaaacttttcaattcattgcag

Basic information

species Vitis vinifera
transcript Vv11s0016g03200.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g03200.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os01g09300.2 (Oryza sativa), 5'ss of exon 6
TCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTGACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAAgt--acgaactctgcagaaaatttttaagctatgttacaattgtatttcacataattttggaagtgaattgaaacttttcaattca---ttgcag
| || | ||  ||||     ||||| | | |||||||||||| |||||||| |||||||| || || ||  ||||||| ||||||||  | || || |||||  | | |   || |   |    |||    ||||| || |  | ||   | | | ||   |    ||| | |  ||| ||  | |    |||||
TAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTGATTATGGCCTAATCACTCTACTGGCAACCGATGATGTAGTTGGTCTCCAAgtaaatgcatcttgaatcgacaccttatcaaatgtttcattgatttt---cgtgacttctaata-aaatggtagttttccatctgaattatgcag

upper sequence: Vv11s0016g03200.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA16G08470.1 (Glycine max), 5'ss of exon 6
TCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTGACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAAgtacgaactctgcagaaaatttttaagctatgttacaattgtatttcacataattttg-gaagtgaattgaaacttttcaattc----attgcag
|||| | || ||||||||||| ||| |||||||||| || || ||| ||||||||||  | ||||| || || |||||||||||||||   || ||||||||| |||     || | |       |   || ||  |||   ||| || ||| ||||| | |   |||| |||   || |  ||    |||||||
TCAAGTTTCGGATCCCTTGAAAGGATTATATGGAGCTGGAGCTCATACTGACTATGGTTTAATTACACTGTTAGCAACAGATGATGTCTCGGGTCTTCAAgtaagaaaggaacacacacacacacacacatattttaat---attacaaatatttttgtgcaaataattaaaaacattgatgtcttctattgcag

upper sequence: Vv11s0016g03200.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA01G01170.2 (Glycine max), 5'ss of exon 6
TCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTGACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAAgtacgaactctgcaga-aaatttttaagctatgt-tacaattgtattt-cacataattttggaagtgaattgaaacttttcaattcat-tgcag-------------------------------------------------------------------------------
|||| | || ||||||| ||| ||| |||||||||| || || ||| | |||| |||  | ||||| || || |||||||||||||||| ||| ||||||||| |||  || |  | | || | ||    || | || |  | ||| |  | |||  | |  |  |  ||  | |  | |  ||  || |  |                                                                                
TCAAGTTTCAGATCCCTCGAAAGGATTATATGGAGCTGGAGCTCATACCGACTTTGGTTTAATTACACTGTTAGCAACAGATGATGTCCCAGGTCTTCAAgtaagaaagctacctatatatatatatataatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatttttttttttttttttttttcaatattacaaatacttttgtgcaactaattaagaacattaatgtcttctattgcag

upper sequence: Vv11s0016g03200.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: PP1S180_67V6.1 (Physcomitrella patens), 5'ss of exon 6
TCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTGACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAAgtacgaactct-----gcagaaaatttttaagctatgt-tacaattgtatttcac--ataattttggaagtgaattgaaacttttcaattcattgcag--
| | |  ||  ||         |||||||||||| | ||||| |||||||| |||||||||||||| ||  | || || || || || |  || || || || | |  | |     |   | | | |||    | |   || || |    | ||    |  | | ||   | ||| ||      |||   || ||     
TGAGAAATCAAATGTTGAACTTGGAATATATGGAACTGGTGCTCATTCTGATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCAGgtcctattttttaaccgtcaatattgttttgtatgtacgtataagttggctgcatctgtgttatcggtcctcaatggatgtacgtcatgacaatgtgtag

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|45771236|gb|CN007088.1|CN007088
EST:     AACAGATGA-GTCCTA-GAC-TCAA                         ATATGCAA-GATAAGGACGCTAGACTTCAGACATGGGAATATGTAGCGCCA
genomic: AACAGATGATGTCCTAGGACTTCAAgtacgaactc ... ttcattgcagATATGCAAGGATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCA
EST: gi|110428851|gb|EC995334.1|EC995334
EST:     ACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAA                         ATATGCAAGGATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCA
genomic: ACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAAgtacgaactc ... ttcattgcagATATGCAAGGATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCA
EST: gi|110390246|gb|EC955146.1|EC955146
EST:     ACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAA                         ATATGCAAGGATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCA
genomic: ACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAAgtacgaactc ... ttcattgcagATATGCAAGGATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCA
EST: gi|71881554|gb|DT030609.1|DT030609
EST:     ACTATGGTCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAA                         ATATGCAAGGATAAGGACGCTAGACC
genomic: ACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAAgtacgaactc ... ttcattgcagATATGCAAGGATAAGGACGCTAGACC
EST: gi|30253347|gb|CB970898.1|CB970898
EST:     ACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAA                         ATATGCAAGGATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCA
genomic: ACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAAgtacgaactc ... ttcattgcagATATGCAAGGATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCA
EST: gi|71887181|gb|DT036236.1|DT036236
EST:     ACTATGGTCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAA                         ATATGCAAGGATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCA
genomic: ACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAAgtacgaactc ... ttcattgcagATATGCAAGGATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCA
EST: gi|77589174|gb|DV223847.1|DV223847
EST:     ACTATGGTCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAA                         ATATGCAAGGATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCA
genomic: ACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAAgtacgaactc ... ttcattgcagATATGCAAGGATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCA
EST: gi|83275983|gb|DV939991.1|DV939991
EST:     CAACAGATGATGTCCTAGGACTTCAA                         ATATGCAAGGATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCA
genomic: CAACAGATGATGTCCTAGGACTTCAAgtacgaactc ... ttcattgcagATATGCAAGGATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCA
EST: gi|71884795|gb|DT033850.1|DT033850
EST:     ACTATGGTCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAA                         ATATGCAAGGATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCA
genomic: ACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAAgtacgaactc ... ttcattgcagATATGCAAGGATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCA
EST: gi|110404543|gb|EC969762.1|EC969762
EST:     ACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAA                         ATATGCAAGGATAAGGACGCTAGACCTCAGACATGGGGATATGTAGCG
genomic: ACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAAgtacgaactc ... ttcattgcagATATGCAAGGATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCG
EST: gi|30253270|gb|CB970821.1|CB970821
EST:     ACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAA                         ATATGCAAGGATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCA
genomic: ACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAAgtacgaactc ... ttcattgcagATATGCAAGGATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCA
EST: gi|110421097|gb|EC987385.1|EC987385
EST:     ACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAA                         ATATGCAAGGATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCA
genomic: ACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAAgtacgaactc ... ttcattgcagATATGCAAGGATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCA
EST: gi|71884047|gb|DT033102.1|DT033102
EST:     ACTATGGTCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAA                         ATATGCAAGGATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCA
genomic: ACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAAgtacgaactc ... ttcattgcagATATGCAAGGATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAAATCTCTGATCCCTTGAAGGGAATATATGGAGCAGGTGCACATTCTGACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCAAgtacgaactctgcagaaaatttttaagctatgttacaattgtatttcacataattttggaagtgaattgaaacttttcaattcattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG