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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGACAAGTTAAATGCTTCACAATTGGAGTTCGCAAAAGATAGGATAATCATGGGAACAGAGCGGAAAACAATGTTCTTATCAGAAGAATCAAAGAAGgtatgaatatcatttatgagacctgtcaaggctagctgtttaacctgtgactcactcggtcgatgcttcacctcattactgtgaagtcacagattcaacc...

Basic information

species Vitis vinifera
transcript Vv16s0050g02630.t01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g02630.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: LOC_Os01g43150.2 (Oryza sativa), 5'ss of exon 5
TGCTGACAAGTTAAATGCTTCACAATTGGAGTTCGCAAAAGATAGGATAATCATGGGAACAGAGCGGAAAACAATGTTCTTATCAGAAGAATCAAAGAAGgtatg-----------------aatatcatttatgagacctgtcaaggctag---ctgt-ttaacctgtgactcactcggtcgatgcttcacctcattactgtgaagtcacagattcaacc---------------------------------------------------------------------
||||||||||||   |||| |||| ||||| || || |||||| | || ||||||||||| ||| ||||| |||||||| |||| || ||||| || |||| |||                 | | |  |||| ||||  |   |    |||   || | || |||| |      |      | || |     |  ||| | |      ||                                                                               
TGCTGACAAGTTGGCTGCTGCACAGTTGGAATTTGCGAAAGATCGTATTATCATGGGAACTGAGAGGAAATCAATGTTCATATCTGACGAATCCAAAAAGgcatgcctcttcaagttactttattttattttaagagagttaatagttatagtgcctatgtttacctatagagtgccgttatggtggtctctattgttagtattctactaccagcattgttgtcgatatgcttttaaatgcagaaatgtgaaatacaatacactgatcattatgcatttttgttatttag

upper sequence: Vv16s0050g02630.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GRMZM2G156069_T01 (Zea mays), 5'ss of exon 13
TGCTGACAAGTTAAATGCTTCACAATTGGAGTTCGCAAAAGATAGGATAATCATGGGAACAGAGCGGAAAACAATGTTCTTATCAGAAGAATCAAAGAAGgtatg-------------aatatcatttatgagacctgtcaaggctagctg--tttaacctgtgactcactcggtcgatgcttcacctca-ttactgtgaagtcacagattcaacc------------------------
||| |||||||| ||||||   || |||||||| || |||||| | || ||||||||||| ||| ||| | |||||||| ||||||| ||||| |  |||| |||             | | || ||| |   | ||   |||   |  |     |||| |  |  |   ||  |  || ||  |    |   |||| ||| ||  | ||| |                           
TGCGGACAAGTTGAATGCTGTTCAGTTGGAGTTTGCCAAAGATCGTATTATCATGGGAACTGAGAGGAGATCAATGTTCATATCAGATGAATCGAGAAAGgcatgtttgtttttgttaactttcctttttcgcaactaaaaagaacaattagtcctaacataaggtt---tccataaattctagattggagcaactgcgaaatcgtatattaattaacttcatttccttgtgctcattag

upper sequence: Vv16s0050g02630.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA13G08160.1 (Glycine max), 5'ss of exon 13
TGCTGACAAGTTAAATGCTTCACAATTGGAGTTCGCAAAAGATAGGATAATCATGGGAACAGAGCGGAAAACAATGTTCTTATCAGAAGAATCAAAGAAGgtatgaatatcatttatgagacctgtcaaggct--agctgtttaacctgtgactcactcggtcgatgcttcacctcattactgtgaagtcacagattcaacc--
||| || ||  |||  ||| ||||||||||||| |||||||| || ||| | ||||| || |||||||||||||||||  |||| ||||| ||||||||||||||  |||     | ||      | |   ||  |    | ||   ||||  | |   | | ||| ||  ||   |    ||   | ||     || ||    
TGCAGAGAAAGTAACAGCTGCACAATTGGAGTTTGCAAAAGACAGAATAGTTATGGGTACTGAGCGGAAAACAATGTTTATATCTGAAGAGTCAAAGAAGgtatgtgtatatgccaggatctggtttagtacttaaaacatgtaggttgtggtttatatgattgat-ctaaactatagggttg---actcttgtttttaaaaga

upper sequence: Vv16s0050g02630.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA14G29810.1 (Glycine max), 5'ss of exon 5
TGCTGACAAGTTAAATGCTTCACAATTGGAGTTCGCAAAAGATAGGATAATCATGGGAACAGAGCGGAAAACAATGTTCTTATCAGAAGAATCAAAGAAGgtatgaatatcatttatgagacctgtcaaggctagctgtttaacctgtgactcactcggtcgatgcttcacctcattactgtgaagtcacagattcaacc----
||| || ||  |||  ||| | || |||||||| |||||||| || ||| | ||||| || |||||||||||||||||  |||||||||| ||||||||||||||  |||     | || | |||     | || ||    ||| |||   |       |  ||| || | || |  | |||    |   | | |   |     
TGCAGAGAAAGTAACAGCTGCGCAGTTGGAGTTTGCAAAAGACAGAATAGTTATGGGTACTGAGCGGAAAACAATGTTTGTATCAGAAGAGTCAAAGAAGgtatgtgtatatgccaggaaatctggtttag-tacctaa--aacatgtaggttgtggtttatatgattgatctaaaca-tgtaggatgggaaacttgtctggcg

upper sequence: Vv16s0050g02630.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA06G13140.1 (Glycine max), 5'ss of exon 13
TGCTGACAAGTTAAATGCTTCACAATTGGAGTTCGCAAAAGATAGGATAATCATGGGAACAGAGCGGAAAACAATGTTCTTATCAGAAGAATCAAAGAAGgta-tgaatatcatttatgagacctg-tcaaggctagctgtttaacctgtgact-cactcggtcgatgcttcacct-cattactgtgaa--gtcacagattcaacc
||| || || |||   ||| |||| || ||||| || |||||||| ||||| ||||| ||||| ||||||||||||| | |||| ||||| ||||| |||||| || | |  || ||||  |     ||  |  ||||  || ||| | |  ||    ||  |  ||| || |  |   |   ||| ||     |||| ||     
TGCAGAGAATTTAGCAGCTGCACAGTTAGAGTTTGCCAAAGATAGAATAATTATGGGTACAGAACGGAAAACAATGTCCATATCCGAAGAGTCAAAAAAGgtaatgtacagtatatatgttatgaaatctggtttagcacttgaacttcttgctgtgatctat--atgattgatatgtgtgggtgtaaatcactacagtttt----

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|110363183|gb|EC926755.1|EC926755
EST:     TCATGGGAACAGAGCGGAAAACAATGTTCTTATCAGAAGAATCAAAGAAG                         CTTACTGCATATCATGAGAGCGGTCATGCAATTGTTGCCTTCAACACAGAT
genomic: TCATGGGAACAGAGCGGAAAACAATGTTCTTATCAGAAGAATCAAAGAAGgtatgaatat ... ctcttttcagCTTACTGCATATCATGAGAGCGGTCATGCAATTGTTGCCTTCAACACAGAT
EST: gi|110420745|gb|EC987025.1|EC987025
EST:     TCATGGGAACAGAGCGGAAAACAATGTTCTTATCAGAAGAATCAAAGAAG                         CTTACTGCATATCATGAGAGCGGTCATGCAATTGTTGCCTTCAACACAGAT
genomic: TCATGGGAACAGAGCGGAAAACAATGTTCTTATCAGAAGAATCAAAGAAGgtatgaatat ... ctcttttcagCTTACTGCATATCATGAGAGCGGTCATGCAATTGTTGCCTTCAACACAGAT
EST: gi|34549961|gb|CF518193.1|CF518193
EST:     ATGTTCTTATCAGAAGGATCAAAGAAG                         CTTACTGCATATCATGAGAGCGGTCATGCAATTGTTGCCTTCAACACAGAT
genomic: ATGTTCTTATCAGAAGAATCAAAGAAGgtatgaatat ... ctcttttcagCTTACTGCATATCATGAGAGCGGTCATGCAATTGTTGCCTTCAACACAGAT
EST: gi|34550831|gb|CF519047.1|CF519047
EST:     GGAAAACAATGTTCTTATCAGAAGGATCAAAGAAG                         CTTACTGCATATCATGAGAGCGGTCATGCAATTGTTGCCTTCAACACAGAT
genomic: GGAAAACAATGTTCTTATCAGAAGAATCAAAGAAGgtatgaatat ... ctcttttcagCTTACTGCATATCATGAGAGCGGTCATGCAATTGTTGCCTTCAACACAGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGACAAGTTAAATGCTTCACAATTGGAGTTCGCAAAAGATAGGATAATCATGGGAACAGAGCGGAAAACAATGTTCTTATCAGAAGAATCAAAGAAGgtatgaatatcatttatgagacctgtcaaggctagctgtttaacctgtgactcactcggtcgatgcttcacctcattactgtgaagtcacagattcaacc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG