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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGCCTCCTCGGGAAACTTGCCTCTGTTAACTTACAGGGCCTAACCCATCAGGAGAAGCTTGCTTTCTGGATCAACACCTATAATTCCTGCATGATGAATgtaagcaaggcctttttgtaaacgtaaatttaaactctatgtttattcttttgcttatctgtttactgtactgcattgcttgctttag

Basic information

species Vitis vinifera
transcript Vv18s0001g11120.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g11120.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os09g28850.2 (Oryza sativa), 5'ss of exon 5
GCGCCTCCTCGGGAAACTTGCCTCTGTTAACTTACAGGGCCTAACCCATCAGGAGAAGCTTGCTTTCTGGATCAACACCTATAATTCCTGCATGATGAATgtaagcaa--ggccttt---ttgtaaacgtaaatttaaactctatgtttattc-ttttgcttatctgtttactgtactgcattgcttgctttag-------
|    |  || |||  ||| | || ||| || |   ||| ||  |||||||| ||||||| || ||||||||||||| ||| ||||| ||||||||||||||||||     |||| |   |  |||  |         |  ||   ||| ||| | ||| | |  | | | || |  |   || || | |  ||       
GGCTTTGATCCGGAGGCTTTCATCGGTTGACCTGACGGGGCTCTCCCATCAGCAGAAGCTGGCATTCTGGATCAACATCTACAATTCGTGCATGATGAATgtaagctgtcagcctgtcactcataattgagcccacccatcctgaatttcttcatcttgatcaattatat-ctttgttcattttctcgttagagggaaatt

upper sequence: Vv18s0001g11120.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G066516_T01 (Zea mays), 5'ss of exon 5
GCGCCTCCTCGGGAAACTTGCCTCTGTTAACTTACAGGGCCTAACCCATCAGGAGAAGCTTGCTTTCTGGATCAACACCTATAATTCCTGCATGATGAATgtaagcaa------ggcctttttgtaaacgtaaatttaaactctatgtttattcttttgcttatctgtttactgtactgcattgcttgctttag------
|  | | ||  |||  ||  | || ||| || |   ||| ||  |||||||| ||||||| || ||||||||||||  ||| ||||||||||||||||| |||||| |       | |   ||  | |  |   | |   ||||   | | |  ||||  |||   |   |    |    | | |    ||  |      
GGCCTTGCTGCGGAGGCTGTCGTCGGTTGACCTGGCGGGGCTCTCCCATCAGCAGAAGCTGGCCTTCTGGATCAACGTCTACAATTCCTGCATGATGAACgtaagccatcgggcagtcacatttcagagttgggtgtttcctcttcttgtgtgtttttttttaaaagaagaagacagcaaaattcgcaattcggtttgct

upper sequence: Vv18s0001g11120.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G442763_T02 (Zea mays), 5'ss of exon 6
GCGCCTCCTCGGGAAACTTGCCTCTGTTAACTTACAGGGCCTAACCCATCAGGAGAA---GCTTGCTTTCTGGATCAACACCTATAATTCCTGCATGATGAATgtaagcaaggcctttttgtaaacgtaaatttaaactctatgtttattcttttgcttatctgtttactgtactgcattgcttgctttag-------------
    || ||| |||| ||  |||  ||| || ||  ||||||  |||| ||| | ||   ||| || |||||||||||||||||  | |||||||||||||| ||||||    |||  |     | | |   |    ||       |   | |    | ||  ||  |  |   |  |   |  |                   
---ACTGCTCCGGAAGCTCTCCTTGGTTGACCTAGCGGGCCTCTCCCACCAGCATAATAGGCTGGCGTTCTGGATCAACACCTACTACTCCTGCATGATGAACgtaagctgcccctaataactgaggcatcctcttgcttctcacctcagcatcca-tgattggtccatagctttatacctcacgtccctttcctgtcgatggg

upper sequence: Vv18s0001g11120.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA17G36350.1 (Glycine max), 5'ss of exon 8
GCGCCTCCTCGGGAAACTTGCCTCTGTTAACTTACAGGGCCTAACCCATCAGGAGAAGCTTGCTTTCTGGATCAACACCTATAATTCCTGCATGATGAATgtaagcaaggcctttttgtaaacgtaa-atttaa---actctatgttt--attcttttgcttatctgtttactgtactgcattgcttgctttag----------------------------------------------------------------------------------
 |  ||  |  ||||| | |||||||| |||||  |   ||| | |||||||||||||||||| ||||||||||||| ||| ||||| || |||||||||||| |  ||   | |   | |    || |||||    | ||| | | |  |   |||| |    |  |||| | ||        |     | ||                                                                                  
-CTACTTTTTAGGAAAGTAGCCTCTGTCAACTTGGAAAACCTCAACCATCAGGAGAAGCTTGCATTCTGGATCAACATCTACAATTCGTGTATGATGAATGtatgtcagttatgtccattacaacaacatttagtataatctgtatctaaacattttttccacgcaatttattataactttcctcaataatcagaataacaaatcttaatttgtgcgcctaattatcctgtcaaaccataataatgatggtattttaagttctactttgcttcagg

upper sequence: Vv18s0001g11120.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA06G04060.1 (Glycine max), 5'ss of exon 7
GCGCCTCCTCGGGAAACTTGCCTCTGTTAACTTACAGGGCCTAACCCATCAGGAGAAGCTTGCTTTCTGGATCAACACCTATAATTCCTGCATGATGAATgtaagcaaggcctttttgtaaacgtaaatttaaactctatgtttattcttttgcttatctg---tttactgtactgcattgcttgctttag--------------------------------
||  || ||  | ||||| || | ||| ||| |  ||  ||| | ||| |||||||||||||| ||||||||||||| ||| ||||| || ||||||||||||||  |    | |  || |   |||  |  ||    || |  | |    |  ||| | |     | || |    ||        ||||                                 
GCTTCTTCTGAGAAAACTAGCTTGTGTCAACATCGAGAACCTCAACCACCAGGAGAAGCTTGCCTTCTGGATCAACATCTACAATTCATGTATGATGAATgtaagtcaattatgtccgttagattaacatgtaatgtcatctgaaatggccttgttaacagaaccattctttgagccaagcacaattttaaagtagtaatagctaagttctgctctgcttcag

upper sequence: Vv18s0001g11120.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA04G03930.1 (Glycine max), 5'ss of exon 6
GCGCCTCCTCGGGAAACTTGCCTCTGTTAACTTACAGGGCCTAACCCATCAGGAGAAGCTTGCTTTCTGGATCAACACCTATAATTCCTGCATGATGAATgtaagcaa-----ggcctttttgtaaacgtaaatttaaactctatgtttattcttttgcttatctgtttactgtactgcattgcttgctttag-----------------------------------
||  || ||  | ||||| |||| ||| ||| |  ||  ||| | ||| |||||||||||||| ||||||||||||| ||| ||||| || ||||||||||||||  |     | || ||   | ||| |  | |   |    |  | |  |  ||  |  | |  ||   || ||   |     | ||  ||                                   
GCTTCTTCTGAGAAAACTAGCCTGTGTCAACATTGAGAACCTCAACCACCAGGAGAAGCTTGCCTTCTGGATCAACATCTACAATTCATGTATGATGAATgtaagtcaattatgtccattagattaacatgtagtgtcatctgaaatgtccttgttgacagaaccattctttgaaccaaacactcttctaaagcagtaatagcttatttaagttccgctttgcttcag

upper sequence: Vv18s0001g11120.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA14G08820.1 (Glycine max), 5'ss of exon 7
GCGCCTCCTCGGGAAACTTGCCTCTGTTAACTTACAGGGCCTAACCCATCAGGAGAAGCTTGCTTTCTGGATCAACACCTATAATTCCTGCATGATGAATgtaagcaaggcctttttgtaaacgtaa-atttaaactctatgtttattcttttgcttatctgtttactgtactgcattgcttgctttag----------------------------------------------------------------------------------------
 |  ||  |  ||||||| ||||| || |||||  |   ||| | |||||||||||||||||| ||||||||||||| ||| || || || |||||||||||| |  ||   | |   | |    || |||||      || | |||         | | | |  ||  |     ||  ||| | |                                                                                           
ACTACTTTTTAGGAAACTAGCCTCGGTCAACTTGGAAAACCTCAACCATCAGGAGAAGCTTGCATTCTGGATCAACATCTACAACTCTTGTATGATGAATgtatgtcagttatgtccattacaacaacatttagttataatttgtatctaaacatctttttctacacaatttattataactttcctcgataatcagaataactaatcttaagtggtgcacttaattatcttctaaaaccataataatgatggtattttaagttctactttgcttcag

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|161720309|gb|FC071162.1|FC071162
EST:     AGGAGAAGCTTGCTTTCTGGATCAACACCTATAATTCCTGCATGATGAAT                         GCATTCCTGGAACATGGAATACCAGGGAATCCAGAGATGGTCGTTGAATTG
genomic: AGGAGAAGCTTGCTTTCTGGATCAACACCTATAATTCCTGCATGATGAATgtaagcaagg ... cttgctttagGCATTCCTGGAACATGGAATACCAGGGAATCCAGAGATGGTTGTTGAATTG
EST: gi|110360425|gb|EC923512.1|EC923512
EST:     AATTCCTGCATGATGAAT                         GCATTCCTGGAACATGGAATACCAGGGAATCCAGAGATGGTCGTTGAATTG
genomic: AATTCCTGCATGATGAATgtaagcaagg ... cttgctttagGCATTCCTGGAACATGGAATACCAGGGAATCCAGAGATGGTTGTTGAATTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGCCTCCTCGGGAAACTTGCCTCTGTTAACTTACAGGGCCTAACCCATCAGGAGAAGCTTGCTTTCTGGATCAACACCTATAATTCCTGCATGATGAATgtaagcaaggcctttttgtaaacgtaaatttaaactctatgtttattcttttgcttatctgtttactgtactgcattgcttgctttag

- - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC