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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTACCAACCACACTTGATTGCCCCTGAACAAGGTTATCGTCGCCTTATTGAGGGGTCGCTGAATTATTTTAGGGGCCCAGCTGAAGCTTCAGTGGATGCTgtgagtagttcttgtttcatctgctatgtatatggaagttcatttggaaagttgtggtatgtatctggaaagaaatttttttaatctgactgatcaagaaattggaacgtag

Basic information

species Vitis vinifera
transcript Vv15s0021g00480.t01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0021g00480.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: LOC_Os10g41820.1 (Oryza sativa), 5'ss of exon 12
TTACCAACCACACTTGATTGCCCCTGAACAAGGTTATCGTCGCCTTATTGAGGGGTCGCTGAATTATTTTAGGGGCCCAGCTGAAGCTTCAGTGGATGCTgtgagtagttcttgtttcatctgctatgta-tatggaagttcatttggaaagttgtggtatgtatctggaaagaaatttttttaatctgactgatcaagaaattggaacgtag
||| ||||| || || ||||| ||||| ||||| || || || || |||||     | || ||||||||||| || |||||||||||||| || |||||||| |     |     |    || || || | | |||  |     |  |  | ||    ||| |||   ||||    ||||   | | |  | |                    
TTATCAACCTCATTTAATTGCTCCTGAGCAAGGGTACCGCCGACTGATTGAATCTGCTCTCAATTATTTTAGAGGGCCAGCTGAAGCTTCTGTAGATGCTgtaatatactaagaatcttcctcctgtggactgtggttgcctgctctggtattt----tatttattctgaaatctcttttaccattgttgcag--------------------

upper sequence: Vv15s0021g00480.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA08G45380.1 (Glycine max), 5'ss of exon 12
TTACCAACCACACTTGATTGCCCCTGAACAAGGTTATCGTCGCCTTATTGAGGGGTCGCTGAATTATTTTAGGGGCCCAGCTGAAGCTTCAGTGGATGCTgtgagtagttcttgtttcatctgctatgtatatggaagttcatttggaaagttgtggtatgtatctggaaagaaatttttttaatctgactgatcaagaaattggaacgtag
||| || || |||||||||||||| || ||||||||  | ||| | ||||||||  | ||   ||| ||||| |||||||||||||||||||| |||||||| |||| | |    ||  | |  | ||  |||  |  ||||| |   |    |   ||   | |||    |   ||  |||  | |                         
TTATCAGCCTCACTTGATTGCCCCAGAGCAAGGTTACAGGCGCTTGATTGAGGGAGCTCTCGGTTACTTTAGAGGCCCAGCTGAAGCTTCAGTAGATGCTgtaagtattcc--agttggtattatctggttattaattttcatctaacagaaagaatta---aactgagtcggtcttgattttctgtag-----------------------

upper sequence: Vv15s0021g00480.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: AT2G44590.2 (Arabidopsis thaliana), 5'ss of exon 11
TTACCAACCACACTTGATTGCCCCTGAACAAGGTTATCGTCGCCTTATTGAGGGGTCGCTGAATTATTTTAGGGGCCCAGCTGAAGCTTCAGTGGATGCTgtgagtagttcttgtttcatctgctatgtatatggaagttcatttgg-aaagttgtggta--tgtatctggaaagaaatttttttaatctgactgatcaagaaattggaacgtag
 || ||||| |||||||| || || |||  |||||||||||| |||||||| || || || ||| ||||||| || |||||||||||||| ||| ||||||| ||    | ||  |   |   || | |  || |   |  || |   ||    ||      |||   || ||                                          
CTATCAACCTCACTTGATAGCACCAGAATTAGGTTATCGTCGTCTTATTGAAGGATCCCTAAATCATTTTAGAGGTCCAGCTGAAGCTTCTGTGAATGCTgtaagctcctttttctcacttcactcttt-catcggtatctatataataagaccgtaacgactgtgattgtaacag---------------------------------------

upper sequence: Vv15s0021g00480.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: AT3G60190.1 (Arabidopsis thaliana), 5'ss of exon 12
TTACCAACCACACTTGATTGCCCCTGAACAAGGTTATCGTCGCCTTATTGAGGGGTCGCTGAATTATTTTAGGGGCCCAGCTGAAGCTTCAGTGGATGCTgtgagtagttct----tgtttcatctgctatgtatatggaagttcatttggaaagttgtggtatgtatctggaaagaaatttttttaatctgactgatcaagaaattggaacgtag
||| ||||| ||||||||||| || ||||| |||||||| || || || || ||| | |||  ||| ||||| || |||||||||||||| ||||||||||| |||  ||||    ||| || ||  ||     | |  || | ||    ||  ||  ||  |  |  |   || | ||                                     
TTATCAACCTCACTTGATTGCACCAGAACAGGGTTATCGCCGTCTAATCGAAGGGGCACTGGGTTACTTTAGAGGTCCAGCTGAAGCTTCTGTGGATGCTgtaagttcttctacagtgtctcctc-acttcacttttataaataca---agaccgtaatgaga-atggcgcaaatgcaacag----------------------------------

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|26264134|gb|CA815197.1|CA815197
EST:     AGGGGTCACTGAATTATTTTAGGGGCCCAGCTGAAGCTTCAGTGGATGCT                         GTTCACTTCGTCTTGAAGGAACTTGTGAGGAAGTCCATTGGAGAAACTCAG
genomic: AGGGGTCGCTGAATTATTTTAGGGGCCCAGCTGAAGCTTCAGTGGATGCTgtgagtagtt ... tggaacgtagGTTCACTTCGTCTTGAAGGAACTTGTGAGGAAGTCCATTGGAGAAACTCAG
EST: gi|33406103|gb|CF211730.1|CF211730
EST:     AGGGGTCACTGAATTATTTTAGGGGCCCAGCTGAAGCTTCAGTGGATGCT                         GTTCACTTCGTCTTGAAGGAACTTGTGAGGAAGTCCATTGGAGAAACTCAG
genomic: AGGGGTCGCTGAATTATTTTAGGGGCCCAGCTGAAGCTTCAGTGGATGCTgtgagtagtt ... tggaacgtagGTTCACTTCGTCTTGAAGGAACTTGTGAGGAAGTCCATTGGAGAAACTCAG
EST: gi|110376479|gb|EC941544.1|EC941544
EST:     AGGGGTCGCTGAATTATTTTAGGGGCCCAGCTGAAGCTTCAGTGGATGCT                         GTTCACTTCGTCTTGAAGGAACTTGTGAGGAAGTCCATTGGAGAAACTCAG
genomic: AGGGGTCGCTGAATTATTTTAGGGGCCCAGCTGAAGCTTCAGTGGATGCTgtgagtagtt ... tggaacgtagGTTCACTTCGTCTTGAAGGAACTTGTGAGGAAGTCCATTGGAGAAACTCAG
EST: gi|46918033|gb|CN547362.1|CN547362
EST:     AGGGGTCACTGAATTATTTTAGGGGCCCAGCTGAAGCTTCAGTGGATGCT                         GTTCACTTCGTCTTGAAGGAACTTGTGAGGAAGTCCATTGGAGAAACTCAG
genomic: AGGGGTCGCTGAATTATTTTAGGGGCCCAGCTGAAGCTTCAGTGGATGCTgtgagtagtt ... tggaacgtagGTTCACTTCGTCTTGAAGGAACTTGTGAGGAAGTCCATTGGAGAAACTCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTACCAACCACACTTGATTGCCCCTGAACAAGGTTATCGTCGCCTTATTGAGGGGTCGCTGAATTATTTTAGGGGCCCAGCTGAAGCTTCAGTGGATGCTgtgagtagttcttgtttcatctgctatgtatatggaagttcatttggaaagttgtggtatgtatctggaaagaaatttttttaatctgactgatcaagaaattggaacgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA