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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCATATTCATTTCAAGCTCAGGAGACCAATCCCATTCAATGAGTGGAAATGgtaaacctacttcttttatttgcccttcatttatttgtaatccatgcacttacagtttggggaaattgagcgtggtagcaaagccactagactttggaat...

Basic information

species Vitis vinifera
transcript Vv08s0007g05170.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g05170.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os03g20310.2 (Oryza sativa), 5'ss of exon 7
GGCATATTCATTTCAAGCTCAGGAGACCAATCCCATTCAATGAGTGGAAATGgtaa-acctac-ttcttttatttgc-ccttcatttatttgtaatccatgcactt-acagtttgg-ggaaattgagcgtggtagcaaagccactagactttggaat
|| || | |||||| ||||||||||||||| | ||| | ||||||||||||||||| | | | | | |||| | | | | | || |||| | ||||| | |||| | || || | || | | || || |
GGAATTTACATTTCGAGCTCAGGAGACCAAACTCATGCTATGAGTGGAAATGgtaagatttgtgtacgcacagttgcacgcgtacctgctcact-tgtgtgtactttagtgtttgttaggggttgaac-tgata--agagtaagttttctctgcag-

upper sequence: Vv08s0007g05170.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G361847_T02 (Zea mays), 5'ss of exon 5
GGCATATTCATTTCAAGCTCAGGAGACCAATCCCATTCAATGAGTGGAAATGgtaaa---cctacttcttttatttgcccttcatttatttgtaatccatgcacttacagtttggggaaattgagcgtggtagcaaagccactagactttggaat------------
|| || |||||||| ||||| ||||||||| ||||| | ||||||||||||||||| | | | || ||| || | | | || | || | | | || | || ||| | || || | || ||
GGAATCTTCATTTCTAGCTCTGGAGACCAAACCCATGCCATGAGTGGAAATGgtaatatttcaattcgttatatctgtgcgtttctggatt-tgattagtctatct-tgattgaatgctatctttatctctagaagtgcatctgaaattataaacttgttgttgcag
















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|110359279|gb|EC920517.1|EC920517
EST:     CATATTCATTTCAAGCTCAGGAGACCAATCCCATTCAATGAGTGGAAATG                         GGGCCTTGGCATTTGATGTAGAATATGCTCGGTGGCTAGAAGAGCACAACA
genomic: CATATTCATTTCAAGCTCAGGAGACCAATCCCATTCAATGAGTGGAAATGgtaaacctac ... tcttctgcagGGGCCTTGGCATTTGATGTAGAATATGCTCGGTGGCTAGAAGAGCACAACA
EST: gi|71884309|gb|DT033364.1|DT033364
EST:     CATATTCATTTCAAGCTCAGGAGACCAATCCCATTCAATGAGTGGAAATG                         GGGCCTTGGCATTTGATGTAGAATATGCTCGGTGGCTAGAAGAGCACAACA
genomic: CATATTCATTTCAAGCTCAGGAGACCAATCCCATTCAATGAGTGGAAATGgtaaacctac ... tcttctgcagGGGCCTTGGCATTTGATGTAGAATATGCTCGGTGGCTAGAAGAGCACAACA
EST: gi|33409731|gb|CF215358.1|CF215358
EST:     ATATTCATTTCAAGCTC-GATAGACCAATCCCATTCAATGAGTGGAAATG                         GGGCCTTGGCATTTGATGTAGAATATGCTCGGTGGCTAGAAGAGCACAACA
genomic: ATATTCATTTCAAGCTCAGG-AGACCAATCCCATTCAATGAGTGGAAATGgtaaacctac ... tcttctgcagGGGCCTTGGCATTTGATGTAGAATATGCTCGGTGGCTAGAAGAGCACAACA
EST: gi|161710152|gb|FC061050.1|FC061050
EST:     CATATTCATTTCAAGCTCAGGAGACCAATCCCATTCAATGAGTGGAAATG                         GGGCCTTGGCATTTGATGTAGAATATGCTCGGTGGCTAGAAGAGCACAACA
genomic: CATATTCATTTCAAGCTCAGGAGACCAATCCCATTCAATGAGTGGAAATGgtaaacctac ... tcttctgcagGGGCCTTGGCATTTGATGTAGAATATGCTCGGTGGCTAGAAGAGCACAACA
EST: gi|71885133|gb|DT034188.1|DT034188
EST:     CATATTCATTTCAAGCTCAGGAGACCAATCCCATTCAATGAGTGGAAATG                         GGGCCTTGGCATTTGATGTAGAATAT
genomic: CATATTCATTTCAAGCTCAGGAGACCAATCCCATTCAATGAGTGGAAATGgtaaacctac ... tcttctgcagGGGCCTTGGCATTTGATGTAGAATAT
EST: gi|71888810|gb|DT037865.1|DT037865
EST:     CATATTCATTTCAAGCTCAGGAGACCAATCCCATTCAATGAGTGGAAATG                         GGGCCTTGGCATTTGATGTAGAATATGCTCGGTGGCTAGAAGAGCACAACA
genomic: CATATTCATTTCAAGCTCAGGAGACCAATCCCATTCAATGAGTGGAAATGgtaaacctac ... tcttctgcagGGGCCTTGGCATTTGATGTAGAATATGCTCGGTGGCTAGAAGAGCACAACA
EST: gi|161719149|gb|FC065719.1|FC065719
EST:     CATATTCATTTCAAGCTCAGGAGACCAATCCCATTCAATGAGTGGAAATG                         GGGCCTTGGCATTTGATGTAGAATATGCTCGGTGGCTAGAAGAGCACAACA
genomic: CATATTCATTTCAAGCTCAGGAGACCAATCCCATTCAATGAGTGGAAATGgtaaacctac ... tcttctgcagGGGCCTTGGCATTTGATGTAGAATATGCTCGGTGGCTAGAAGAGCACAACA
EST: gi|71883209|gb|DT032264.1|DT032264
EST:     CATATTCATTTCAAGCTCAGGAGACCAATCCCATTCAATGAGTGGAAATG                         GGGCCTTGGCATTTGATGTAGAATATGCTCGGTGGCTAGAAGAGCACAACA
genomic: CATATTCATTTCAAGCTCAGGAGACCAATCCCATTCAATGAGTGGAAATGgtaaacctac ... tcttctgcagGGGCCTTGGCATTTGATGTAGAATATGCTCGGTGGCTAGAAGAGCACAACA
EST: gi|71874124|gb|DT023179.1|DT023179
EST:     CCCATTCAATGAGTGGAAATG                         GGGCCTTGGCATTTGATGTAGAATATGCTCGGTGGCTAGAAGAGCACAACA
genomic: CCCATTCAATGAGTGGAAATGgtaaacctac ... tcttctgcagGGGCCTTGGCATTTGATGTAGAATATGCTCGGTGGCTAGAAGAGCACAACA
EST: gi|161720288|gb|FC070549.1|FC070549
EST:     CATATTCATTTCAAGCTCAGGAGACCAATCCCATTCAATGAGTGGAAATG                         GGGCCTTGGCATTTGATGTAGAATATGCTCGGTGGCTAGAAGAGCACAACA
genomic: CATATTCATTTCAAGCTCAGGAGACCAATCCCATTCAATGAGTGGAAATGgtaaacctac ... tcttctgcagGGGCCTTGGCATTTGATGTAGAATATGCTCGGTGGCTAGAAGAGCACAACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCATATTCATTTCAAGCTCAGGAGACCAATCCCATTCAATGAGTGGAAATGgtaaacctacttcttttatttgcccttcatttatttgtaatccatgcacttacagtttggggaaattgagcgtggtagcaaagccactagactttggaat

- - - - - - CAAGCT
- - - - - - - AGCTCA
- - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggaaat