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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTTGCGTTCATCACCAAGAGCGAAGTTGATCATCTTGACGATGGATACAGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAGgtatatcaaatcccgatcttggtccccttattcatttaattattttcttaattatgaagcaaaaggaaaaaaaaaagtgtggaagtaactaaacattttcttaattttcag

Basic information

species Vitis vinifera
transcript Vv05s0077g00730.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g00730.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA07G36640.1 (Glycine max), 5'ss of exon 2
GATTTGCGTTCATCACCAAGAGCGAAGTTGATCATCTTGACGATGGATACAGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAGgtata----tcaaatcccgatc--ttggtccccttattcat---------ttaattattttcttaattatgaagc---------------aaaaggaaaaaaaaaagtgtgga--agtaactaaacattttcttaattttcag---------
||||||||||||| || ||||| ||||| ||||| || |||||||| ||||||||| | |||||||| |||||||| || || ||||||||| ||| ||||||| |||| || ||| | | ||| || ||||||| ||| | | | ||| | | | | || ||| | ||| |||| |||||| | ||
GATTTGCGTTCATGACAAAGAGTGAAGTGGATCACCTCGACGATGGCTACAGATGGCGCAAGTACGGTCAAAAAGCCGTCAAAAACAGCCCTCATCCAAGgtatacccatcaatatataattatttgcacatttcattgatcgtcaaatcttaattaattttgtcactttgattctttcttctcctttttagtactttggatttgggttgggactaataattaaaatatttcttgcggtgcacgcaaaacag

upper sequence: Vv05s0077g00730.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA17G03950.2 (Glycine max), 5'ss of exon 2
GATTTGCGTTCATCACCAAGAGCGAAGTTGATCATCTTGACGATGGATACAGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAGgtatat---caaatcccgatcttg-gtccccttattcatttaattatt------ttcttaat-tatgaagcaaaaggaaaaaa-----aaaagtgtggaagtaactaaacattttcttaattttcag------------------------------------------------------
||||||||||||| || ||||| ||||| ||||| || |||||||| || |||||| | |||||||| |||||||| || || ||||||||| ||| |||||||| | || || | | ||| | || |||||||| | ||| |||| | | | ||| | | | | | | | | || | | |||| ||
GATTTGCGTTCATGACAAAGAGTGAAGTGGATCACCTCGACGATGGCTATAGATGGCGCAAGTACGGTCAAAAAGCCGTCAAAAACAGCCCTCATCCAAGgtatatatatatatatatatatcatatacccatgagtatataattattaatcaatatcaaatatatgcatttcatttatcaaaccttaattcattttgtcattatgattcgttcttctcctttttagtactttggattgggactaataattaaactatttcttgcggtgcacgcaaaacag

upper sequence: Vv05s0077g00730.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: PP1S25_173V6.1 (Physcomitrella patens), 5'ss of exon 4
GATTTGCGTTCATCACCAAGAGCGAAGTTGATCATCTTGACGATGGATACAGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAGgtatatcaaatcccgatcttggtccccttattcatttaatt--attttcttaattatgaagcaaaaggaaaaaaaaaagtgtggaagtaacta-aacattttcttaattttcag
|| ||| | || | || |||||| | |||||||| | | ||| | ||||||||||| |||||||| || |||||||||| ||| ||||| |||| || | | | | | | | || || | | | || | | | | ||| | |||| | | ||
TATATGCCATTGAAACTCGCACGGATGTTGATATAATGGACGATGGCTTTAAGTGGCGCAAGTACGGCCAGAAAGCTGTCAAAAACAGCCCTTATCCCAGgtacatcatgtcgatacccttcttatcatgacagtaagatcgaatatgcctcatgtcgggacgggacagattgaaatcatttggatttggatgcggcag---------------

upper sequence: Vv05s0077g00730.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ10059 (Selaginella moellendorffii), 5'ss of exon 1
GATTTGCGTTCATCACCAAGAGCGAAGTTGATCATCTTGACGATGGATACAGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAGgtatatcaaatcccgatcttggtccccttattcatttaattattttcttaattatgaagcaaaaggaaaaaaaaaagtgtggaagt--aactaaacattttcttaattttcag
| | ||| | ||||||||||| || | |||||||| ||| | |||||||||||||| ||||| || || ||||||||||| | || |||| | | | || | | | | | | | || | | | || || || | | | | || | | || |
GGTATGCCATACAAACCAAGAGCGACAAGGAGATCATGGACGATGGCTACCGGTGGAGGAAGTACGGACAAAAGGCCGTCAAGAACAGCCCATACCCAAGgtgcgt---------acggcaggcctcca--ttgtgagaggagagagagagagagagaggcgaggaatgcgttgaattggggccattggattgaccacctccacgatcgac--

upper sequence: Vv05s0077g00730.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ34931 (Selaginella moellendorffii), 5'ss of exon 1
GATTTGCGTTCATCACCAAGAGCGAAGTTGATCATCTTGACGATGGATACAGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAGgtatatcaaatcccgatcttggtccccttattcatttaattattttcttaattatgaagcaaaaggaaaaaaaaaagtgtggaagtaactaaacattttcttaattttcag--
| | ||| | ||||||||||| || | |||||||| ||| | |||||||||||||| ||||| || |||||||||||||| | || |||| | | | || || || || | | | | || | | | || | | | | || | | | | |
GGTATGCCATACAAACCAAGAGCGACAAGGAGATCATGGACGATGGCTACCGGTGGAGGAAGTACGGACAAAAGGCCGTGAAGAACAGCCCATACCCAAGgtgcgt--acggcagacct-----ccattgtgagaggagagag------agaggcgaggaatgcgttgaattggggccattggattgaccacctccacgatcgacggtgaaat

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|27583690|gb|CB006385.1|CB006385
EST:     AGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAG                         GAGCTACTATCGTTGCACCACTGCCGCCTGCGGAGTGAAAAAGAGGGTGGA
genomic: AGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAGgtatatcaaa ... taattttcagGAGCTACTATCGTTGCACCACTGCCGCCTGCGGAGTGAAAAAGAGGGTGGA
EST: gi|110395866|gb|EC961540.1|EC961540
EST:     AGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAG                         GAGCTACTATCGTTGCACCACTGCCGCCTGCGGAGTGAAAAAGAGGGTGGA
genomic: AGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAGgtatatcaaa ... taattttcagGAGCTACTATCGTTGCACCACTGCCGCCTGCGGAGTGAAAAAGAGGGTGGA
EST: gi|22009147|gb|BQ794181.1|BQ794181
EST:     AGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAG                         GAGCTACTATCGTTGCACCACTGCCGCCTGCGGAGTGAAAAAGAGGGTGGA
genomic: AGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAGgtatatcaaa ... taattttcagGAGCTACTATCGTTGCACCACTGCCGCCTGCGGAGTGAAAAAGAGGGTGGA
EST: gi|156737123|gb|EV241244.1|EV241244
EST:     AGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAG                         GAGCTACTATCGTTGCACCACTGCCGCCTGCGGAGTGAAAAAGAGGGTGGA
genomic: AGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAGgtatatcaaa ... taattttcagGAGCTACTATCGTTGCACCACTGCCGCCTGCGGAGTGAAAAAGAGGGTGGA
EST: gi|110719220|gb|EE096949.1|EE096949
EST:     AGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAG                         GAGCTACTATCGTTGCACCACTGCCGCCTGCGGAGTGAAAAAGAGGGTGGA
genomic: AGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAGgtatatcaaa ... taattttcagGAGCTACTATCGTTGCACCACTGCCGCCTGCGGAGTGAAAAAGAGGGTGGA
EST: gi|110372689|gb|EC936875.1|EC936875
EST:     AGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAG                         GAGCTACTATCGTTGCACCACTGCCGCCTGCGGAGTGAAAAAGAGGGTGGA
genomic: AGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAGgtatatcaaa ... taattttcagGAGCTACTATCGTTGCACCACTGCCGCCTGCGGAGTGAAAAAGAGGGTGGA
EST: gi|46917930|gb|CN547259.1|CN547259
EST:     AGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAG                         GAGCTACTATCGTTGCACCACTGCCGCCTGCGGAGTGAAAAAGAGGGTGGA
genomic: AGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAGgtatatcaaa ... taattttcagGAGCTACTATCGTTGCACCACTGCCGCCTGCGGAGTGAAAAAGAGGGTGGA
EST: gi|22014586|gb|BQ799620.1|BQ799620
EST:     AGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAG                         GAGCTACTATCGTTGCACCACTGCCGCCTGCGGAGTGAAAAAGAGGGTGGA
genomic: AGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAGgtatatcaaa ... taattttcagGAGCTACTATCGTTGCACCACTGCCGCCTGCGGAGTGAAAAAGAGGGTGGA
EST: gi|22014202|gb|BQ799236.1|BQ799236
EST:     AGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAG                         GAGCTACTATCGTTGCACCACTGCCGCCTGCGGAGTGAAAAAGAGGGTGGA
genomic: AGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAGgtatatcaaa ... taattttcagGAGCTACTATCGTTGCACCACTGCCGCCTGCGGAGTGAAAAAGAGGGTGGA
EST: gi|27582871|gb|CB005566.1|CB005566
EST:     AGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAG                         GAGCTACTATCGTTGCACCACTGCCGCCTGCGGAGTGAAAAAGAGGGTGGA
genomic: AGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAGgtatatcaaa ... taattttcagGAGCTACTATCGTTGCACCACTGCCGCCTGCGGAGTGAAAAAGAGGGTGGA
EST: gi|110712223|gb|EE089600.1|EE089600
EST:     AGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAG                         GAGCTACTATCGTTGCACCACTGCCGCCTGCGGAGTGAAAAAGAGGGTGGA
genomic: AGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAGgtatatcaaa ... taattttcagGAGCTACTATCGTTGCACCACTGCCGCCTGCGGAGTGAAAAAGAGGGTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTTGCGTTCATCACCAAGAGCGAAGTTGATCATCTTGACGATGGATACAGATGGAGGAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTTTCCTAGgtatatcaaatcccgatcttggtccccttattcatttaattattttcttaattatgaagcaaaaggaaaaaaaaaagtgtggaagtaactaaacattttcttaattttcag

- - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC