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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCCGTCCACAAGGGCATGCCCCACAAGTTCTACCATGGCCGCACTGGTAAGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAGgtctctcctctacatctctatctctctctgatgtgttgttgttgtgttttgatcgtagtttatgggtttaatgttttgtttgtgtgaaaatggtggttga...

Basic information

species Vitis vinifera
transcript Vv08s0007g06890.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g06890.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os03g04750.1 (Oryza sativa), 5'ss of exon 1
CGCCGTCCACAAGGGCATGCCCCACAAGTTCTACCATGGCCGCACTGGTAAGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAGgtctc-tcctctacatctctatctctctctgatgtgttgttgttgtgttttgatcgtagtttatgggtttaatgttttgtttgtgtgaaaatggtggttga
|||||| |||||||||||||| |||||||||||||| |||||||| ||    ||||||||||||||||||||||||||||| || ||  | ||||||||||| |  ||| || |    |   |        ||   ||  | ||      |  |      | |   |      | |||| | |        || ||| |  
CGCCGTGCACAAGGGCATGCCGCACAAGTTCTACCACGGCCGCACCGGCCGCGTCTGGAACGTCACCAAGCGCGCCATCGGCGTCGAGATCAACAAGCAGgtataatccgctccgctccggccatagcggcatcctttcctcttcctccctcttttcttctcaacaggcggtagatttggtagatctgtgctgttggctc-

upper sequence: Vv08s0007g06890.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os10g32820.1 (Oryza sativa), 5'ss of exon 1
CGCCGTCCACAAGGGCATGCCCCACAAGTTCTACCATGGCCGCACTGGTAAGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAGgtctctcctctacatctctatctctctctgatgtgttgttgttgtgttttgatcgtag-tttatgggtttaatgttttgtttgtgtgaaaatg-gtggttga--
|||||| |||||||| ||||| |||||||||||||| |||||||| ||    ||||||||||||||||||||||||||||| || ||  | ||||||||||| |  || |     | | | | | |      | |  |  |  |  | ||  || ||| | | ||| | |   | ||   |    ||       ||  |||   
CGCCGTGCACAAGGGGATGCCGCACAAGTTCTACCACGGCCGCACCGGCCGCGTCTGGAACGTCACCAAGCGCGCCATCGGCGTCGAGATCAACAAGCAGgtataacccccgatccccaaacaccccg----gcggcggcgccgcctctttgtcatagatctgtggttgtgtcgcttaagtgacttggtgtcatgtttttgccc

upper sequence: Vv08s0007g06890.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G149257_T01 (Zea mays), 5'ss of exon 1
CGCCGTCCACAAGGGCATGCCCCACAAGTTCTACCATGGCCGCACTGGTAAGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAGgtctctcctctacatctctatctctctctgatgtgttgttgttgtgttttgatcgt-agtttatgggtttaatgttttgtttgtgtgaaaatggtg-gttga
|||||| |||||||||||||| |||||||||||||| |||||||| |||   ||||||||||||||||||||||||||||| |||||  | ||||||||||| |  |  |  || |   ||  | || || |||  | | |||  || |    ||   ||||    | |   || |     ||  |||      |     ||
CGCCGTGCACAAGGGCATGCCGCACAAGTTCTACCACGGCCGCACCGGTCGCGTCTGGAACGTCACCAAGCGCGCCATCGGCGTTGAGATCAACAAGCAGgtataacgcccgcaccagcatacc-ctgtgttgtcat-tcgttccgtatgcgccgccggtttgctagatgtgtgctgctgctggttgatggcaatacagcga

upper sequence: Vv08s0007g06890.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G026216_T01 (Zea mays), 5'ss of exon 1
CGCCGTCCACAAGGGCATGCCCCACAAGTTCTACCATGGCCGCACTGGTAAGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAGgtctctcctctacatctctatct-----ctctctgatgtgttgttgt-tgtgttttgatcgtagtttatgggtttaatgttt-tgttt-gtgtgaaaatggtggttga
||||||||||||||| ||||| |||||||||||||| |||||||| |||   ||||||||||||||||||||||||||||| || ||  ||||||||||||| |  |      ||| || |       ||| |||||  |||| ||   |      | |   |   | || |      | ||  |||| ||| |   | |        
CGCCGTCCACAAGGGGATGCCGCACAAGTTCTACCACGGCCGCACCGGTCGCGTCTGGAACGTCACCAAGCGCGCCATCGGCGTCGAGATAAACAAGCAGgtataccacacggatcccttttcgctagctcgctgataggttgctgggcgcaggcagttgaaatcgtttgtgcacggcgcttacgtttagtgcgcggacg--------

upper sequence: Vv08s0007g06890.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G089421_T01 (Zea mays), 5'ss of exon 1
CGCCGTCCACAAGGGCATGCCCCACAAGTTCTACCATGGCCGCACTGGTAAGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAGgtctctcctctacatct-ctatctctctctgatgtgttgttgttgtgttttgatcgtagtttatgggtttaatgttt-tgtttgtgtgaaaatg-gtggttga
|||||| |||||||||||||| |||||||||||||| |||||||| || |  ||||||||||||||||||||||||||||| || ||  | ||||||||||| |  |  |  || |  ||| |   || |  |  |||     |  |  ||  |  |   |||    | |  || |  || |  |      |||  | | |  
CGCCGTGCACAAGGGCATGCCGCACAAGTTCTACCACGGCCGCACCGGGAGCGTCTGGAACGTCACCAAGCGCGCCATCGGCGTCGAGATCAACAAGCAGgtataactcccgcaccagctaccatgctgtcgttcgttccgtatcagcattcgttttg--ttagatctatgctgctgatgctaatacacggatgcataggta-

upper sequence: Vv08s0007g06890.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA03G36560.1 (Glycine max), 5'ss of exon 1
CGCCGTCCACAAGGGCATGCCCCACAAGTTCTACCATGGCCGCACTGGTAAGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAGgtctctcctctacatctctatctctctctgatgtgttgttgttgtgttttgatcgtagtttatgggtttaatgttttgtttgtgtgaaaatggtggttga--
||||||||||||||| ||||| ||||||||||||||||||||||| |||   |||||||| |||||||| || ||  | || || ||||| |||||||||||||| |     | ||  || | ||  |       ||  | || || ||   |||   | | | | | |    ||||  | |||  |  || |      |  
CGCCGTCCACAAGGGAATGCCACACAAGTTCTACCATGGCCGCACCGGTCGCGTCTGGAATGTCACCAAACGTGCTGTTGGGGTCGAAGTCAACAAGCAGgtctcgcactctcttccttaaccctaacactctatttacttttctgcttc--tcgatctgttttgttatgtcttttttatcgtgatactatcgcttccaatt

upper sequence: Vv08s0007g06890.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA19G39240.1 (Glycine max), 5'ss of exon 1
CGCCGTCCACAAGGGCATGCCCCACAAGTTCTACCATGGCCGCACTGGTAAGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAGgtctc----tcctctacatctctatctctctctgatgtgttgttgttgtgttttgatcgtagtttatgggtttaatgttttgtttgtgtgaaaatggtg-gttga-
 ||||| |||||||| ||||||||||| ||||||||||||||||| ||    |||||||| |||||||| || ||  | || || ||||| ||||||||||||||    || ||   | | ||| | |   |     |    ||  ||  ||| ||||     |  || ||||  |||||  | | ||||| | |   | || || 
TGCCGTTCACAAGGGAATGCCCCACAAATTCTACCATGGCCGCACCGGACGCGTCTGGAATGTCACCAAACGTGCTGTTGGCGTCGAAGTCAACAAGCAGgtctcacactcttccttaaccctagcaccacccttctttccttttctgcttttcgatc-----tgttgtgttttctgtttcttat-tgtgatattctcgtgtcgaa

upper sequence: Vv08s0007g06890.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EDO99609 (Chlamydomonas reinhardtii), 5'ss of exon 2
CGCCGTCCACAAGGGCATGCCCCACAAGTTCTACCATGGCCGCACTGGTAAGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAGgtctctcctctacatctctatctctctctgatgtgttgttgttgtgttttgatcgtagtttatgggtttaatgttttgtttgtgtgaaaatgg-tggttga
             ||||||||||||||||  ||||| |||   || ||||  |||||||||||||||||||||||||||||||| || || ||||||| |||   || | |   |||   || ||       |    |||    |||    || ||   |  || |  |||||         ||  ||  |||  ||  ||
-------------GGCATGCCCCACAAGTGGTACCAGGGCAAGACCGGTACCGTCTGGAACGTCACCAAGCGCGCCATCGGTGTGGAGGTCAACAAGCGGgtgggtcttgt-tgtcttgctcgcttgtgtgggccgggttcacttgtcaaaattgtttgtcctgagaataatgccaccaagctgcaaagctggacggcgga

upper sequence: Vv08s0007g06890.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S91_107V6.1 (Physcomitrella patens), 5'ss of exon 1
CGCCGTCCACAAGGGCATGCCCCACAAGTTCTACCATGGCCGCACTGGTAAGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAGgtc---tctcctctacatct-ctatctctctctgatgtgttgttgttgtgttttgatcgtagtttatgggtttaatgtttt-gtttgtgtgaaaatggtggttga
 ||||| |||||||| |||||||||||||||||||| ||||||||||| |  |||||||||||||||||||||||| |||| ||||   | |||||||||||    |   |||   |||   | | | | | || ||   |   | | |||||   |||  |||   | |||   |||||  | ||     | |||  ||  |||
AGCCGTTCACAAGGGTATGCCCCACAAGTTCTACCACGGCCGCACTGGAATTGTCTGGAACGTCACCAAGCGCGCCGTCGGCGTTGTGATGAACAAGCAGgtacggttctctcgctatccgttttttttttttggtggaatccagct-tgtttcagtcg--gttccggcgttccttgtttcagcttacaccagaatattg--tga

upper sequence: Vv08s0007g06890.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S1_780V6.1 (Physcomitrella patens), 5'ss of exon 1
CGCCGTCCACAAGGGCATGCCCCACAAGTTCTACCATGGCCGCACTGGTAAGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAGgtctc-tcctctacatctctatctctctctgatgtgttgttgttgtgttttgatcgtagtttatgggtttaatgttttgtttgtgtgaaaatggtggttga
 |||||||||||||| ||||| |||||||||||||| || ||||| || |  |||||||||||||||||||| ||| ||||||| |   | ||||||||||| |  |   |    || ||  ||| | |  |   |  |  |    ||  ||   |       |   |     ||| |     | |        ||| || 
AGCCGTCCACAAGGGTATGCCTCACAAGTTCTACCACGGGCGCACCGGCATCGTCTGGAACGTCACCAAGCGTGCCGTCGGTGTCGTGATGAACAAGCAGgtatgattgaccttctccctccctcccccgaagccgaagccgcctggtcgtgggagctcccccttcctgcttcgttctagggtttttccttctttggctg-

upper sequence: Vv08s0007g06890.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S107_181V6.1 (Physcomitrella patens), 5'ss of exon 1
CGCCGTCCACAAGGGCATGCCCCACAAGTTCTACCATGGCCGCACTGGTAAGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAGgtctctcctctacatctctatctctctctgatgtgttgttgttgtgttttgatcgtagtttatgggtttaatgttttgtttgtgtgaaaatggtggttga--
 || ||||||||||| ||||| |||||||||||||| || ||||| || |  |||||||||||||||||||||||| | ||||| |   | ||||||||||| |   ||||   |  || |    || |  | |  | |||  |  | |   ||    || |||  |||  |  | ||  || ||           ||    
TGCTGTCCACAAGGGTATGCCTCACAAGTTCTACCACGGACGCACCGGCATCGTCTGGAACGTCACCAAGCGCGCCGTTGGTGTCGTGATGAACAAGCAGgtatggtctctttgtacctcttcggctgtcgtctacttttggag-atgtctgtctggcttaatgactttcgt-ctgtgggtgcgtcttcgccactattctcg

upper sequence: Vv08s0007g06890.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S298_23V6.1 (Physcomitrella patens), 5'ss of exon 1
CGCCGTCCACAAGGGCATGCCCCACAAGTTCTACCATGGCCGCACTGGTAAGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAGgtct-----ctcctctacatctctatctct-ctctgatgtgttgttgttgtg----ttttgatcgtagttta--tgggtttaatgttttgtttgtgtgaaaatggtggttga
 |||||||||||||| |||||||||||||||||||| || ||||| ||||  |||||||| ||||||||||||||  | ||||| |   | ||||||||||| |      |  | |||    | |   |   |||  || ||| ||||||||    || ||  | ||  | |   |  | ||   || ||||| |||  |            
AGCCGTCCACAAGGGAATGCCCCACAAGTTCTACCACGGGCGCACCGGTATCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgttttttttacgatccaacggcaattcttgtg-gtttttgttgtgccccttgtgtccttacatcagacgcatgtagcattctgtttctgtccat-----------

upper sequence: Vv08s0007g06890.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EFJ28214 (Selaginella moellendorffii), 5'ss of exon 1
CGCCGTCCACAAGGGCATGCCCCACAAGTTCTACCATGGCCGCACTGGTAAGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAGgtctctcctctacatc--tctatctctc---tctgatgtgttgttgttgtgttttgatcgtagttt----atgggtttaatgttttgtttgtgtgaaaatggtggttga
|||  |||||||||||||||| ||||| || ||||| |||||||| ||    || ||||| ||||||||||||||  |||| || ||  | ||||||||||| |  |      |||  || |||| ||   | | |  | ||    ||    || |||    ||||    | |  ||| ||||    ||  ||||    |  || | | 
CGCGATCCACAAGGGCATGCCGCACAAATTTTACCACGGCCGCACCGGGGTTGTGTGGAATGTCACCAAGCGCGCGGTCGGAGTCGAGATGAACAAGCAGgtatgcctcgcggatcgatcaatctttcgagttttagctctttcctttccaattcgatgtgggttttcgcaagattttgatgtgg-attcctgtgcttcttctgctag-

upper sequence: Vv08s0007g06890.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EFJ29711 (Selaginella moellendorffii), 5'ss of exon 1
CGCCGTCCACAAGGGCATGCCCCACAAGTTCTACCATGGCCGCACTGGTAAGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAGgtctctcctctac--atctctatctctctctgatgtgttgttgttgtgttttgatcgtagtttatgggtttaatgttttgtttgtgtgaaaatggtggttga
|||  |||||||||||||||| ||||| |||||||| |||||||| ||    || ||||| ||||||||||||||  |||| || ||  | ||||||||||| |  |    |   |||| |   ||| |||  |    | | | ||||  ||      || || ||   |  ||  || | || |      |          
CGCGATCCACAAGGGCATGCCGCACAAATTCTACCACGGCCGCACCGGGGTTGTGTGGAATGTCACCAAGCGCGCGGTCGGAGTCGAGATGAACAAGCAGgtatgcctcgcatcaatcttttcgtctttctattccaat-tcgatgtgggttttcgcaagattttgatgtggattcttggcttcttctgctag---------

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|37188184|gb|CF607533.1|CF607533
EST:     AGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAG                         GTGGGTAACAGGATAATCAAGAAGCGGATCCATGTGCGAGTGGAGCATGTG
genomic: AGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAGgtctctcctc ... cccaatccagGTGGGTAACAGGATAATCAAGAAGCGGATCCATGTGCGAGTGGAGCATGTG
EST: gi|30296896|gb|CB973690.1|CB973690
EST:     AGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAG                         GTGGGTAACAGGATAATCAAGAAGCGGATCCATGTGCGAGTGGAGCATGTG
genomic: AGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAGgtctctcctc ... cccaatccagGTGGGTAACAGGATAATCAAGAAGCGGATCCATGTGCGAGTGGAGCATGTG
EST: gi|71871499|gb|DT020554.1|DT020554
EST:     AGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAG                         GTGGGTAACAGGATAATCAAGAAGCGGATCCATGTGCGAGTGGAGCATGT
genomic: AGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAGgtctctcctc ... cccaatccagGTGGGTAACAGGATAATCAAGAAGCGGATCCATGTGCGAGTGGAGCATGT
EST: gi|37184511|gb|CF603865.1|CF603865
EST:     AGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAG                         GTGGGTAACAGGATAATCAAGAAGCGGATCCATGTGCGAGTGGAGCATGTG
genomic: AGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAGgtctctcctc ... cccaatccagGTGGGTAACAGGATAATCAAGAAGCGGATCCATGTGCGAGTGGAGCATGTG
EST: gi|34416327|gb|CF415081.1|CF415081
EST:     AGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAG                         GTGGGTAACAGGATAATCAAGAAGCGGATCCATGTGCGAGTGGAGCATGTG
genomic: AGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAGgtctctcctc ... cccaatccagGTGGGTAACAGGATAATCAAGAAGCGGATCCATGTGCGAGTGGAGCATGTG
EST: gi|37188484|gb|CF607833.1|CF607833
EST:     AGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAG                         GTGGGTAACAGGATAATCAAGAAGCGGATCCATGTGCGAGTGGAGCATGTG
genomic: AGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAGgtctctcctc ... cccaatccagGTGGGTAACAGGATAATCAAGAAGCGGATCCATGTGCGAGTGGAGCATGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCCGTCCACAAGGGCATGCCCCACAAGTTCTACCATGGCCGCACTGGTAAGGTCTGGAACGTCACCAAGCGCGCCATCGGTGTTGAAGTAAACAAGCAGgtctctcctctacatctctatctctctctgatgtgttgttgttgtgttttgatcgtagtttatgggtttaatgttttgtttgtgtgaaaatggtggttga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaatg