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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCAACAACATTCGGTATTATATCCTTCCCGACAGCTTGAATCTTGAGACCCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAGgtattgctctatctctttggctctaattctatgcattttcgtatgatttatgttccccttgttttaattttttttaatgcttttttccatttcag

Basic information

species Vitis vinifera
transcript Vv07s0104g00160.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os02g37430.1 (Oryza sativa), 5'ss of exon 3
GGCAACAACATTCGGTATTATATCCTTCCCGACAGCTTGAATCTTGAGACCCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAGgt------attgctctatctctttggctctaattctatgcattttcgtatgatttatgttccccttgttttaattttttttaatgcttttttccatttcag
|| ||||||||||| ||||| || ||||| |||||||| || || |||||  |  |||| || || ||||| ||||||||| | ||||||||||| ||||||      |||| | | ||||| |   |  | ||   ||   |   | |   ||| |  |   |     |||||        |                  
GGAAACAACATTCGCTATTACATTCTTCCTGACAGCTTAAACCTGGAGACATTGCTGGTTGAGGATACACCGAGGGTCAAGGCTAAGAAGCCAACTGCAGgtttgataattgttttgtctctctaagttgattttactgagctgctgaactgtttgt-ctgatcaaaccttaatccggaaacag-----------------

upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G416061_T01 (Zea mays), 5'ss of exon 4
GGCAACAACATTCGGTATTATATCCTTCCCGACAGCTTGAATCTTGAGACCCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAGgt-attgctctatctctttggctctaattctatgcattttcgtatgatttatgttccccttgttttaattttttttaatgcttttttccatttcag
|| |||||||| || |||||||||||||| |||||| | || || |||||  |  |||| || || ||||| ||||||||||| |||||||| ||  | ||| |  | ||| | |||     |  ||   |    |||| |       |    ||  | ||   |  || ||  | ||                  
GGAAACAACATCCGCTATTATATCCTTCCTGACAGCCTAAACCTGGAGACTTTGCTGGTTGAGGAAACACCAAGGGTCAAGCCTAAGAAGCCTACTTCTGgtcagagttctttttctcccatttcaaccttcgagatttaccacctgctagcattatcatttcatccatcttcatcaaaaaccag-----------

upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA03G30880.1 (Glycine max), 5'ss of exon 3
GGCAACAACATTCGGTATTATATCCTTCCCGACAGCTTGAATCTTGAGACCCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAGgtattgctctatctctttggctctaattctatgcattttcgtatgatttatgttccccttgttttaattttttttaatgcttttttccatttcag--------------------
|||||||||||||| |||||||||||||| ||||||||||||||||||||  |  |||| |||||| | |||| | ||||||| ||||||||||| || ||||||| | ||| | |||| || | | |  |   || ||  |  ||  |   ||    |    || | | || | || |  | | |   | |||                     
GGCAACAACATTCGATATTATATCCTTCCTGACAGCTTGAATCTTGAGACTTTACTGGTTGAAGAGGCTCCTAAGATCAAGCCTAAGAAGCCAACTGCTGgtattg-tatat-tatttgactgtcactaaa---atgtttatcagaagttaattatgttcaggttgactgttatcaagggatatctggttctcaaagttttgattttatttgcag

upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA19G33700.1 (Glycine max), 5'ss of exon 3
GGCAACAACATTCGGTATTATATCCTTCCCGACAGCTTGAATCTTGAGACCCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAGgtattgctctatctctttggctctaattctatgcattttcgtatg--atttatgttccccttg-ttttaattt-----tttttaatgcttt---tttccatttcag------
|||||||||||||| |||||||||||||| ||||||||||||||||||||  |  |||| |||||| | |||| | ||||||| ||||||||||| || ||||||| | ||| | |||| || | | |  |    || ||  | |  | ||||||||   |||  | | || |     | | |  | ||     |||  |||| |       
GGCAACAACATTCGATATTATATCCTTCCTGACAGCTTGAATCTTGAGACTTTACTGGTTGAAGAGGCTCCTAAGATCAAGCCTAAGAAGCCAACTGCTGgtattg-tatat-tatttgactttcactagaatgtttatcagaggccaattatgttcaggttgactgttatctaggaatatctggttctcaaagttttgattttatttacag

upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA02G10640.1 (Glycine max), 5'ss of exon 4
GGCAACAACATTCGGTATTATATCCTTCCCGACAGCTTGAATCTTGAGACCCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAGgtattgctc------tatctctttggctctaattc-tatgcattttcgtatgatt---------tatgttccccttgttttaattttttttaatgcttttttccatttcag
|| |||||||| || || ||||| ||||| ||||||||||||||||||||| |  |||||||||||||||| | | |||| |||||||||||||| || |||| || |       |  ||       | | || | ||  || ||   | | |||         |  |||||||  |||||||||||     ||  |  || |  || |||
GGTAACAACATCCGTTACTATATTCTTCCTGACAGCTTGAATCTTGAGACCTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgtttatagtttgactacaaaattttcatccatactcaattcactctaattgtttcttggtgagttccccaggttttaattttagcatattttcattacatttccag

upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA18G52210.1 (Glycine max), 5'ss of exon 4
GGCAACAACATTCGGTATTATATCCTTCCCGACAGCTTGAATCTTGAGACCCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAGgtattgc------tctatct-----ctttggctcta-attctatgcattttcgtatgatttatgt---tccccttgttttaattttttttaatgcttttttccatttcag--
 | |||||||| || || || || ||||| |||||||||||||| ||||||||  | |||||||||||||||| | |||| |||||||||||||| || |||| ||       | || ||      |||   || |   || || |||| |  |    | |  ||   | ||   | ||||||||||   |    ||  |  ||||||    
-GTAACAACATCCGTTACTACATTCTTCCTGACAGCTTGAATCTCGAGACCCTGCTTGTGGAAGAGACACCTAAGATCAAACCCAAGAAGCCAACTGCTGGtactgtatatagtttaactacaaaatttacatccatgctcaattcattctaattgtttcttggtgagttcctcaggtttaatttttaacatattttcatcgcatttccagg

upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT4G02840.2 (Arabidopsis thaliana), 5'ss of exon 4
GGCAACAACATTCGGTATTATATCCTTCCCGACAGCTTGAATCTTGAGACCCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAGgtattgctctatctctttggctctaattctatgcattttcgtatgatttatgttccccttgttttaattttttttaatgcttttttccatttcag
|| ||||||||||| |||||||| ||||| ||||| |||||||| |||||  |  |||| ||||| || || ||  |||| ||||| |||||||| |||||||       || |||||      ||  |||||| |||   | || |||   ||   |||    | || ||| | | || | | ||   | ||||
GGAAACAACATTCGCTATTATATTCTTCCGGACAGTTTGAATCTGGAGACTTTGCTGGTTGAAGACACTCCAAGAATCAAACCCAAAAAGCCAACTGCAGgtaacaaaacatttcttttttctgaa--ctatgcctttgtttttgtttttgtttttgcttagactcatctttct-attgttctctttggtatcag

upper sequence: Vv07s0104g00160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: PP1S37_118V6.1 (Physcomitrella patens), 5'ss of exon 3
GGCAACAACATTCGGTATTATATCCTTCCCGACAGCTTGAATCTTGAGACCCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAGgtattgctct--atctctttggctctaa--ttctatgcattttcgtatgatttatgttccccttgttttaattttttttaatgcttttttccatttcag-
|||||||||||||| ||||||||| | || ||||||||||||||||| || ||| | || || || |||||  | || ||   |||||| ||    |||||| |   | |  | | |||||  ||  |  |  |||  | |    | |  ||  |  |   |||   |  | || ||  | ||  |     ||  |    
GGCAACAACATTCGATATTATATCTTGCCTGACAGCTTGAATCTTGACACGCTTCTTGTTGACGATACACCGCGCGTGAAAGTCAAGAAACCTGTTGCAGgtctctttgttaaaccctttgagtcagaagtcttatctagtactctttttttattccttggctttactagaattgttacattgtatcccagcacgttgtg

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|77578860|gb|DV218230.1|DV218230
EST:     CCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAG                         GGAGACCCATGGGACGTGGGCGGGGCCGTGGTCGCGGGCGTGGACGTGGGC
genomic: CCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAGgtattgctct ... tccatttcagGGAGACCCATGGGACGTGGGCGGGGCCGTGGTCGTGGGCGTGGACGTGGGC
EST: gi|110715316|gb|EE093229.1|EE093229
EST:     CCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAG                         GGAGACCCATGGGACGTGGGCGGGGCCGTGGTCGCGGGCGTGGACGTGGGC
genomic: CCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAGgtattgctct ... tccatttcagGGAGACCCATGGGACGTGGGCGGGGCCGTGGTCGTGGGCGTGGACGTGGGC
EST: gi|32246247|gb|CD712066.1|CD712066
EST:     CCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAG                         GGAGACCCATGGGACGTGGGCGGGGCCGTGGTCGCGGGCGTGGACGTGGGC
genomic: CCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAGgtattgctct ... tccatttcagGGAGACCCATGGGACGTGGGCGGGGCCGTGGTCGTGGGCGTGGACGTGGGC
EST: gi|71873275|gb|DT022330.1|DT022330
EST:     CCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAG                         GGAGACCCATGGGACGTGGGCGGGGCCGTGGTCGCGGGCGTGGACGTGGGC
genomic: CCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAGgtattgctct ... tccatttcagGGAGACCCATGGGACGTGGGCGGGGCCGTGGTCGTGGGCGTGGACGTGGGC
EST: gi|27583587|gb|CB006282.1|CB006282
EST:     CCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAG                         GGAGACCCATGGGACGTGGGCGGGGCCGTGGTCGCGGGCGTGGACGTGGGC
genomic: CCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAGgtattgctct ... tccatttcagGGAGACCCATGGGACGTGGGCGGGGCCGTGGTCGTGGGCGTGGACGTGGGC
EST: gi|110726188|gb|EE101761.1|EE101761
EST:     CCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAG                         GGAGACCCATGGGACGTGGGCGGGGCCGTGGTCGCGGGCGTGGACGTGGGC
genomic: CCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAGgtattgctct ... tccatttcagGGAGACCCATGGGACGTGGGCGGGGCCGTGGTCGTGGGCGTGGACGTGGGC
EST: gi|77578278|gb|DV217913.1|DV217913
EST:     CCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAG                         GGAGACCCATGGGACGTGGGCGGGGCCGTGGTCGCGGGCGTGGACGTGGGC
genomic: CCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAGgtattgctct ... tccatttcagGGAGACCCATGGGACGTGGGCGGGGCCGTGGTCGTGGGCGTGGACGTGGGC
EST: gi|110717228|gb|EE092911.1|EE092911
EST:     CCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAG                         GGAGACCCATGGGACGTGGGCGGGGCCGTGGTCGCGGGCGTGGACGTGGGC
genomic: CCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAGgtattgctct ... tccatttcagGGAGACCCATGGGACGTGGGCGGGGCCGTGGTCGTGGGCGTGGACGTGGGC
EST: gi|30131461|gb|CB916800.1|CB916800
EST:     CCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAG                         GGAGACCCATGGGACGTGGGCGGGGCCGTGGTCGCGGGCGTGGACGTGGGC
genomic: CCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAGgtattgctct ... tccatttcagGGAGACCCATGGGACGTGGGCGGGGCCGTGGTCGTGGGCGTGGACGTGGGC
EST: gi|110690320|gb|EE067314.1|EE067314
EST:     CCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAG                         GGAGACCCATGGGACGTGGGCGGGGCCGTGGTCGCGGGCGTGGACGTGGGC
genomic: CCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAGgtattgctct ... tccatttcagGGAGACCCATGGGACGTGGGCGGGGCCGTGGTCGTGGGCGTGGACGTGGGC
EST: gi|110419993|gb|EC986253.1|EC986253
EST:     CCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAG                         GGAGACCCATGGGACGTGGGCGGGGCCGTGGTCGCGGGCGTGGACGTGGGC
genomic: CCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAGgtattgctct ... tccatttcagGGAGACCCATGGGACGTGGGCGGGGCCGTGGTCGTGGGCGTGGACGTGGGC
EST: gi|71872888|gb|DT021943.1|DT021943
EST:     CCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAG                         GGAGACCCATGGGACGTGGGCGGGGCCGTGGTCGCGGGCGTGGACGTGGGC
genomic: CCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAGgtattgctct ... tccatttcagGGAGACCCATGGGACGTGGGCGGGGCCGTGGTCGTGGGCGTGGACGTGGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCAACAACATTCGGTATTATATCCTTCCCGACAGCTTGAATCTTGAGACCCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAGgtattgctctatctctttggctctaattctatgcattttcgtatgatttatgttccccttgttttaattttttttaatgcttttttccatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC