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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTCTGAGAGTTATTCTGGCCAAAGAAGAATTGGCACCTGATGTTGGTTTGGAAGCAGTTGCAAATATGACTGATGGGTATTCTGGAAGTGACCTAAAGgttgcctaatctcctctctattatatatgatatgccttaaacatagaactttggcctatattagtttcctctaatcaaattaccgtttgcag

Basic information

species Vitis vinifera
transcript Vv07s0005g00200.t01
intron # 24
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 5'ss of exon 24
lower sequence: GLYMA10G02410.1 (Glycine max), 5'ss of exon 21
AATTCTGAGAGTTATTCTGGCCAAAGAAGAATTGGCACCTGATGTTGGTTTGGAAGCAGTTGCAAATATGACTGATGGGTATTCTGGAAGTGACCTAAAGgttgcct---aatctcctctctattatatatgat-atgccttaaacatagaactttggcctatattagtttcctctaatcaaattaccgtttgcag-------
|||| | || |||||| | || ||||||||||||||||||||||||| ||| |||||| | ||||||||||||||||| |||||||| ||||||||||||||||  |    || |    |||| |  |  |  | ||  ||     | |  || |     || || |  | |   |   |  |||    | |           
AATTGTTAGTGTTATTTTAGCAAAAGAAGAATTGGCACCTGATGTTGATTTCGAAGCAATAGCAAATATGACTGATGGATATTCTGGGAGTGACCTAAAGgttgtatttctatgtatcttctacttcaattcttgatcgctggggaagatgacatgattttacatgaaatactcattgactcattgttatcttttcactgcag

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 5'ss of exon 24
lower sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 21
AATTCTGAGAGTTATTCTGGCCAAAGAAGAATTGGCACCTGATGTTGGTTTGGAAGCAGTTGCAAATATGACTGATGGGTATTCTGGAAGTGACCTAAAGgttgcctaatctcctctctattatatatgatatgccttaaacat--agaactttggcct---atattagtttcctctaatcaaattaccgtttgcag
|||| | ||||||||| | || |||||||| |||||||||||||||| ||| |||||| | ||||||||||||||||| ||||| |||||||||||||||||||  |    | || | |||  | ||    |   ||| | ||    | |   || | |   ||| |  ||  |||      |  |   |  |||||
AATTGTCAGAGTTATTTTAGCAAAAGAAGATTTGGCACCTGATGTTGATTTTGAAGCAATAGCAAATATGACTGATGGATATTCAGGAAGTGACCTAAAGgttgtat----ttctatatatcttttacttcaattcttgatcactggggaagatgacatgaaatactcattgactcattgttatcttttgactgcag

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 5'ss of exon 24
lower sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 24
AATTCTGAGAGTTATTCTGGCCAAAGAAGAATTGGCACCTGATGTTGGTTTGGAAGCAGTTGCAAATATGACTGATGGGTATTCTGGAAGTGACCTAAAGgttgcctaatctcctctctattatatatgatatgcctta----------aacatagaactttggcctatattag-tttcctctaatcaaattaccgtttgcag
|||||| ||||| ||| | |  |||||||| ||||||||||| |||| ||| |||||| | || |||||||||||||| |||||||| ||||||||||||||||  |       | | |||| |  |     |  |||           ||  ||  |  |    ||| || |  | | |||      |  |   | ||||||
AATTCTCAGAGTCATTTTAGTGAAAGAAGATTTGGCACCTGACGTTGATTTTGAAGCAATAGCTAATATGACTGATGGATATTCTGGGAGTGACCTAAAGgttgtatgtatatttatgtatttttcacttcctttcttggtttctggagaaggtaccatctgtttctacataaaatattctcattgttatcttttgattgcag

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 5'ss of exon 24
lower sequence: GLYMA02G17410.1 (Glycine max), 5'ss of exon 20
AATTCTGAGAGTTATTCTGGCCAAAGAAGAATTGGCACCTGATGTTGGTTTGGAAGCAGTTGCAAATATGACTGATGGGTATTCTGGAAGTGACCTAAAGgttgccta---atctcctctctattatatatgata--tgcctta-aacatagaactttggcctatattagtttcctctaatcaaattacc-gtttgcag
|||||| || || ||| |||| |||||||| |||||||||||  ||| ||| |||||| | || |||||||| ||||| |||||||| |||||| |||||||||  ||   || |  | |  | |   | |  |   ||| | | ||  ||| |  |    ||| || |  |     || |   ||     | ||||||
AATTCTCAGTGTCATTTTGGCGAAAGAAGATTTGGCACCTGACATTGATTTTGAAGCAATAGCTAATATGACAGATGGATATTCTGGGAGTGACTTAAAGgttgtatatctatgtatttttcacttcctctcttggttgcttgagaaggtagcatctctttctacataaaatattcttattgttatcgtttgattgcag

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 5'ss of exon 24
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 5'ss of exon 24
AATTCTGAGAGTTATTCTGGCCAAAGAAGAATTGGCACCTGATGTTGGTTTGGAAGCAGTTGCAAATATGACTGATGGGTATTCTGGAAGTGACCTAAAGgttgcctaatctcctctctattatatatgatatgccttaaacatagaactttggcctatattagtttcctctaatcaaattaccgtttgcag
 ||  |||| |||||||| || ||||||||| | ||||| || || | ||| |||||  | ||||||||||| |||||||| || ||||||||| |||||||  |    |    |  |  |        || | | |      || ||      |  | |   || | || |  |    || | |       
GATCTTGAGCGTTATTCTAGCAAAAGAAGAAATAGCACCAGACGTCGATTTAGAAGCTATAGCAAATATGACAGATGGGTACTCAGGAAGTGACTTAAAGgtctcgactttctataaccttccctctcaatctccttcccctgtaaaaa---aactcacacacgtattcttt--tttggttgcag-------

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|34547757|gb|CF515989.1|CF515989
EST:     TGGAAGCAGTTGCAAATATGACTGATGGGTATTCTGGAAGTGACCTAAAG                         AATCTTTGTGTGACTGCAGCCCACT-TCG-ATCGAAGAGAGATTTTAGAAC
genomic: TGGAAGCAGTTGCAAATATGACTGATGGGTATTCTGGAAGTGACCTAAAGgttgcctaat ... ccgtttgcagAATCTTTGTGTGACTGCAGCCCACTGTCCCAT--AAGAGAGATTTTAGAAC
EST: gi|37183620|gb|CF602974.1|CF602974
EST:     TGGAAGCAGCTGCAAATATGACTGATGGGTATTCTGGAAGTGACCTAAAG                         AATCTTTGTGTGACTGCAGCCCACTGTCCCATAAGAGAGATTTTAGAACGA
genomic: TGGAAGCAGTTGCAAATATGACTGATGGGTATTCTGGAAGTGACCTAAAGgttgcctaat ... ccgtttgcagAATCTTTGTGTGACTGCAGCCCACTGTCCCATAAGAGAGATTTTAGAACGA
EST: gi|30300649|gb|CB977443.1|CB977443
EST:     TGGAAGCAGTTGCAAATATGACTGATGGGTATTCTGGAAGTGACCTAAAG                         AATCTTTGTGTGACTGCAGCCCACTGTCCCATAAGAGAGATTTTAGAACG
genomic: TGGAAGCAGTTGCAAATATGACTGATGGGTATTCTGGAAGTGACCTAAAGgttgcctaat ... ccgtttgcagAATCTTTGTGTGACTGCAGCCCACTGTCCCATAAGAGAGATTTTAGAACG
EST: gi|71881952|gb|DT031007.1|DT031007
EST:     TGGAAGCAGTTGCAAATATGACTGATGGGTATTCTGGAAGTGACCTAAAG                         AATCTTTGTGTGACTGCAGCCCACTGTCCCATAAGAGAGATTTTAGAACGA
genomic: TGGAAGCAGTTGCAAATATGACTGATGGGTATTCTGGAAGTGACCTAAAGgttgcctaat ... ccgtttgcagAATCTTTGTGTGACTGCAGCCCACTGTCCCATAAGAGAGATTTTAGAACGA
EST: gi|30300714|gb|CB977508.1|CB977508
EST:     TGGAAGCAGTTGCAAATATGACTGATGGGTATTTTGGAAGTGACCTAAAG                         AATCTTTGTGTGACTGCAGCCCCCTGTCCCATAAGAGAGATTTTAGAACG
genomic: TGGAAGCAGTTGCAAATATGACTGATGGGTATTCTGGAAGTGACCTAAAGgttgcctaat ... ccgtttgcagAATCTTTGTGTGACTGCAGCCCACTGTCCCATAAGAGAGATTTTAGAACG
EST: gi|30134135|gb|CB919473.1|CB919473
EST:     TGGAAGCAGTTGCAAATATGACTGATGGGTATTCTGGAAGTGACCTAAAG                         AATCTTTGTGTGACTGCAGCCCACTGTCCCATAAGAGAGATTTTAGAACGA
genomic: TGGAAGCAGTTGCAAATATGACTGATGGGTATTCTGGAAGTGACCTAAAGgttgcctaat ... ccgtttgcagAATCTTTGTGTGACTGCAGCCCACTGTCCCATAAGAGAGATTTTAGAACGA
EST: gi|30130536|gb|CB915875.1|CB915875
EST:     TGGAAGCAGTTGCAAATATGACTGATGGGTATTCTGGAAGTGACCTAAAG                         AATCTTTGTGTGACTGCAGCCCACTGTCCCATAAGAGAGATTTTAGAACGA
genomic: TGGAAGCAGTTGCAAATATGACTGATGGGTATTCTGGAAGTGACCTAAAGgttgcctaat ... ccgtttgcagAATCTTTGTGTGACTGCAGCCCACTGTCCCATAAGAGAGATTTTAGAACGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTCTGAGAGTTATTCTGGCCAAAGAAGAATTGGCACCTGATGTTGGTTTGGAAGCAGTTGCAAATATGACTGATGGGTATTCTGGAAGTGACCTAAAGgttgcctaatctcctctctattatatatgatatgccttaaacatagaactttggcctatattagtttcctctaatcaaattaccgtttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG