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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattgataagtagcttcttttttctatcccttgatctctatagtgggttgttatttttttttttctcagctggtttctcatctttcttgttgcag

Basic information

species Vitis vinifera
transcript Vv17s0000g01550.t01
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 5'ss of exon 22
TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattgataagtagcttcttttt-tctatcccttgatctctatagtgggttgttatttttttttttctcagctggtttctcatctttcttgttgcag
|||||| ||||| ||||| |||||||||||||| || ||||| ||||| || |||||||| || ||||| ||||| |||||||| |||||| | || |||||  |  ||  ||| |   | || ||  || ||   ||  | | |  | |  |  |  || |      || |   |   |  | ||               
TGGCCCGCCTGGTACAGGAAAGACAATGCTTGCCAAAGCTGTGGCTACAGAGGCTGGTGCGAATTTCATAAATATATCAATGTCGAGCATCTCTTCAAAGgtatt--ttactaaatgattgctattagtccatggttttgtttttgcattttg--ggcatctgaaacattgtgtaccattaccacag--------------

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 22
TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattgataagtagcttcttttttctatcccttgatctctatagtgggttgttatttttttttttctcagctggtttctcatctttcttgttgcag
||| || ||||| || || || || |||||||||||||| || || |||||||| ||||| |||||||| || || |||||||||||||| ||||| ||||| || || |  |   |  || |   ||        |||  | || ||||   | |      |  || ||  ||||   | ||  | |||||  || |||
TGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgt-atgat-ggcatccaaattttgcattaa------tgaggtgtacagtgtactatg-----tgattctcaaagctaaatgctgttttttctactttcag

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: GRMZM2G042074_T01 (Zea mays), 5'ss of exon 22
TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattgataagt--agcttcttttttctatcccttga---tctctatagtgggttgttatttttttttttctcagctggtttctcatctttcttgttgcag
|||||| ||||| || || ||||||||||||||||||||||| || ||||| |||||||| || ||||| || || || |||||||||||| | || |||||  | ||  ||  |   ||| ||| |||| |  |  ||||   |||  ||  | |  | | | |    | |||  |||                          
TGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATATCGATGTCAAGCATCTCTTCAAAGgtacttatcaattggacaagcctctgttttttggcagttgagtatctgcattatagcatctaaataacctattttccag--------------------------

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: GRMZM2G435582_T01 (Zea mays), 5'ss of exon 2
TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattgata-agtagcttcttttttctatcccttgatctct-atagtgggttgttatttttttttttctcagctggtttctcatctttcttgttgcag
 || || ||||| || || || || |||||||| || || || || |||||||| || || || ||||||||||| |||||||| ||||| |||||||||||  |  || |   | | |     |  |   || |  |  | ||| |  |        |  ||| ||   | ||||                          
CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCTAAGgtattatttcacctaatgggcaactgatgagattcactactgtctcaaggctaaccagtggtttgttaactttcag--------------------------

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: GRMZM2G354532_T01 (Zea mays), 5'ss of exon 1
TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattgata-agtagcttcttttttctatcccttgatctctatagtgggttgttatttttttttttctcagctggtttctcatctttcttgttgcag
 || || ||||| || || || || |||||||| || || || || |||||||| || || || ||||||||||| |||||||| ||||| |||||||||||  |  || |   | | |     |  |   || |  |  | |||  ||                                                    
CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCTAAGgtattatttcacctaatgggcaactgatgagattcactactgtctcaag----------------------------------------------------

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: GRMZM2G157621_T03 (Zea mays), 5'ss of exon 22
TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattgataagtagcttcttttttctatcccttgatctctatagtgggttgttatttttttttttctcagctggtttctcatct-ttcttgttgcag
||| || ||||| || || ||||| |||||||| || |||||||| || || |||||||| || || ||||| || ||||||||||||||  | || |||||  |  |      | | | |  |  |  |     ||| || | ||   | ||  |||||  |||        |||| ||||    || |   | |  |||
TGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATATCAATGTCAAGCATTGCTTCAAAGgtacttgt------gcaacgttatactcatcaagtttgttcccgatttggagtacttattacttt--------gctgatttcaaccctgtaactataacag

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: GRMZM2G126453_T02 (Zea mays), 5'ss of exon 7
TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattgata-agtagcttcttttttctatcccttgatctct-atagtgggttgttatttttttttttctcagctggtttctcatctttcttgttgcag
 || || ||||| || || || || |||||||| || || || || |||||||| || || || ||||||||||| |||||||| ||||| ||||| |||||  |  || |   | | |     |  |   || |  |  | ||| |  |        |  ||| ||   | ||||                          
CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCGAAGgtattatttcacctaatgggcaactgatgagattcactactgtctcaaggctaaccagtggtttgttaactttcag--------------------------

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 13
TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattga--taagtagcttcttttttctatcccttgatctctatagtgggttgttatttttttttttctcagctggtttctcatctttcttgttgcag
 || || ||||| || || || || |||||||| || || || || |||||||| ||||| || ||||||||||| |||||||| ||||| || || |||||  |  ||||  ||    ||  ||  |     || ||||      |           |  ||  |||  | ||||                          
CGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttgacctagcgggcaactgatgagattcacttgtgtctcaagcctaaccagtggttcgtttactttcag--------------------------

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: GLYMA04G37050.1 (Glycine max), 5'ss of exon 5
TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattgataagtagcttcttttt-tctatcccttgatctctatagtgggttgttatttttttttttctcagctggtttctcatctttcttgttgcag
||| |||||||||||||| |||||||||||||| ||||| |||||||| |||||||||||||| |||||||| ||||| |||||||| ||||||||||||||||        || | |||||  |   | |||       |||||    |  |||  |  ||  |||| |||  | |  |||| ||| || |||    |||
TGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTTCCATGTCAAGTATCACATCTAAGgtta--------aatttgcttcactgggtttattttaatgtctctgctatcagttagttgttcattttatctgtgttcttttcccattttgctt----cag

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: GLYMA06G17940.1 (Glycine max), 5'ss of exon 22
TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattgataagtagcttcttttttctatcccttgatctctatagtgggttgttatttttttttttctcagctggtttctcatctttcttgttgcag
||| |||||||||||||| |||||||||||||| ||||| |||||||| |||||||||||||| |||||||| ||||| |||||||| ||||||||||||||||     |||| |    |   |   | |||       ||||| |  |  |||  |  ||  ||||  ||    |  |||| ||| || |||    |||
TGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTTCCATGTCAAGTATCACATCTAAGgtta-----gatatgc--ttcactgggtttattttaatgtctctgttatcagttagttgttcattttaactgcattcttttcccattttgctt----cag

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: GLYMA17G13850.1 (Glycine max), 5'ss of exon 20
TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattgataagtagcttcttttttctatcccttgatctctatagtgggttgttatttttttttttct-cagctggttt-ctcatct-ttcttgttgcag
||| ||||||||||| || || ||||||||||| |||||  ||||||||||||||||||| ||||||||||| ||||| |||||||| ||||||||||||||||   |||        ||   | |   | |   ||||| ||         || ||| |||  | |   | || ||  ||| ||   || || ||| | |||
TGGTCCCCCTGGAACTGGTAAAACAATGCTTGCAAAGGCAATTGCTACTGAAGCTGGTGCTAACTTCATCAACATTTCTATGTCAAGTATCACATCTAAGgttaaatttgt-------ctctctctaagtgtatattgatttcacct-----ttattagtttgctgtgcatacaactcattttcttgcctctttttgcttcag

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: GLYMA05G03270.1 (Glycine max), 5'ss of exon 18
TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattgataagtagcttcttttttctatcccttgatctctatagtgggttgttatttttttttttctcagctggtttctcatctttcttgttgcag
||| ||||||||||| || || |||||||| || |||||  | ||||||||||||||||||||||||||||| ||||| |||||||| || || ||||||||||   |||        |    |     | |   |||||||| |   |   | |||   | |   | ||    |  |||  |   | |  ||| | |||
TGGTCCCCCTGGAACTGGTAAAACAATGCTCGCAAAGGCAATAGCTACTGAAGCTGGTGCAAACTTCATCAACATTTCTATGTCAAGTATTACCTCTAAGgttaaatttgt-------ccctctccaagtgtatattgatctc-acctttattagtttgctgtgcatatcaactcatgttcttgcccctctttgcttcag

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: AT4G24860.1 (Arabidopsis thaliana), 5'ss of exon 21
TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattgataagtagcttcttttttctatcccttgatctctatagtgggttgttatttttttttttctcagctggtttctcatctttcttgttgcag
||| || |||||||| || ||||| |||||||| || || || || |  ||||||| ||| ||||||||||| || |||||||||||||||||||||||||| |    |||  | |   |      ||||| |    ||| |  | |  || |         ||||||||  |  ||  ||||     ||  |  |||||
TGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCTCAATGTCAAGCATCACATCTAAGgtaac---tgaatactctatgaaaagttctacc----gatttacacacgggatc--------tttttttcaaacttgtgttctt---cttaatactgcag

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: AT1G62130.1 (Arabidopsis thaliana), 5'ss of exon 21
------------TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattgataagtagcttcttttttctatcccttgatctctatagtgggttgttatttttttttttctcagctggtttctcatctttcttgttgcag
            ||| ||  ||||||| || ||||| |||||||| ||||| || || || ||||||||||| ||| ||||||| || |||||||||||  | |||     |  |||| |||| |||| |         |||| |     || | || |  |  |         | || |||  |  ||  ||||  ||  | |||  |   
AATTCTCTTATTTGGACCTTCTGGAACTGGAAAGACCATGCTTGCAAAGGCAGTGGCAACGGAAGCTGGTGCTAACCTCATCAACATGTCAATGTCAAGGgtaaca-----gaatatccttgaaaagttggac------tctacc----aatttatacacggaatc--------tcttgttcaaacttgtgttcttctcaatattgcag---

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: PP1S3_184V6.1 (Physcomitrella patens), 5'ss of exon 18
TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattgataagtagcttcttttttctatcccttgatctctatagtgggttgttatttttttttttctcagctggtttctcatctttcttgttgcag----------
||| || || || ||||| ||||| ||| | |||||||||||||| |||||||| || || |||||||| || ||||| ||||| | |||  | || |||||  |  ||| |       || ||       | |   ||| |   |   | || || | | ||    |  | |  |  |     || |      || |||          
TGGACCACCAGGTACAGGGAAGACTATGTTAGCTAAGGCTGTTGCAACTGAAGCAGGGGCTAACTTCATAAACATTTCCATGTCTACCATTGCTTCCAAGgtgctttttggt-------tttttcgaaagttgctacgatgt---tgaagagtagtcaatgttcaactcatgaaattataatatatgtagacattttcagttgctccaca

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: EFJ31084 (Selaginella moellendorffii), 5'ss of exon 9
TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattgataagtagcttcttttttctatcccttgatctctatagtgggttgttatttttttttttctcagctggtttctcatctttcttgttgcag
||| || || ||||| || ||||| |||||||||||||| |||||||| || ||||||||||| |||||||||||||||||||| |  ||  ||||||| || | || |                    || | | ||||   | |    | ||    |||| ||| ||| |||                          
TGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaagcact--------------------taccacgtgatag-tgttcaagtttaccgttttctttcttcgcag--------------------------

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|37186767|gb|CF606120.1|CF606120
EST:     AAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAG                         TGGTTTGGAGAGGGCGAGAAGTATGTGAAGGCCGTTTTCTCACTTGCCAGT
genomic: AAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattg ... cttgttgcagTGGTTTGGAGAGGGCGAGAAGTATGTGAAGGCCGTTTTCTCACTTGCCAGT
EST: gi|110720420|gb|EE096327.1|EE096327
EST:     AAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAG                         TGGTTTGGAGAGGGTGAGAAGTATGTGAAGGCCGTTTTCTCACTTGCCAGT
genomic: AAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattg ... cttgttgcagTGGTTTGGAGAGGGCGAGAAGTATGTGAAGGCCGTTTTCTCACTTGCCAGT
EST: gi|110711745|gb|EE088578.1|EE088578
EST:     AGCTGGTGCAAACTTCATCAATATTTCAATGTNCA-GCATCACATCTAAN                         TGGTTTGGGAGAGGT-GAGAAATATGTGAAGGCCGTTTTCTCACT-GCCAG
genomic: AGCTGGTGCAAACTTCATCAATATTTCAATGT-CAAGCATCACATCTAAGgttatcattg ... cttgttgcagTGGTTTGG-AGAGGGCGAGAAGTATGTGAAGGCCGTTTTCTCACTTGCCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattgataagtagcttcttttttctatcccttgatctctatagtgggttgttatttttttttttctcagctggtttctcatctttcttgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG