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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttacttttctgtgttgctaacactctaatcattgtagttttcacggatttgtatttttttcttactaaatctagactattcgttcatttccagTTTGATTATCTCAAGAGTTTGGAAATAGAGGAGAAAATCAATAAGATTAGATGGTGTCAAACAGCTAACAATGCATTGTTTCTTCTCTCCACCAATGACA

Basic information

species Vitis vinifera
transcript Vv11s0016g02550.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 3
-----gtatt-tacttttctgtgttgctaacactctaatcat-tgtagttttcacggatttgtatttttttcttactaaatctagactattcgttcatttccagTTTGATTATCTCAAGAGTTTGGAAATAGAGGAGAAAATCAATAAGATTAGATGGTGTCAAACAGCTAACAATGCATTGTTTCTTCTCTCCACCAATGACA
     | |||  | | || ||   ||||     | |  || |   |   || |  | || || |   |    |  |||  | |     ||    |   ||| |||||||||| ||||| |||||||||||||||||||| ||||| ||||| || ||||| || ||||| || ||| || | |  ||||| || || ||||| |
atgaagcattacattattgtgctatgctcttgttttgttcttgcttgaattacttgcatatggaaactcacat--ctatgtttttttgatgaactg--ttctagTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA

upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 3
gtatttacttttctgtgttgctaacactctaatcattgtagttttcacggatttgtatttttttcttactaaatctagactattcgttcattt--ccagTTTGATTATCTCAAGAGTTTGGAAATAGAGGAGAAAATCAATAAGATTAGATGGTGTCAAACAGCTAACAATGCATTGTTTCTTCTCTCCACCAATGACA
             | | ||| ||  |  ||||    | ||||    | | |  |||| ||| |  |   |||  |||   | |    ||||      ||||||||||||| ||||| |||||||| || ||||| || || ||||| |  ||||| |||||||| ||    |||||||||||||| ||||| ||||| |
------------gtatattg-tacaagactaactgct-tagtg---aagtacctgtaatttctgttgtttaa--ctaatttgtcttgtcatgcgattagTTTGATTATCTGAAGAGCTTGGAAATTGAAGAGAAGATTAACAAGATAAAGTGGTGCCAAACAGCAAATGGAGCATTGTTTCTTCTGTCCACAAATGATA

upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 3
gtatttacttttctgtgttgctaacactctaatcattgtagttttcacggatttgtatttttttcttactaaatctagactattcgttcatttccagTTTGATTATCTCAAGAGTTTGGAAATAGAGGAGAAAATCAATAAGATTAGATGGTGTCAAACAGCTAACAATGCATTGTTTCTTCTCTCCACCAATGACA
|||| | ||        ||| |||     |  |  |  | || |||  | |||   | ||     ||  ||||   |   | ||     ||   |||||||||||||| ||||| |||||||| || ||||| || ||  | || | |||||||||| |||| ||   |||||||| |||||| ||||| |||||||
gtatattctcacaaacattgttaag----tggtattatttgtcttc-tgaatt---acttgaaatttgataaagtgatgttgttatggaat---cagTTTGATTATCTTAAGAGCTTGGAAATTGAAGAGAAGATTAACCAAATAAAATGGTGTCAAGCAGCAAATGGTGCATTGTATCTTCTATCCACAAATGACA

upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 3
gtatttacttttctgtgttgc-taacactctaatcattgtagttttcacggatttgtatttttttcttactaaatctagactattcgttcatttc--cagTTTGATTATCTCAAGAGTTTGGAAATAGAGGAGAAAATCAATAAGATTAGATGGTGTCAAACAGCTAACAATGCATTGTTTCTTCTCTCCACCAATGACA
|   ||  | |    |   |  |  |  |    |  ||| | ||       | || ||| ||  |  | |    | |     ||  |||   ||   |||||||||||| | ||||||||||||||||||||||| |||||||| ||||| ||||| || || |||||   |||   ||| || || || || |||||||
gggattgttctgagatacagtatggcgttgattttgttgcacttcgtttccagttctatcttactgatgcctgcttttttgaatatgtttggttatgcagTTTGATTATTTGAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGGTGGTGCCAGACTGCTAATGCTGCTCAGTTCCTACTTTCTACAAATGACA

upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------------------gtatttacttttctgtgttgctaacactctaatcattgtagttttcacggatttgtatttttttcttactaaatctagactattcgttc-----------atttc------cagTTTGATTATCTCAAGAGTTTGGAAATAGAGGAGAAAATCAATAAGATTAGATGGTGTCAAACAGCTAACAATGCATTGTTTCTTCTCTCCACCAATGACA
                                                                          || || | ||    |  |  || ||   |     ||  |  |||      |||| |  || |  |||  | ||  |   | |||| |            |||||      |||||||||||  | ||||||||||||||||||||||| |||||||| |||||||||||||| || || |||   ||   |||  |  | || || |||||||
gtaatgttagcaacgctaaggtgagtcgtggtaatttttcaagattgcgcccacatagttttctagaatattgatagtttccttaaaatcattatatcaacttctctttttcatatttactaagtttgcaagttatctttatcatattgaccgtgttcggtttacgatactgtatttctttctgcagTTTGATTACTTGAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGTCAGACTGCCAACGCCGCTCAGTTCTTAATTTCTACGAATGACA

upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S10_312V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------------------------------------gtatttacttttctgtgtt-gctaacactctaatcattgtagttttcacggatttgtatttttttcttactaaa---tctagactattcgttcatttccagTTTGATTATCTCAAGAGTTTGGAAATAGAGGAGAAAATCAATAAGATTAGATGGTGTCAAACAGCTAACAATGCATTGTTTCTTCTCTCCACCAATGACA
                                                                             ||    || | ||||   | |    |  |  |   ||   | ||   | |||   |  |||    |  | ||   | | |  |  |  ||  | | |||||||||||  | || ||||||||||| |||||||| |||||||| || ||||||||  | ||  ||||   |||    || || |||||||| ||||| |
gtacgttcttgcacttctcttgagcgttagatttccatgtttcactttatttttggtttctacgtgtcacctcaatcataagtttctatgtgccaggtggagcatttttttctgatttgttgtagcattgacaagtttgatgtcttgaactgttttgtttggtactttttgtgcagTTTGATTACTTGAAAAGTTTGGAAATTGAGGAGAAGATCAATAAAATCAGATGGTGCGACACTACTAATGGTGCCCGATTGCTGCTCTCCACAAATGATA

upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 3
gtatttacttttctgtgttgctaacactctaat--cattgtagttttcacggatttgtatttttttcttactaaatcta--gactattcgttcatttccagTTTGATTATCTCAAGAGTTTGGAAATAGAGGAGAAAATCAATAAGATTAGATGGTGTCAAACAGCTAACAATGCATTGTTTCTTCTCTCCACCAATGACA
 | | ||    |     |||     | || | |  ||||  | || |     | |  ||||||      ||    | |   || | |   ||  | | ||||| ||||| || ||||||||||||||||||||||| ||||| || || |||||||| || ||  | ||   |||   |||||| || || || |||||||
-tgtgtagggatactgtttgacggtaatccagttgcattacacttgttggtcaatcctattttacgaacacgtgcttttctgaatgtattttgttatgcagTTCGATTACCTGAAGAGTTTGGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACA

upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 3
gtatttacttttctgtgttgctaacactctaatcattgtagttttcacggatttgtatttttt--tcttactaaatctagactattcgt-tcatttccagTTTGATTATCTCAAGAGTTTGGAAATAGAGGAGAAAATCAATAAGATTAGATGGTGTCAAACAGCTAACAATGCATTGTTTCTTCTCTCCACCAATGACA
 |||||  | |  ||| ||| |        ||  |||||| |  |      ||    ||   |  || |  | | | | |  ||| | | |  ||| |||||||||||  | ||||||||||||||||||||||| |||||||| ||||||||||| || || || ||    ||   |||||| || || |||||||| |
ttatttgttgtgttgttttgattttttgaaaaaaattgtaataattttaatttgaagttcactgatcgttttcactttcgtatatgcttcttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATA

upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ09063 (Selaginella moellendorffii), 3'ss of exon 3
gtatttacttttctgtgttgctaacactctaatcattgtagttttcacggatttgtatttttttcttactaaatctagactattcgttcatttccagTTTGATTATCTCAAGAGTTTGGAAATAGAGGAGAAAATCAATAAGATTAGATGGTGTCAAACAGCTAACAATGCATTGTTTCTTCTCTCCACCAATGACA
                                    ||   ||         ||| |   | ||  | ||| ||      | ||    | |  ||||||||| || ||||||||  |||| |||||||| || ||||| || || ||||||||||| || ||||||   ||    ||| || | ||||| |||||||
-----------------------------------gtgcgcttgctctatcgttgaagcgtgttgatgctacattacttttgttttggcttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA

upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 3
gtatttacttttctgtgttgctaacactctaatcattgtagttttcacggatttgtatttttttcttactaaatctagactattcgttcatttcc--agTTTGATTATCTCAAGAGTTTGGAAATAGAGGAGAAAATCAATAAGATTAGATGGTGTCAAACAGCTAACAATGCATTGTTTCTTCTCTCCACCAATGACA
                                    ||   ||         ||| |   | ||  | ||| ||      | ||  ||   ||||  ||||||| || ||||||||  |||| |||||||| || ||||| || || ||||||||||| || ||||||   ||    ||| || | ||||| |||||||
-----------------------------------gtgcgcttgctctatcgttgaagcgtgttgatgctacattactttttttttttggcttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA

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|30134123|gb|CB919461.1|CB919461
EST:     CACATCCTGAGTTCCGGTATAAAACAGAGTTTCAAAGTCACGAACCTGAG                         TTTGATTATCTCAAGAGTTTGGAAATAGAGGAGAAAATCAATAAGATTAGA
genomic: CACATCCTGAGTTCCGGTATAAAACAGAGTTTCAAAGTCACGAACCTGAGgtatttactt ... tcatttccagTTTGATTATCTCAAGAGTTTGGAAATAGAGGAGAAAATCAATAAGATTAGA
EST: gi|27755257|gb|CB036012.1|CB036012
EST:     CACATCCTGAGTTCCGGTATAAAACAGAGTTTCAAAGTCACGAACCTGAG                         TTTGATTATCTCAAGAGTTTGGAAATAGAGGAGAAAATCAATAAGATTAGA
genomic: CACATCCTGAGTTCCGGTATAAAACAGAGTTTCAAAGTCACGAACCTGAGgtatttactt ... tcatttccagTTTGATTATCTCAAGAGTTTGGAAATAGAGGAGAAAATCAATAAGATTAGA
EST: gi|71860554|gb|DT009609.1|DT009609
EST:     CACGAACCTGAG                         TTTGATTATCTCAAGAGTTTGGAAATAGAGGAGAAAATCAATAAGATTAGA
genomic: CACGAACCTGAGgtatttactt ... tcatttccagTTTGATTATCTCAAGAGTTTGGAAATAGAGGAGAAAATCAATAAGATTAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcacggatttgtatttttttcttactaaatctagactattcgttcatttccagTTTGATTATCTCAAGAGTTTGGAAATAGAGGAGAAAATCAATAAGATTAGATGGTGTCAAACAGCTAACAATGCATTGTTTCTTCTCTCCACCAATGACA
                        tactaaa  putative branch site (score: 1)
                                            ttcatttcc  putative PPT
        atttgtatttttttct  TA-rich tract