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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatatcccacaacttgctgggaaatccttccctgacccctgtttgctctttatttatactcttgagccccaaaataagcacatggaccttaattttggaattgttatttgtcttacagCTGTTCTATTTAAGTGCCATTCTCACTGTGTTCTTTTGCGGGATTGTCATGTCTCACTACACATGGCATAATGTGACTGAAAGTTCAAGAGTGACTACCA

Basic information

species Vitis vinifera
transcript Vv05s0020g01960.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os05g05590.1 (Oryza sativa), 3'ss of exon 9
gtaagatatcccacaacttgctgggaaatccttccctgacccctgtttgctctttatttatactcttgagccccaaaataagc-acatggaccttaattttggaattgt----tatttgtcttacagCTGTTCTATTTAAGTGCCATTCTCACTGTGTTCTTTTGCGGGATTGTCATGTCTCACTACACATGGCATAATGTGACTGAAAGTTCAAGAGTGACTACCA
                            |      |||     | |||  |||   |||  ||         ||||| ||    | || ||  ||  |||||    | |    ||| | | || |||||| |  || | |||| |||||||||||||||||| |  || || || ||||| || ||||| |||||||||||||| ||||| || ||  | |||||||
---------------------------ttggcagtctgtaatttctttaatctcactttgcaccagcatcttccaaagtacatgatattgatattttttttgaccctttcatatatatatatttcagCTGCTAGATCTGAGTGGCATTCTCACTGTGTTCTTCTCTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCA

upper sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA17G02560.1 (Glycine max), 3'ss of exon 7
gtaagatatcccacaacttgctgggaaatccttccctgacccctgtttgctctttatttatactcttgagccccaaaataagcacatggaccttaattttggaattgttatttgtcttacagCTGTTCTATTTAAGTGCCATTCTCACTGTGTTCTTTTGCGGGATTGTCATGTCTCACTACACATGGCATAATGTGACTGAAAGTTCAAGAGTGACTACCA
                                               | ||||  |  |  || |   | |     | |    | |   |    |||  |       |||||| | |  ||||| || | ||||||||||||||| ||||| ||||| ||||| ||||| |||||||||||||| |||||||||||||| || |||||||||||||| ||||
--------------------------------------gtaagaaaattctctgaaactcgacccaccacctttgtagtgtaaaaa---attccaatgctaaccaatttatttctttggcagCTATTTTCTTTAAGTGCCATTCTGACTGTTTTCTTCTGCGGCATTGTTATGTCTCACTACACGTGGCATAATGTGACAGAGAGTTCAAGAGTGACAACCA

upper sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA07G38160.1 (Glycine max), 3'ss of exon 8
gtaagatatcccacaacttgctgggaaatccttccctgacccctgtttgctctttatttatactcttgagccccaaaataagcacatggaccttaattttggaattgttatttgtcttacagCTGTTCTATTTAAGTGCCATTCTCACTGTGTTCTTTTGCGGGATTGTCATGTCTCACTACACATGGCATAATGTGACTGAAAGTTCAAGAGTGACTACCA
                                            ||  |   ||| | |  |  ||||  | ||    ||     |   |     ||  |       |||||| | | |||||| || | ||||||||||||||| ||||| ||||| ||||| ||||| |||||||||||||| |||||||||||||| || |||||||||||||| ||||
--------------------------------------------gtaagaattttctctgaaa-cttggccacctttttagtgtaaataattcccatgctaaccgatttatttctttgacagCTATTTTCTTTAAGTGCCATTCTGACTGTTTTCTTCTGCGGCATTGTTATGTCTCACTACACGTGGCATAATGTGACAGAGAGTTCAAGAGTGACAACCA

upper sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT3G06370.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagatatcccacaacttgctgggaaatccttccctgacccctgtttgctctttatttatactcttgagccccaaaataagcacatggaccttaattttggaattgttatttgtcttacagCTGTTCTATTTAAGTGCCATTCTCACTGTGTTCTTTTGCGGGATTGTCATGTCTCACTACACATGGCATAATGTGACTGAAAGTTCAAGAGTGACTACCA
                                           |  |         || | ||  ||  |   ||   |   || |  ||   | |       ||   ||| |   || ||||| ||| | || ||  | ||  | ||||||||||| ||||||||||| ||||||||||| |||||||| ||||| || || |  || |  || ||||| |
------------------------------------------gtaataagaaaaatttgaaacgttttggttacattttttcca-acagaaaatgaaaacatgatacatatatcctttgcagCTATTCCACTTGAGCTCTATCTTGACTGTGTTCTTCTGCGGGATTGTTATGTCTCACTATACATGGCACAATGTTACAGATAAATCCAAGGTCACTACAA

upper sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 8
------------------------------gtaagatatc-----ccacaacttgctgggaaatccttccctgacccctgtttgctctttatttatactcttgagccccaaa---ataagcacatggaccttaattttggaattgttatttgtcttacagCTGTTCTATTTAAGTGCCATTCTCACTGTGTTCTTTTGCGGGATTGTCATGTCTCACTACACATGGCATAATGTGACTGAAAGTTCAAGAGTGACTACCA
                               | | || |      |  || ||||||    ||     |   ||  |  |  | || | ||    |  |    |     |||   | | |     | |   | | ||| | || |   | | | || ||||| ||||| || ||||  |||||| | |||||||||||||| ||||| |||||||| ||||| |||||||| || || || | |||  || | || | ||
gttagctcgactgttcatgcgaattgtttgttcaaatgtttgttactgcagcttgctatttaacttgacgaggaaacgggcat-ctgtgtaggagtttttgcaacttgtaaatgcacaggttttagaaatcttactttagtat-gcggtcttttttgcagCTTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCA

upper sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S207_23V6.2 (Physcomitrella patens), 3'ss of exon 9
---------------------------------gtaa-gatatcccacaacttgctgggaaatccttc---cctgacccctgtttgctctttatttatactcttgagccccaaaataagcacatggacctt------aattttggaattgttatttgtctt-------------acagCTGTTCTATTTAAGTGCCATTCTCACTGTGTTCTTTTGCGGGATTGTCATGTCTCACTACACATGGCATAATGTGACTGAAAGTTCAAGAGTGACTACCA
                                 |||  |  |||  | |   |  | |  | |  |||   ||  |  |   | ||   |  |   |   ||  |   ||      ||| |  | || | |       | | || | |   |  |||| ||              ||||| ||||| || ||||  ||||| ||||| |||||||| || ||||| ||||| ||||| || ||||||||||| |||||||| ||  || | || ||||
gtctactttctctctctctactatgtcaattatgtattgggatcatatattgtattagttacttgttcaatcccaattctgttctgacttgcacgcagcttccagcttccttggcgaagtatgttgatccttttctggactatgaactcaatgcttgtttttcgtttattgcatgcagCTTTTCTACTTGAGTGGGATTCTTACTGTCTTCTTTTGTGGCATTGTAATGTCCCACTATACCTGGCATAATGTTACTGAAAGCTCCCGAATAACCACCA

upper sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S113_117V6.1 (Physcomitrella patens), 3'ss of exon 7
----------------------gtaagatatcccacaacttgctgg-gaaatccttcc--ctgacccctg------tttgctctttatttatactcttg-agccccaaaataagca-----catggaccttaattttg-gaattgttatttgtcttacagCTGTTCTATTTAAGTGCCATTCTCACTGTGTTCTTTTGCGGGATTGTCATGTCTCACTACACATGGCATAATGTGACTGAAAGTTCAAGAGTGACTACCA
                       |      ||| |  |  || |   | |||  |||     || |  ||      |  ||     ||||  | | ||  | |    ||||  | |     ||   |  ||| ||| | |  | || ||| |   | ||||| ||||| || ||||  || ||| | ||||||||||| || ||||| |||||||| ||||| ||||||||||| || |||| |||  ||   || ||||
gtcagtttgaccttctatgtggattgttcgtccaattatctgttcctggaatttttcaaatagatcgatgaggaaatgagcatacgatttggattgttacaacttgtaaatctgaaattttcagaaattttactttcgcgtgtcgtcattgg---tgcagCTTTTCTACTTGAGTGGAATACTCTCAGTGTTCTTTTGTGGCATTGTAATGTCTCATTACACTTGGCATAATGTCACGGAAAATTCTCGAACCACAACCA

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|110696446|gb|EE072580.1|EE072580
EST:     AGGTTGCAATCATGATACTCATGGCTTACCTTTCGTATATGCTGGCTGAA                         CTGTTCTATTTAAGTGCCATTCTCACTGTGTTCTTTTGCGGGATTGTCATG
genomic: AGGTTGCAATCATGATACTCATGGCTTACCTTTCGTATATGCTGGCTGAAgtaagatatc ... tgtcttacagCTGTTCTATTTAAGTGCCATTCTCACTGTGTTCTTTTGCGGGATTGTCATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagccccaaaataagcacatggaccttaattttggaattgttatttgtcttacagCTGTTCTATTTAAGTGCCATTCTCACTGTGTTCTTTTGCGGGATTGTCATGTCTCACTACACATGGCATAATGTGACTGAAAGTTCAAGAGTGACTACCA
                       ccttaat  putative branch site (score: 4)
                                           tttgtctt  putative PPT
                         ttaattttggaattgt  TA-rich tract