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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcatgctgcaaatgctgcccctttttttttttaagagattccctcctttgatatgtttaatttgatatttttcaagttcaagtttgttggcttttgtggtacaactcacttgtcataaatttttaaaccagGTTGTGGCAATTGCATCTACTGCACTGGAAGGGTTTAAGAATGAGGCAAAGAAAATGGTTGTTGCACTTGTTGATATGGAGCGTGCATTTGTTCCCCCTC

Basic information

species Vitis vinifera
transcript Vv12s0035g01740.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 11
gtaatcatgctgcaaatgctgcccctttttttttttaagagattccctcctttgatatgtttaatttgatatttttcaagttcaagtttgttggcttttgtggtacaactcacttgtcataaatttttaaaccagGTTGTGGCAATTGCATCTACTGCACTGGAAGGGTTTAAGAATGAGGCAAAGAAAATGGTTGTTGCACTTGTTGATATGGAGCGTGCATTTGTTCCCCCTC
                   |  | | |   | ||||| ||| |||  ||||||         | ||| |  ||  |  |||| |   |||||| ||  ||||    ||   |  | |  |   |  ||   | ||||  | ||||| ||||| | |||||| ||  | || || ||||| ||||| || ||||||||||||||||||||||||||||| || |||||||| ||||
------------------gtatcacctagctatttta-gagtttctttcctttcg-------agtttcacgttggtagagttta---ttgttgactgatgtga-gtaaaaaatctatgtt---tcctttcgcaagGTCATTGCAATAGCATCAAATGCACTAGACAGCTTCAAAAATGATGCAAAAAAGATGGTTGTTGCACTTGTTGATATGGAGCGCGCCTTTGTTCCTCCTC

upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 11
gtaatcatgctgcaaatgctgcccctttttttttttaagagattccctcctttgatatgtttaatttgatat-ttttcaagttcaagtttgttggcttttgtggtacaactcacttgtcataaatttttaaaccagGTTGTGGCAATTGCATCTACTGCACTGGAAGGGTTTAAGAATGAGGCAAAGAAAATGGTTGTTGCACTTGTTGATATGGAGCGTGCATTTGTTCCCCCTC
                                         |   | |  ||  || |    || ||   ||   ||| | |||   ||     ||||     | |||||   |   ||||   ||||   |  |||| || | ||||||| | | |||| |||| |  || || | ||| ||||| || ||||| |||||||||||||||||||||||||| ||||| || || |
---------------------------------------gtaccactttgttctatttcaccaacttacaatgcattctacttccctttcacctgcttcctgagcacaacat-cccatcatctcttttctga--agGTCGTTGAAATTGCAACCAATGCATTGGATGTCTTCAAAAGTGATGCAAAAAAGATGGTAGTTGCACTTGTTGATATGGAGCGTGCCTTTGTCCCACCAC

upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G485898_T02 (Zea mays), 3'ss of exon 11
gtaatcatgctgcaaatgctgcccctttttttttttaagagattccctcctttgatatgtttaatttgatatttttcaagttcaag-tttgttggcttttgtggtacaactcacttgtcataaatttttaaaccagGTTGTGGCAATTGCATCTACTGCACTGGAAGGGTTTAAGAATGAGGCAAAGAAAATGGTTGTTGCACTTGTTGATATGGAGCGTGCATTTGTTCCCCCTC
                                                    | | |  |||||  || |||||   | |   ||  ||| || | |  || |  |    |   |  | ||   ||| |  || ||||  | ||||| ||||||||||| || || || || |||||||||||||  || ||||| |||||||| ||||| |||||| | ||||| || || || |
---------------------------------------------------gtaaaagttttaaagtg-tatttaataggcaaaaaatttattagttaatgagtaattgttt-ttaattatttctttgtccacaagGTAATTGCAATAGCATCTACTGCTCTAGATGGTTTCAAGAATGAGGCAAGAAAGATGGTCGTTGCACTAGTTGACATGGAGAGGGCATTCGTACCTCCCC

upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 11
gtaatcatgctgcaaatgctgcccctttttttttttaagagattccctcctttgatatgtttaatttgatatttttcaagttcaagtttgttggcttttgtggtacaactcacttgtcataaatttttaaaccagGTTGTGGCAATTGCATCTACTGCACTGGAAGGGTTTAAGAATGAGGCAAAGAAAATGGTTGTTGCACTTGTTGATATGGAGCGTGCATTTGTTCCCCCTC
                   |  | | |||| | ||| | | |||   |||| |  | || ||   |||||| | |    ||||  |  |      ||||| |||  || |   || |  |     | |   | ||||||| ||||| ||||| | |||| ||||    || || || || || || || ||||| ||||| |||||||||||||| ||||| |||||||| || |
------------------gtatcaccttttctgtttcacacattttttcctctt-tctgcttg--ttgatagtgt----gttctggcct------ttttggggtgtaaatt--ttattttg----tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAAAAGATGGTCGTTGCGCTTGTTGATATGGAACGTGCTTTTGTTCCTCCCC

upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 11
gtaatcatgctgcaaatgctgcccctttttttttttaagagattccctcctttgatatgtttaatttgatatttttcaagttcaagtttgttggctttt----gtggtacaactcacttgtcataaatttttaaaccagGTTGTGGCAATTGCATCTACTGCACTGGAAGGGTTTAAGAATGAGGCAAAGAAAATGGTTGTTGCACTTGTTGATATGGAGCGTGCATTTGTTCCCCCTC
                                                       ||   || || || | |   | |  |  || || ||| | ||||     |       |||| ||||   || ||||      || ||||||||||||||  | | || || || |  ||||| |||||  | || |||||||| |||||||| |||||||||||||||||||||||||| || |
------------------------------------------------------gtaacattgatgtgctgtaacttacatgtaacttggtttgtttttagaaattaccttgctcatttgttgcaattttt------agATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCACCAC

upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 11
gtaatcatgctgcaaatgctgcccctttttttttttaagagattccctcctttgatatgtttaatttgatatttttcaagttcaagtttgttggctttt-----gtggtacaactcacttgtcataaatttttaaaccagGTTGTGGCAATTGCATCTACTGCACTGGAAGGGTTTAAGAATGAGGCAAAGAAAATGGTTGTTGCACTTGTTGATATGGAGCGTGCATTTGTTCCCCCTC
                                                       ||    |  | || | |   | |  |  || || ||| | ||||      |  |    |||| ||||   || |||      ||| ||||||||||||||  | | || || || |  ||||| |||||  | || |||||||| |||||||| |||||||||||||||||||||||||| || |
------------------------------------------------------gtaacaatgctgtgctgtaagttacatgtaacttggtttgttttttagaaattatcttgctcatttgttgcaatttt------cagATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCTCCCC

upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaatcatgctgcaaatgctgcccctttttttttttaagagattccctcctttgatatgtttaatttgatatttttcaagttcaagtttgttggcttttgtggtacaactcacttgtcataaat--ttttaaaccagGTTGTGGCAATTGCATCTACTGCACTGGAAGGGTTTAAGAATGAGGCAAAGAAAATGGTTGTTGCACTTGTTGATATGGAGCGTGCATTTGTTCCCCCTC
                                                   |   |||| ||   ||  |  | ||  ||||  | |||  | |  ||  |  ||    |  ||| || |||||  |  | ||||||||||| || || |||  | | ||||| || || || |||||||| || ||||| ||||| |||||| | ||||||||||||||||||||||| || ||||
--------------------------------------------------gtaattatgctt---ttactgctctttcagttgcatttt--tcgtcttactaatagctgtttcttttcttaaataatcgtcaaccagGTTGTAGCTATAGCAAGTGCCGCACTTGATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTC

upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaatcatgctgcaaatgctgcccctttttttttttaagagattccctcctttgatatgtttaatttgatatttttcaagttcaagtttgttggcttttgtggta-caactcacttgtcataaatttttaaaccagGTTGTGGCAATTGCATCTACTGCACTGGAAGGGTTTAAGAATGAGGCAAAGAAAATGGTTGTTGCACTTGTTGATATGGAGCGTGCATTTGTTCCCCCTC
                                                    | |||    |  |||| |  |||      | |  |||  |   ||  ||   |   | ||  || | |  |||  | || ||||||||| || || |||  | | ||||| || || || |||||||| || ||||||||||| |||||||| ||||||||||| || || ||||| || ||||
---------------------------------------------------gtaataatgattttttggtgctttattcagtaatattttatcatttcggtaacagttattcctttctgactaatcatcaa-ccagGTTGTAGCTATAGCAAGTGCAGCACTTGATGGTTTCAAGAATGAAGCCAAGAAAATGGTGGTTGCACTAGTTGATATGGAACGCGCTTTTGTACCACCTC

upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: PP1S33_163V6.1 (Physcomitrella patens), 3'ss of exon 11
gtaatcatgctgcaaatgctgcccctttttttttttaagagattccctcctttgatatgtttaatttgatattttt--caagttcaagtttgttggctt----ttgtggtacaactcacttgtcataaatttttaaaccagGTTGTGGCAATTGCATCTACTGCACTGGAAGGGTTTAAGAATGAGGCAAAGAAAATGGTTGTTGCACTTGTTGATATGGAGCGTGCATTTGTTCCCCCTC
                               ||| ||  |  |    ||||| |   | | |  || ||||  | |   |  ||  ||| ||||||  |    || |   |  | ||  |     ||    |||    ||| |||| || |||||   | | || ||||| |  |  | |  |||  ||||||||||||||||||| |||||||| ||||||||||||||| | || ||||
------------------------------gtttgtacaatttcggttccttcgtagtatctgcttcgataaatgtggtacattatagtgtgttgggctaaaattattcaatgattctttgaggctatgcgtttg---cagATTGTTGCCATTGCCAGTTCAGCGCTGGACGAATACAGGGTTGAATCAAAGAAAATGGTTGTTGCTCTTGTTGACATGGAGCGTGCATTTATCCCACCTC

upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: PP1S109_214V6.1 (Physcomitrella patens), 3'ss of exon 11
gtaatcatgctgcaaatgctgcccctttttt--tttttaagagattccctcctttgatatgtt-taatttgatatttttcaagttcaagtttgt----tggcttttgtggtaca--actcacttgtcataaatttttaaac-----cagGTTGTGGCAATTGCATCTACTGCACTGGAAGGGTTTAAGAATGAGGCAAAGAAAATGGTTGTTGCACTTGTTGATATGGAGCGTGCATTTGTTCCCCCTC
||  | ||      |   ||  |   | |    | || |  | ||||  |   |  | |  || || ||    || |||    || || ||       ||   || |   ||||  | ||| | || |     | ||| |      ||| |||| || |||||  || |||| ||||| | || ||     || |||||||||||||||||||| |||||||||||||||||||||||| |||||||||
gtgcttatagatttatctctttctactatcaaatgttcactaaattctgtgactgcaaaaattatagttacccatctttttcattgaatttcacacaatgtgcttgggcttacagtattcaatggttactcggtgttataatcctgcagATTGTTGCCATTGCTACTGCTGCGCTGGATGAGTATAGAGCAGAAGCAAAGAAAATGGTTGTTGCGCTTGTTGATATGGAGCGTGCATTTATTCCCCCTC

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|30298644|gb|CB975438.1|CB975438
EST:     CTGCAAATGCTACACCGGGCCTGGGAAGATACCCTCCTTTTAAGAGAGAG                         GTTGTGGCAATTGCATCTACTGCACTGGAAGGGTTTAAGAATGAGGCAAAG
genomic: CTGCAAATGCTACACCGGGCCTGGGAAGATACCCTCCTTTTAAGAGAGAGgtaatcatgc ... tttaaaccagGTTGTGGCAATTGCATCTACTGCACTGGAAGGGTTTAAGAATGAGGCAAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaagtttgttggcttttgtggtacaactcacttgtcataaatttttaaaccagGTTGTGGCAATTGCATCTACTGCACTGGAAGGGTTTAAGAATGAGGCAAAGAAAATGGTTGTTGCACTTGTTGATATGGAGCGTGCATTTGTTCCCCCTC
                          aactcac  putative branch site (score: 2)
                                           ttttt  putative PPT
                                 ttgtcataaattttta  TA-rich tract