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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcagagatactatccatccaccaacctttcccacatctgctgcatgtggaaactccattgctgaaaatttactctcttttccccttgaatggattttacatcgtttatctcttattttttgttttcctatacctcactttgtcagcaacttttatgctagttttcactgtccaacttgctgtctgagttttccagGGAGTCATCACTCAGCTCTCAGAACAAATTTCCACACTGAATGAGAGAATGGATGAGTTCACATCTCGCATTGAAGAGTTAAATTCCAAGTTCTCTATCA

Basic information

species Vitis vinifera
transcript Vv17s0000g04650.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g04650.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 10
gtaatcagagatactatccatccaccaacctttcccacatctgctgcatgtggaaactccattgctgaaaatttactctcttttccccttgaatggattttacatcgtttatctcttattttttgttttcctatacctcactttgtcagcaacttttatgctagttttcactgtccaacttgctgtctgagttttccagGGAGTCATCACTCAGCTCTCAGAACAAATTTCCACACTGAATGAGAGAATGGATGAGTTCACATCTCGCATTGAAGAGTTAAATTCCAAGTTCTCTATCA
                                                                       |   |  |||      |||| ||   || ||  |    ||    |||     | |||| ||       |  ||| ||   |   | |  ||   |   | | |||  |||| |  |||    ||  |||| |  ||||||||||| || ||||| ||||| ||  |||||||||| ||||| |||||||| |||||  |||||||  | || |  || ||  | || |
----------------------------------------------------------------------gtggtcattctagaatacttgtattagttatagctaccatactaattaaaacatttttttcttgtgaaaaacttgacataga---taacactgactcaaaat-tcctccttgtttgctgctgcttgtagGGTGCTATCACTCAGCTATCCGAACAGATTTCAACGTTGAATGAGAGGATGGACGAGTTCACCTCTCGAGTTGAAGAACTCAACTGTAAATTTGCAATAA

upper sequence: Vv17s0000g04650.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA17G09080.1 (Glycine max), 3'ss of exon 10
gtaatcagagatactatccatccaccaacctttcccacatctgctgcatgtggaaactccattgctgaaaatttactctcttttccccttgaatggattttacatcgtttatctcttattttttgttttcctatacctcactttgtcagcaacttttatgctagttttcactgtccaacttgctgtctgagttttccagGGAGTCATCACTCAGCTCTCAGAACAAATTTCCACACTGAATGAGAGAATGGATGAGTTCACATCTCGCATTGAAGAGTTAAATTCCAAGTTCTCTATCA
                                                                                |       |  |||      |||||  |  |    | || |    |||  |||  | ||      | |   | | || | ||  | ||  ||             | |||||| |||||||||||||||| ||||| || || |||||||||||| | ||||| |||||||| || ||||| || || ||||||||| | ||||| |||||| ||||||
--------------------------------------------------------------------------------tagaatattctaataataaatacattatcaagacataatctcacatttctctacccatc------taaattattcttctactgatatttgct-------------tttgagttgtccagGGAGTCATCACACAGCTTTCTGATCAAATTTCCACATTAAATGAAAGAATGGACGAATTCACCTCCCGTATTGAAGAGCTGAATTCAAAGTTCGCTATCA

upper sequence: Vv17s0000g04650.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA05G07610.1 (Glycine max), 3'ss of exon 11
gtaatcagagatactatccatccaccaacctttcccacatctgctgcatgtggaaactccattgctgaaaatttactctcttttccccttgaatggattttacatcgtttatctctta-ttttttgttttcctatacctcactttgtcagcaacttttatgctagttttc-actgtccaacttgctgtctgagttttccagGGAGTCATCACTCAGCTCTCAGAACAAATTTCCACACTGAATGAGAGAATGGATGAGTTCACATCTCGCATTGAAGAGTTAAATTCCAAGTTCTCTATCA
                                                                                         |  ||  || |  |  | ||| | ||| | |  |||  ||| || |   |  || ||       | | ||   || | ||| ||||    | |||||    ||||| ||||||||||||||||||| || || || |||||||| ||| | ||||| ||||||||||| ||||| || || ||||||||| | ||||| |||||| ||||||
-----------------------------------------------------------------------------------------ttgataaatgt--ctgcttttgtgtctaagtggtttaattttctgtttatttctctgct-----catctaaattattcttctactgat--atttgct---cgagttgtccagGGAGTCATCACTCAACTTTCTGATCAAATTTCAACATTAAATGAAAGAATGGATGAATTCACCTCCCGTATTGAAGAGCTGAATTCAAAGTTCGCTATCA

upper sequence: Vv17s0000g04650.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G73980.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaatcagagatactatccatccaccaacctttcccacatctgctgcatgtggaaactccattgctgaaaatttactctcttttccccttgaatggattttacatcgtttatctcttattttttgttttcctatacctcactttgtcagcaacttttatgctagttttcact---gtccaacttgctgtctgagttttccagGGAGTCATCACTCAGCTCTCAGAACAAATTTCCACACTGAATGAGAGAATGGATGAGTTCACATCTCGCATTGAAGAGTTAAATTCCAAGTTCTCTATCA
                                                                                        |    |||| | ||  |  ||   ||   || |||    |  |||||  ||   ||||    || |  ||   | | || || |    || ||  |   || |  ||| |  ||||  | |||||||| || ||||| ||||| || |||||||| ||||| |||||||| |||||||| |||||||||||||| ||||||||| || | | ||
---------------------------------------------------------------------------------------gtaatgtggactctatgt--ttcccctgagatctttcaaat--ctatagttc-tgttgttgcaaagtgatactttggcttacaattaaatcaaatgtatggtgtt-gttctatagGGTTTTATCACTCAACTTTCAGACCAAATATCAACACTGAACGAGAGGATGGATGAATTCACATCCCGCATTGAAGAGTTGAATTCCAAGATCCCGAACA

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|71865288|gb|DT014343.1|DT014343
EST:     GAAGGTTTGATGTAAGAACCCCAGATTCTCCTGCAACAGTTCCAAATCAG                         GGAGTCATCACTCAGCTCTCAGAACAAATTTCCACACTGAATGAGAGAATG
genomic: GAAGGTTTGATGTAAGAACCCCAGATTCTCCTGCAACAGTTCCAAATCAGgtaatcagag ... agttttccagGGAGTCATCACTCAGCTCTCAGAACAAATTTCCACACTGAATGAGAGAATG
EST: gi|110423731|gb|EC990082.1|EC990082
EST:     GAAGGTTTGATGTAAGAACCCCAGATTCTCCTGCAACAGTTCCAAATCAG                         GGAGTCATCACTCAGCTCTCAGAACAAATTTCCACACTGAATGAGAGAATG
genomic: GAAGGTTTGATGTAAGAACCCCAGATTCTCCTGCAACAGTTCCAAATCAGgtaatcagag ... agttttccagGGAGTCATCACTCAGCTCTCAGAACAAATTTCCACACTGAATGAGAGAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcagcaacttttatgctagttttcactgtccaacttgctgtctgagttttccagGGAGTCATCACTCAGCTCTCAGAACAAATTTCCACACTGAATGAGAGAATGGATGAGTTCACATCTCGCATTGAAGAGTTAAATTCCAAGTTCTCTATCA
                                               ttttcc  CT-rich tract
      aacttttat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcagagatactatccatccaccaacctttcccacatctgctgcatgtggaaactccattgctgaaaatttactctcttttccccttgaatggattttacatcgtttatctcttattttttgttttcctatacctcactttgtcagcaacttttatgctagttttcactgtccaacttgctgtctgagttttccagGGAGTCATCACTCAGCTCTCAGAACAAATTTCCACACTGAATGAGAGAATGGATGAGTTCACATCTCGCATTGAAGAGTTAAATTCCAAGTTCTCTATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA