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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataacttatgcctttttctattgtgaagagaagtaaaatttacgagataattttttccattgtctttttcttagtctttttttttgtggacaattatcagGCTGATAATCTGCGCCAGCAGACGCTACAGCAGATGCACCGTATATTGACAACCCGGCAGTCTGCACGTGCTCTTCTTGCAATAAATGACTACTTCTCCC

Basic information

species Vitis vinifera
transcript Vv08s0007g05170.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g05170.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os01g59350.2 (Oryza sativa), 3'ss of exon 10
ataacttatg-cctttttctattgtgaagagaagtaaaatttacgagataattttttccattgtctttt-----tcttagtctttttttttg-tggacaattatcagGCTGATAATCTGCGCCAGCAGACGCTACAGCAGATGCACCGTATATTGACAACCCGGCAGTCTGCACGTGCTCTTCTTGCAATAAATGACTACTTCTCCC
       ||  || ||        |    |||| || |  |   || ||   | ||||  |||    ||     | || ||    | |   | ||    ||   ||||||||||||||||| |  ||||| || ||||| ||||| || ||||| || || || ||||| ||||| ||||| |||||||||| ||||||||||||||
-------ataaccattaaacggaataccaagaaatagacatagagaaatgtatatttctgttgcaaattgtaacttttggtgaactataacgatgccttatctgcagGCTGATAATCTGCGGCTTCAGACTCTTCAGCAAATGCAGCGCATATTAACCACTCGCCAGTCAGCACGAGCTCTACTTGCAATAAGTGACTACTTCTCCC

upper sequence: Vv08s0007g05170.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G056099_T01 (Zea mays), 3'ss of exon 9
----------------------------------------------------------------------ataacttatgcctttttctattgtgaagagaagtaaaatttacgagataattttttccattgtct--ttttcttagtcttt----ttttttgtggacaattatc---agGCTGATAATCTGCGCCAGCAGACGCTACAGCAGATGCACCGTATATTGACAACCCGGCAGTCTGCACGTGCTCTTCTTGCAATAAATGACTACTTCTCCC
                                                                        |  | ||| | |||  |    |  |        |  |||| || |||  | | |  |     |  | ||| |||   |      |||| |||  | ||||||   ||||||| ||||| || ||||||||  |||| |||||||| |||||  |||||| ||| ||  |||| ||||| |||||||||||  |||||||||| || |
gtaaacttttcagatacctccaaccctggcaaacatttagttttgttgtttctgttgttgactgtcatagggagatcatgtcatttgattcgatacattttctctacttttaagaaatatatgtatgtagctcttggtgttcctagctctgaagacttttggtgttctattatcgttagGCTGACAATCTACGACAGCAGACCTTACATCAGATGCAACGTATCCTGACAATCCGACAAGCTGCTCGTGCGCTTCTTGCAATCCATGACTACTTTTCAC
















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|110363172|gb|EC926744.1|EC926744
EST:     TGGCCATGGCAATGGGTAAGCTAGGGACTCTTGAGGGATTTCTTCGTCAG                         GCTGATAATCTGCGCCAGCAGACGCTACAGCAGATGCACCGTATATTGACA
genomic: TGGCCATGGCAATGGGTAAGCTAGGGACTCTTGAGGGATTTCTTCGTCAGgtaatctccc ... caattatcagGCTGATAATCTGCGCCAGCAGACGCTACAGCAGATGCACCGTATATTGACA
EST: gi|33407846|gb|CF213473.1|CF213473
EST:     TGGCCATGGCAATGGGTAAGCTAGGGACTCTTGAGGGATTTCTTCGTCAG                         GCTGATAATCTGCGCCAGCAGACGCTACAGCAGATGCACCGTATATTGACA
genomic: TGGCCATGGCAATGGGTAAGCTAGGGACTCTTGAGGGATTTCTTCGTCAGgtaatctccc ... caattatcagGCTGATAATCTGCGCCAGCAGACGCTACAGCAGATGCACCGTATATTGACA
EST: gi|351040876|gb|FQ438420.1|FQ438420
EST:     TGGCCATGGCAATGGGTAAGCTAGGGACTCTTGAGGGATTTCTTCGTCAG                         GCTGATAATCTGCGCCAGCAGACGCTACAGCAGATGCACCGTATATTGACA
genomic: TGGCCATGGCAATGGGTAAGCTAGGGACTCTTGAGGGATTTCTTCGTCAGgtaatctccc ... caattatcagGCTGATAATCTGCGCCAGCAGACGCTACAGCAGATGCACCGTATATTGACA
EST: gi|33402332|gb|CF207959.1|CF207959
EST:     TGGCCATGGCAATGGGTAAGCTAGGGACTCTTGAGGGATTTCTTCGTCAG                         GCTGATAATCTGCGCCAGCAGACGCTACAGCAGATGCACCGTATATTGACA
genomic: TGGCCATGGCAATGGGTAAGCTAGGGACTCTTGAGGGATTTCTTCGTCAGgtaatctccc ... caattatcagGCTGATAATCTGCGCCAGCAGACGCTACAGCAGATGCACCGTATATTGACA
EST: gi|110358865|gb|EC923392.1|EC923392
EST:     TGGCCATGGCAATGGGTAAGCTAGGGACTCTTGAGGGATTTCTTCGTCAG                         GCTGATAATCTGCGCCAGCAGACGCTACAGCAGATGCACCGTATATTGACA
genomic: TGGCCATGGCAATGGGTAAGCTAGGGACTCTTGAGGGATTTCTTCGTCAGgtaatctccc ... caattatcagGCTGATAATCTGCGCCAGCAGACGCTACAGCAGATGCACCGTATATTGACA
EST: gi|161719149|gb|FC065719.1|FC065719
EST:     TGGCCATGGCAATGGGTAAGCTAGGGACTCTTGAGGGATTTCTTCGTCAG                         GCTGATAATCTGCGCCAGCAGACGCTACAGCAGATGCACCGTATATTGACA
genomic: TGGCCATGGCAATGGGTAAGCTAGGGACTCTTGAGGGATTTCTTCGTCAGgtaatctccc ... caattatcagGCTGATAATCTGCGCCAGCAGACGCTACAGCAGATGCACCGTATATTGACA
EST: gi|30295958|gb|CB972752.1|CB972752
EST:     NNNNNNTGGCAATGGGTAAGCTAGGGACTCTTGAGGGATTTCTTCGTCAG                         GCTGATAATCTGCGCCGGCAGACGCTACAG
genomic: GCCA--TGGCAATGGGTAAGCTAGGGACTCTTGAGGGATTTCTTCGTCAGgtaatctccc ... caattatcagGCTGATAATCTGCGCCAGCAGACGCTACAG
EST: gi|71874124|gb|DT023179.1|DT023179
EST:     TGGCCATGGCAATGGGTAAGCTAGGGACTCTTGAGGGATTTCTTCGTCAG                         GCTGATAATCTGCGCCAGCAGACGCTACAGCAGATGCACCGTATATTGACA
genomic: TGGCCATGGCAATGGGTAAGCTAGGGACTCTTGAGGGATTTCTTCGTCAGgtaatctccc ... caattatcagGCTGATAATCTGCGCCAGCAGACGCTACAGCAGATGCACCGTATATTGACA
EST: gi|351025955|gb|FQ427967.1|FQ427967
EST:     TGGCCATGGCAATGGGTAAGCTAGGGACTCTTGAGGGATTTCTTCGTCAG                         GCTGATAATCTGCGCCAGCAGACGCTACAGCAGATGCACCGTATATTGACA
genomic: TGGCCATGGCAATGGGTAAGCTAGGGACTCTTGAGGGATTTCTTCGTCAGgtaatctccc ... caattatcagGCTGATAATCTGCGCCAGCAGACGCTACAGCAGATGCACCGTATATTGACA
EST: gi|33402254|gb|CF207881.1|CF207881
EST:     TGGCCATGGCAATGGGTAAGCTAGGGACTCTTGAGGGATTTCTTCGTCAG                         GCTGATAATCTGCGCCAGCAGACGCTACAGCAGATGCACCGTATATTGACA
genomic: TGGCCATGGCAATGGGTAAGCTAGGGACTCTTGAGGGATTTCTTCGTCAGgtaatctccc ... caattatcagGCTGATAATCTGCGCCAGCAGACGCTACAGCAGATGCACCGTATATTGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gataattttttccattgtctttttcttagtctttttttttgtggacaattatcagGCTGATAATCTGCGCCAGCAGACGCTACAGCAGATGCACCGTATATTGACAACCCGGCAGTCTGCACGTGCTCTTCTTGCAATAAATGACTACTTCTCCC
                   tttttcttagtctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataacttatgcctttttctattgtgaagagaagtaaaatttacgagataattttttccattgtctttttcttagtctttttttttgtggacaattatcagGCTGATAATCTGCGCCAGCAGACGCTACAGCAGATGCACCGTATATTGACAACCCGGCAGTCTGCACGTGCTCTTCTTGCAATAAATGACTACTTCTCCC

- - - tatgcct
- - - - - - - - - - - - -aagagaa