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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttattgatatttgatattgtttctgttttttcttgatgatgctcaacattgctaccttatcctttttttctttttctttttctcttttttttttccagAGCTGAGGAGCTGGAGACAGCATTGATGGAGATGGTCAAACAGGATAACCGGCGGCAATTGAGTGCAAGG

Basic information

species Vitis vinifera
transcript Vv13s0067g03420.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g03420.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os05g38950.2 (Oryza sativa), 3'ss of exon 12
ctttattgatatttgatattgtttctgttttttcttga-tgatgctcaacattgctacct-tatcctttttttctttttctttttctcttttttttttccagAGCTGAGGAGCTGGAGACAGCATTGATGGAGATGGTCAAACAGGATAACCGGCGGCAATTGAGTGCAAGG
 |  ||| ||   | || ||     | |   | ||||| |  || ||    |  |||||  | |    | ||  ||    ||||  |||||||  | ||||||||||| || || ||||| ||||||||||| |||||||| || |||||  |||||||||| ||||||| |
-tagatttatggctaat-ttacccgtatcagtccttgagtcctgatctggttgtctaccagtctgaagtattaattccaattttcttctttttgatatccagAGCTGATGAACTAGAGACGGCATTGATGGAAATGGTCAAGCAAGATAATAGGCGGCAATTAAGTGCAAAG

upper sequence: Vv13s0067g03420.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 12
ctttattgatatttgatattgtttctgttttttcttgatgatgctcaacattgctaccttatcctttttttctttttctttttctctttttttttt-ccagAGCTGAGGAGCTGGAGACAGCATTGATGGAGATGGTCAAACAGGATAACCGGCGGCAATTGAGTGCAAGG
 | |||  || |  | |   |       |||  | |||  ||    |   |  ||   ||   | |    | | || ||||   | |  | |||||  |||||| ||||||||||| |||||||| ||||| |||||||| ||||||||  |||||||| ||||||| | |
gtgtatgtatgtaag-tggagagagaagtttcccctgaaaattgagagattcacttttttgcacatagcatttattcctttcaatttcctctttttatcagAGCGGAGGAGCTGGAAACAGCATTAATGGAAATGGTCAAGCAGGATAATAGGCGGCAACTGAGTGCCAAG

upper sequence: Vv13s0067g03420.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA10G44110.1 (Glycine max), 3'ss of exon 12
---ctttattgatatttgatattgtttctgttttttcttgatgatgctcaacattgctaccttatcctttttttctttttctttttctcttttttttttccagAGCTGAGGAGCTGGAGACAGCATTGATGGAGATGGTCAAACAGGATAACCGGCGGCAATTGAGTGCAAGG
    | | |   ||| ||           |||||  ||  | | ||    |  |  ||   ||    |  ||| ||  ||    ||   | ||||| |  |||||| ||||||||||| |||||||| ||||| |||||||  || |||||  |||||||| ||||||| | |
aatgtatgtatgtatatggagagagagaagttttccctgaaagttgagagat-tcacttttttgcaatcatttactcctttcaatttcttctttttat--cagAGCGGAGGAGCTGGAAACAGCATTAATGGAAATGGTCAGGCAAGATAATAGGCGGCAACTGAGTGCTAAG

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|30136499|gb|CB921837.1|CB921837
EST:     GCTCTGCTCAG                         AGCTGAGGAGCTGGAGACAGCATTGATGGAGATGGTCAAACAGGATAACCG
genomic: GCTCTGCTCAGgttagcattt ... ttttttccagAGCTGAGGAGCTGGAGACAGCATTGATGGAGATGGTCAAACAGGATAACCG
EST: gi|30135773|gb|CB921111.1|CB921111
EST:     GCTCTGCTCAG                         AGCTGAGGAGCTGGAGACAGCATTGATGGAGATGGTCAAACAGGATAACCG
genomic: GCTCTGCTCAGgttagcattt ... ttttttccagAGCTGAGGAGCTGGAGACAGCATTGATGGAGATGGTCAAACAGGATAACCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacattgctaccttatcctttttttctttttctttttctcttttttttttccagAGCTGAGGAGCTGGAGACAGCATTGATGGAGATGGTCAAACAGGATAACCGGCGGCAATTGAGTGCAAGG
           ccttatcctttttttc  CT-rich tract
                   tttttttctttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttattgatatttgatattgtttctgttttttcttgatgatgctcaacattgctaccttatcctttttttctttttctttttctcttttttttttccagAGCTGAGGAGCTGGAGACAGCATTGATGGAGATGGTCAAACAGGATAACCGGCGGCAATTGAGTGCAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - -cttgatg