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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaaatctgttcccatttccactacccagtagtctctgagtgttcatataatctattctctcactctttcttagaagattgttttgatatttttatcagGAATGCCTTGTACGAGTGGCGGTCTGGTGCATTGGAGAATATGGTGAAATGTTAGTCAATAATGTTGGAATGCTTGATATAGAGGAACCTATAACT

Basic information

species Vitis vinifera
transcript Vv01s0026g00310.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os06g07090.1 (Oryza sativa), 3'ss of exon 10
aaaaaatctgttcccatttccactacccagtagtctctgagtgttcatataatctattctctcactctttcttagaagattgttttgatatttttatcagGAATGCCTTGTACGAGTGGCGGTCTGGTGCATTGGAGAATATGGTGAAATGTTAGTCAATAATGTTGGAATGCTTGATATAGAGGAACCTATAACT
      | ||     ||   || |   |  ||   |||      |    |      || ||| ||   | | |  |    |  |    |   ||  | ||||| |  | ||  | || || || ||||||||||| || |||||||||||| | || || |||||||| ||||| || ||||||||||| || || 
-----gtatggagaaatagtcagtcttctttatgatctataccattgagttgctacttatctgaca--tacctgaatctcttctacattgaattatttagGAAAGTTTGGTTAGGGTAGCTGTATGGTGCATTGGTGAGTATGGTGAAATGCTGGTGAACAATGTTGGTATGCTGGACATAGAGGAACCAATCACG

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os02g56110.1 (Oryza sativa), 3'ss of exon 10
aaaaaatctgttcccatttccactacccagta-gtctctgagtgttcatataatctattct----ctcactctttcttagaagattgttttgatatttttatcagGAATGCCTTGTACGAGTGGCGGTCTGGTGCATTGGAGAATATGGTGAAATGTTAGTCAATAATGTTGGAATGCTTGATATAGAGGAACCTATAACT
                |||  |  |   | |  || | | |   | |||||  |     ||    || |||  ||  |  ||  | |||    ||   |    ||| | |  | ||| ||||||| || |||||||| || ||||||||||||||| |||| || |||||||| |||||  |    ||||||||||| || 
---------------gtttggaaaaaaaaatgtgtttgttatgatgcatattgttccaccttaacctaactgatttgtgtaacttggttgcactacactgtgtagGGAAGTTTAGTAAGAGTGGCTGTTTGGTGCATCGGTGAATATGGTGAAATGCTAGTTAACAATGTTGGCATGCTGCAAGGGGAGGAACCTATTACG

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G054210_T01 (Zea mays), 3'ss of exon 10
aaaaaatctgttcccatttccactacccagtagtctctgagtgttcatataatctattc--tctcactct------ttcttagaagattgttt-tgatatttttatcagGAATGCCTTGTACGAGTGGCGGTCTGGTGCATTGGAGAATATGGTGAAATGTTAGTCAATAATGTTGGAATGCTTGATATAGAGGAACCTATAACT
                       ||      ||| | | | | | |||  | || ||||  |||||  ||      | | |  || | |||   |  |||  | || ||| | |  | ||| |||| || || ||||||||||| ||||||||||||||| | || || |||||||| ||||| |||   ||||| || || |  
---------------------gttaggggaaagtttat-actctccatgcattccattccatctcatcctacttgatgcctgtaacactgtcaatattataatgattagGGAAGTTTAGTAAGAGTAGCTGTTTGGTGCATTGGTGAATATGGTGAAATGCTGGTGAACAATGTTGGCATGCTGGATGGGGAGGAGCCAATTAAG

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA02G03800.1 (Glycine max), 3'ss of exon 9
aaaaaatctgttcccatttccactacccagtagtctctgagtgttcatataatctattctctcactctttcttagaagattgttttgatatttttatcagGAATGCCTTGTACGAGTGGCGGTCTGGTGCATTGGAGAATATGGTGAAATGTTAGTCAATAATGTTGGAATGCTTGATATAGAGGAACCTATAACT
         || | || |||  ||       |   |||  |        |||| |  | |      ||||| || || |||   |     |||| |||||||    || || |||||  | || ||||||||||| || |||||||| |||||||||||||||||||||||||| || ||||| || || ||||| 
---------gtgctcacttctgct--ttgacaaaatctaggcacattgttaatttgcttttgatgcctttcatataatattacctaatacttttcatcagGAGACTCTAGTTCGAGTTACAGTGTGGTGCATTGGGGAGTATGGTGACATGTTAGTCAATAATGTTGGAATGCTAGACATAGAAGATCCAATAACA

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA01G03890.1 (Glycine max), 3'ss of exon 10
aaaaaatctgttcccatttccactacccagtagtctctgagtgttcatataatctattctctcactctttcttagaagattgttttgatatttttatcagGAATGCCTTGTACGAGTGGCGGTCTGGTGCATTGGAGAATATGGTGAAATGTTAGTCAATAATGTTGGAATGCTTGATATAGAGGAACCTATAACT
         || | || |||  ||           |||  |    |   |||| |  | |      ||||| || || |||   |   | |||| |||||||    || || |||||  | || ||||||||||| || |||||||| |||||||| |||||||||||||||||||| ||||| || || ||||| 
---------gtgctcacttctgct--ttgaccaaatctaggcacactgttaatttgcttttgatgcctttcatataatattacctaattcttttcatcagGAGACTCTAGTTCGAGTTACAGTGTGGTGCATTGGGGAGTATGGTGACATGTTAGTTAATAATGTTGGAATGCTTGACATAGAAGATCCAATAACA

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA08G39930.1 (Glycine max), 3'ss of exon 10
aaaaaatctgttcccatttccactacccagtagtctctgagtgttcatataatctattctctcactctttcttagaagattgtt--ttgatattttt-atcagGAATGCCTTGTACGAGTGGCGGTCTGGTGCATTGGAGAATATGGTGAAATGTTAGTCAATAATGTTGGAATGCTTGATATAGAGGAACCTATAACT
         || | | ||||  ||       |   ||||    | |   | || |  |||  |   | ||  |  || ||  ||     |||||||| ||||||||   ||||| || || || || |||||||| ||||| |||||||| || ||| ||||||||| ||||||||||||| |||| || ||  |||||
---------gtgctcttttctgct--ttgacaaaatctgttcatgctgttgattttctcttactgccattaatgtaatatcattgacgaatatttttcatcagGAAACTCTTGTTCGCGTTGCAGTTTGGTGCATCGGAGAGTATGGTGACATCTTAATCAATAATGCTGGAATGCTTGATGTAGAAGATCCAGTAACT

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|71889458|gb|DT038513.1|DT038513
EST:     GATATACAGTAAGGTCCCTTTACAGAGCATTCCAAGCATCAGTGGAACAG                         GAATGCCTTGTACGAGTGGCGGTCTGGTGCATTGGAGAATATGGTGAAATG
genomic: GATATACAGTAAGGTCCCTTTACAGAGCATTCCAAGCATCAGTGGAACAGgtatgcaggt ... tttttatcagGAATGCCTTGTACGAGTGGCGGTCTGGTGCATTGGAGAATATGGTGAAATG
EST: gi|110416791|gb|EC982796.1|EC982796
EST:     GATATACAGTAAGGTCCCTTTACAGAGCATTCCAAGCATCAGTGGAACAG                         GAATGCCTTGTACGAGTGGCGGTCTGGTGCATTGGAGAATATGGTGAAATG
genomic: GATATACAGTAAGGTCCCTTTACAGAGCATTCCAAGCATCAGTGGAACAGgtatgcaggt ... tttttatcagGAATGCCTTGTACGAGTGGCGGTCTGGTGCATTGGAGAATATGGTGAAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catataatctattctctcactctttcttagaagattgttttgatatttttatcagGAATGCCTTGTACGAGTGGCGGTCTGGTGCATTGGAGAATATGGTGAAATGTTAGTCAATAATGTTGGAATGCTTGATATAGAGGAACCTATAACT
                                             tttttatc  CT-rich tract
                              aagattgttttgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaaatctgttcccatttccactacccagtagtctctgagtgttcatataatctattctctcactctttcttagaagattgttttgatatttttatcagGAATGCCTTGTACGAGTGGCGGTCTGGTGCATTGGAGAATATGGTGAAATGTTAGTCAATAATGTTGGAATGCTTGATATAGAGGAACCTATAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
aaaaaat
- - - - - - -ccatttc
- - - - - - - - - - - ctaccca
- - - - - - - - - - - - - - - - - - -tgagtgt