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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACAGATGGGCGAGAGCTTGTAGCTGGAAGTAGTGATGATTCAATATATGTTTATGATCTTGAAGCAAATAAGCTTTCCCTTAGAATTTTGGCACACACGgtatagattatgtgtgataaacgattttcttatattattcttcagttgatttggaaattttgtttggctgatcattgctttttgtttcccattgaatgtg...

Basic information

species Vitis vinifera
transcript Vv07s0104g00900.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0104g00900.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os05g33710.1 (Oryza sativa), 5'ss of exon 5
CACAGATGGGCGAGAGCTTGTAGCTGGAAGTAGTGATGATTCAATATATGTTTATGATCTTGAAGCAAATAAGCTTTCCCTTAGAATTTTGGCACACACGgtatagattatgtgtgataaacgattttcttatattattcttcagttgatttggaaattttgtttggctgatcattgcttttt-----gtttcccattgaatgtg-------------------
  | ||||| ||||||||||| ||||| ||||  ||||||||||||||||||||||| ||||  ||||| || ||  |  |  |  |    || ||    |||| ||| || || | |       |  ||| |||  || || | |    ||      ||| ||  | || | || |  | ||      |||    |  ||||||                   
TTCTGATGGCCGAGAGCTTGTTGCTGGCAGTAACGATGATTCAATATATGTTTATGACCTTGTGGCAAACAAACTAACGTTGCGTTTGCCTGCTCATCATgtat-gataatttg-gttgttttcatggcttgtatctttatttaatcttcttaatctatttcttaagttggttatgggctctttccatatttgatctctaatgtgttcccccctacttttccag

upper sequence: Vv07s0104g00900.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA02G17000.1 (Glycine max), 5'ss of exon 6
CACAGATGGGCGAGAGCTTGTAGCTGGAAGTAGTGATGATTCAATATATGTTTATGATCTTGAAGCAAATAAGCTTTCCCTTAGAATTTTGGCACACACGgtatagattatgtgtgataaacgattttcttatattattcttcagttgatttggaaattttgtttggctgatcattgctttttgt-ttcccattgaatgtg----
     | ||| ||||  | || || |||||||||| |||||| || ||||| ||||||||||||||||||||||| || ||| ||||||| ||||||||||||| | |||   |  |||||   |    |||| |    ||||   || ||| |   | |||||||  |    |||| ||| ||| ||    ||| |   |    
-----ACGGGAGAGAATTAGTTGCAGGAAGTAGTGGTGATTCTATTTATGTATATGATCTTGAAGCAAATAAGCTCTCACTTCGAATTTTAGCACACACGgtattg-ttactaggcataaatactacatttatttag--cttcgtgtgctttaggc-tattgtttga-tatctattggtttatgtatttttgttgcagaaggatt

upper sequence: Vv07s0104g00900.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA10G02800.1 (Glycine max), 5'ss of exon 5
CACAGATGGGCGAGAGCTTGTAGCTGGAAGTAGTGATGATTCAATATATGTTTATGATCTTGAAGCAAATAAGCTTTCCCTTAGAATTTTGGCACACACGgtatagattatgtgtgataaacgattttcttatattattcttcagttgatttggaaattttgtttggctgatcattgctttttgt-ttcccattg---aatgtg-
 | |||||||  |||  | || || |||||||||| |||||| |||||||| || |||||||||||||||||||| || ||| ||||||| || |||||||||| | |||   |  |||||   |    |||| |    |||||  || ||| |   | |||||||  |    |||| ||| ||| ||    |||   ||| |  
AAAAGATGGGAAAGAATTAGTTGCAGGAAGTAGTGGTGATTCTATATATGTATACGATCTTGAAGCAAATAAGCTCTCACTTCGAATTTTAGCTCACACGgtattg-ttactaggcataaatactacatttatttag--cttcatatgctttaggc-tattgtttga-tatctattggtttatgtatttttgttgcagaatattt

upper sequence: Vv07s0104g00900.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT4G03020.2 (Arabidopsis thaliana), 5'ss of exon 5
CACAGATGGGCGAGAGCTTGTAGCTGGAAGTAGTGATGATTCAATATATGTTTATGATCTTGAAGCAAATAAGCTTTCCCTTAGAATTTTGGCACACACGgtatagat-tatgtgtgataaacgattttcttatattattcttcagttgatttggaaattttgtttggctgatcattgcttt-ttgtttcc-cattgaatgtg------------------
 |||||||| |||||  |||| ||||| || ||||||||||| || ||||||||||| ||||||||||||    |||| ||  | | | | |||||||||||| |    | | |  | | |   | |||||  ||  |||  | |  ||  |    |  |   | | | |  |  |  | || | ||||   || |||  |                    
AACAGATGGCCGAGAAGTTGTTGCTGGGAGCAGTGATGATTCCATTTATGTTTATGACCTTGAAGCAAATCGAGTTTCACTCCGGACTGTTGCACACACGgtaaattcctttatcggttgaggcaatttctcctaagatttgt-acctgtgtgtagatctacctgttgttagtggtaacgttatcgttttagcactgatagcattttctccatttctgcag

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|71859982|gb|DT009037.1|DT009037
EST:     TTTATGATCTTGAAGCAAATAAGCTTTCCCTTAGAATTTCGGCACACACG                         TCTGATGTCAATACTGTATGCTTTGCTGATGAAAGTGGGCATC
genomic: TTTATGATCTTGAAGCAAATAAGCTTTCCCTTAGAATTTTGGCACACACGgtatagatta ... cctatggcagTCTGATGTCAATACTGTATGCTTTGCTGATGAAAGTGGGCATC
EST: gi|27579975|gb|CB002670.1|CB002670
EST:     TTTATGATCTTGAAGCAAATAAGCTTTCCCTTAGAATTTCGGCACACACG                         TCTGATGTCAATACTGTATGCTTTGCTGATGAAAGTGGGCATCTTATTTAT
genomic: TTTATGATCTTGAAGCAAATAAGCTTTCCCTTAGAATTTTGGCACACACGgtatagatta ... cctatggcagTCTGATGTCAATACTGTATGCTTTGCTGATGAAAGTGGGCATCTTATTTAT
EST: gi|110711873|gb|EE088850.1|EE088850
EST:     TTTATGATCTTGAAGCAAATAAGCTTTCCCTTANAATTTTGGCACACACG                         TCTGATGTNCA-TACTGTATGCTTTGCTGATGAAAGTGG-CATC
genomic: TTTATGATCTTGAAGCAAATAAGCTTTCCCTTAGAATTTTGGCACACACGgtatagatta ... cctatggcagTCTGATGT-CAATACTGTATGCTTTGCTGATGAAAGTGGGCATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACAGATGGGCGAGAGCTTGTAGCTGGAAGTAGTGATGATTCAATATATGTTTATGATCTTGAAGCAAATAAGCTTTCCCTTAGAATTTTGGCACACACGgtatagattatgtgtgataaacgattttcttatattattcttcagttgatttggaaattttgtttggctgatcattgctttttgtttcccattgaatgtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttggaaa