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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatattcatttacctatataatgtgttaggggtttttgtgtagttaatattgtcgtttcgcctgatcttttgactatcatttattattcttgtattcagAGACTGGCATCTGGTGAATGGTTTACTGCTCGAGTTTCTGCATGTGGACTGTTTCATATTGCTTACCCAAGTGCCCCAGAGATGTTAAAGATGGAGTTGC

Basic information

species Vitis vinifera
transcript Vv01s0011g03280.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 2
gcatattcatttacctatataatgtgttaggggtttttgtgtagttaatattgtcgtttcgcctgatcttttgactatcatttat-tattcttg---tattcagAGACTGGCATCTGGTGAATGGTTTACTGCTCGAGTTTCTGCATGTGGACTGTTTCATATTGCTTACCCAAGTGCCCCAGAGATGTTAAAGATGGAGTTGC
   |||  |   ||  | |  |  |||    |      ||  | |||   |   | ||   |   ||| |||  | || |  |    || ||||    | ||||||  ||||    ||||| |||||||| |||||||||||| ||||||| || |||||||| || || || ||||| || ||     | |||   ||  || 
---tata-acaaacgcaaagcacttgtgtatgtgggaagtacaattacgttctacattgttctatatcatttagcaattaactggacatacttgatcaactcagAGGTTGGCGGTAGGTGAGTGGTTTACAGCTCGAGTTTCTTCATGTGGCCTTTTTCATATCGCCTATCCTAGTGCACCTGAACAACTGAAGGCAGAACTGA

upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 2
gcatattcatttacctatataatgtgttaggggtttttgtgtagttaa--tattgtcgtttcgcctg------atcttttgactatcatttattattcttgtattcagAGACTGGCATCTGGTGAATGGTTTACTGCTCGAGTTTCTGCATGTGGACTGTTTCATATTGCTTACCCAAGTGCCCCAGAGATGTTAAAGATGGAGTTGC
      ||| ||    ||  | ||| | ||    |  | ||| |  |   ||   ||||||  |  |      ||| ||| |  ||  | | ||| | | || |||||||| ||||||| ||||||||||| ||||||||||| ||| |||||||||| ||||||||||||||||| || || || || |||| |||||| || ||| 
------tcaatttatgatgcattgtat-agatcctgctatgttggcagtttacattcgttttactggttgaacatcctttcaacattttcttttaatttggt-ttcagAGATTGGCATCAGGTGAATGGTTCACTGCTCGAGTGTCTTCATGTGGACTATTTCATATTGCTTACCCTAGCGCACCTGAAATGTCAAAGATAGAATTGA

upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 2
gcatattcatttacctata-taatgtgttaggggtttttgtgtagttaatattg-tcgtttcgcctgatc-ttttgacta--tcat-ttattattcttgtattcagAGACTGGCATCTGGTGAATGGTTTACTGCTCGAGTTTCTGCATGTGGACTGTTTCATATTGCTTACCCAAGTGCCCCAGAGATGTTAAAGATGGAGTTGC
      |  |||  |  || |  ||||||    || |     |||||   |||| |    | |  ||| | || || | |  ||||  | | ||| || | |||||||| ||||| | ||||||||||||||||||||||| |||||||||||||| ||||||||||| ||||| || || ||||| |  | |||||  |||||| 
------ttgtttgtcattaatggtgtgttgtatgtatcctgctagttcccattgattaagttgattgaacattctgtccaattcatgctgtgattattttgttcagAGATTGGCAGCAGGTGAATGGTTTACTGCTCGAGTCTCTGCATGTGGACTATTTCATATTGCATACCCTAGCGCACCAGAAACATCAAAGACAGAGTTGA

upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 2
gcatattcatttacc-tatataatgtgttaggggtttttgtgtagttaatattg-tcgtttcgcctgatc-ttttgactatcatttatta----ttcttgtattcagAGACTGGCATCTGGTGAATGGTTTACTGCTCGAGTTTCTGCATGTGGACTGTTTCATATTGCTTACCCAAGTGCCCCAGAGATGTTAAAGATGGAGTTGC
         |||  | | |||  | || |    || |     |||||   |||| |    | |  ||| | || || | |     |  |     || || | |||||||| ||||| | |||||||||||||| || ||||| |||||||||||||| ||||||||||| ||||| || || ||||| |  | |||||  |||||| 
-------tgtttgtcatttatggtctgctgtatgtatcctgctagttcccattgattaagttgattgaacattctgtccaattcatgctgcgattttttttgttcagAGATTGGCAGCAGGTGAATGGTTTACCGCCCGAGTCTCTGCATGTGGACTATTTCATATTGCATACCCTAGCGCACCAGAAACATCAAAGACAGAGTTGA

upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 2
gcatattcatttacctatataatgtgttaggggtttttgtgtagttaatattgtcgtttcgcctgatcttttgactatcatttattattcttgtatt-cagAGACTGGCATCTGGTGAATGGTTTACTGCTCGAGTTTCTGCATGTGGACTGTTTCATATTGCTTACCCAAGTGCCCCAGAGATGTTAAAGATGGAGTTGC
      |  |     | |||       ||      |  || ||| |  |  |   ||    || ||  |    | ||      | | |  |||| |  ||| ||||  || ||||||||||||| || ||  |||| || ||||||||  | || |||||||| |||||||||||||||||  || |||||| |||| |  
tttgggttgtggttgtgtatgtgaccatacatacctcggtataggtgctcgtaatgtgaaacc-gacttaagcattactgaacactgtcattgtgtaacagCGACTTTCAGCTGGTGAATGGTTCACAGCCAGAGTATCAGCATGTGGGATTTTCCATATTGCATACCCAAGTGCCCCAGATGTGCTAAAGACGGAGCTAA

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|161713352|gb|FC063363.1|FC063363
EST:     CTCGAATGAAAGAAAATGATTTGATTAACTGGTTTATTCCTTTGGTGAAG                         AGACTGGCATCTGGTGAATGGTTTACTGCTCGAGTTTCTGCATGTGGACTG
genomic: CTCAAATGAAGGAAAATGATTTGATTAACTGGTTTATTCCTTTGGTGAAGgtgacttaac ... ttgtattcagAGACTGGCATCTGGTGAATGGTTTACTGCTCGAGTTTCTGCATGTGGACTG
EST: gi|161706094|gb|FC056244.1|FC056244
EST:     CTCAAATGAAGGAAAATGATTTGATTAACTGGTTTATTCCTTTGGTGAAG                         AGACTGGCATCTGGTGAATG
genomic: CTCAAATGAAGGAAAATGATTTGATTAACTGGTTTATTCCTTTGGTGAAGgtgacttaac ... ttgtattcagAGACTGGCATCTGGTGAATG
EST: gi|30303369|gb|CB980163.1|CB980163
EST:     CTCAAATGAAGGAAAATGATTTGATTAACTGGTTTATTCCTTTGGTGAAG                         AGACTGGCATCTGGTGAATGGTTTACCGCTCGAGTTTCTGCATGTGGACTG
genomic: CTCAAATGAAGGAAAATGATTTGATTAACTGGTTTATTCCTTTGGTGAAGgtgacttaac ... ttgtattcagAGACTGGCATCTGGTGAATGGTTTACTGCTCGAGTTTCTGCATGTGGACTG
EST: gi|110724591|gb|EE100555.1|EE100555
EST:     CTCAAATGAAGGAAAATGATTTGATTAACTGGTTTATTCCTTTGGTGAAG                         AGACTGGCATCTGGTGAATGGTTTACCACTCGAGTTTCTGCATGTGGACTG
genomic: CTCAAATGAAGGAAAATGATTTGATTAACTGGTTTATTCCTTTGGTGAAGgtgacttaac ... ttgtattcagAGACTGGCATCTGGTGAATGGTTTACTGCTCGAGTTTCTGCATGTGGACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatattgtcgtttcgcctgatcttttgactatcatttattattcttgtattcagAGACTGGCATCTGGTGAATGGTTTACTGCTCGAGTTTCTGCATGTGGACTGTTTCATATTGCTTACCCAAGTGCCCCAGAGATGTTAAAGATGGAGTTGC
                       ttttgac  putative branch site (score: 3)
                                       ttattctt  putative PPT
                              tatcatttattattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatattcatttacctatataatgtgttaggggtttttgtgtagttaatattgtcgtttcgcctgatcttttgactatcatttattattcttgtattcagAGACTGGCATCTGGTGAATGGTTTACTGCTCGAGTTTCTGCATGTGGACTGTTTCATATTGCTTACCCAAGTGCCCCAGAGATGTTAAAGATGGAGTTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - -catttac
- - - - - - - - - - - - - - -ggggttt