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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctacttgtttgacctgaaaggttgatttgtgagctgtaacttctattggcaaatttgtcaattccaatacctttaaaatttatatatgtctgtgctgcagCTTGATGCAGGTATAAAAGAAGCATTTGATGTGGCATATGATAACATTTTTGCATTTCATGCTGCTCAAAAGTCAGCTGAAAAAATTGTTGAGAACATGA

Basic information

species Vitis vinifera
transcript Vv18s0166g00300.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 3
--------------ctacttgtttgacctgaaaggttgatttgtgagctgtaacttctattggcaaatttg---tcaattccaatacctttaaaatttatatatgtctgtgctgcagCTTGATGCAGGTATAAAAGAAGCATTTGATGTGGCATATGATAACATTTTTGCATTTCATGCTGCTCAAAAGTCAGCTGAAAAAATTGTTGAGAACATGA
               ||    |     |||||    ||  || |||  | | | |    || |  |  |||   |     | | ||  ||     |||       | | |  ||||||||||  |   ||| || ||||| |||||||| || |||||||| |||| |||||||||||||||||| |||||| | || |||| ||||||||||||||
gtatgtttgtttggatatgcatacattctgaagatatgcctt-tga-ttatgattcactttagtgatgttggtttgggcgctattatattcttgtttttgtgccttttattttgcagCTTGAACCGCCTATTAAGGAAGCTTTTGATGTCGCCTATGATAATATTTATGCATTTCATGCTGCTCAGAAGTCATCCGAGAAAAGTGTTGAGAACATGA

upper sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA15G13910.1 (Glycine max), 3'ss of exon 3
--------------ctacttgtttgacctgaaaggttgatttgt--gagctgtaacttctattgg----caaatt-----tgtcaattccaatacctttaaaat-ttatatatgt-----ctgtgctgcagCTTGATGCAGGTATAAAAGAAGCATTTGATGTGGCATATGATAACATTTTTGCATTTCATGCTGCTCAAAAGTCAGCTGAAAAAATTGTTGAGAACATGA
               ||    |   |  ||||   ||  |||||   || | |  |||  |||      ||  ||     |||   ||      |  ||| | | || | | |||      |||  ||||||||||| ||  ||| || ||||| || ||||| || || || || |||| |||||||||||||||||| |||||| | || |||| ||||||||||||||
gtatgtttgtttggatatgcatacaatatgaagttttattttgttgaagatatgcctttgattatgattcactttagtgatgttggtttgggcgctattatattcttgtttttgtgccttttgttttgcagCTTGATCCACCTATTAAGGAAGCTTTCGATGTTGCCTACGACAATATTTATGCATTTCATGCTGCTCAGAAGTCACCCGAGAAAAGTGTTGAGAACATGA
















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|351014573|gb|FQ437575.1|FQ437575
EST:     TTGAACTAGATAGATTAATTGAAAATGTTGCTGAACTTCCAGATCCAGAG                         CTTGATGCAGGTATAAAAGAAGCATTTGATGTGGCATATGATAACATTTTT
genomic: TTGAACTAGATAGATTAATTGAAAATGTTGCTGAACTTCCAGATCCAGAGgtattccttc ... tgtgctgcagCTTGATGCAGGTATAAAAGAAGCATTTGATGTGGCATATGATAACATTTTT
EST: gi|351043930|gb|FQ431361.1|FQ431361
EST:     TTGAACTAGATAGATTAATTGAAAATGTTGCTGAACTTCCAGATCCAGAG                         CTTGATGCAGGTATAAAAGAAGCATTTGATGTGGCATATGATAACATTTTT
genomic: TTGAACTAGATAGATTAATTGAAAATGTTGCTGAACTTCCAGATCCAGAGgtattccttc ... tgtgctgcagCTTGATGCAGGTATAAAAGAAGCATTTGATGTGGCATATGATAACATTTTT
EST: gi|349825486|gb|FQ419403.1|FQ419403
EST:     TTGAACTAGATAGATTAATTGAAAATGTTGCTGAACTTCCAGATCCAGAG                         CTTGATGCAGGTATAAAAGAAGCATTTGATGTGGCATATGATAACATTTTT
genomic: TTGAACTAGATAGATTAATTGAAAATGTTGCTGAACTTCCAGATCCAGAGgtattccttc ... tgtgctgcagCTTGATGCAGGTATAAAAGAAGCATTTGATGTGGCATATGATAACATTTTT
EST: gi|351028553|gb|FQ444834.1|FQ444834
EST:     TTGAACTAGATAGATTAATTGAAAATGTTGCTGAACTTCCAGATCCAGAG                         CTTGATGCAGGTATAAAAGAAGCATTTGATGTGGCATATGATAACATTTTT
genomic: TTGAACTAGATAGATTAATTGAAAATGTTGCTGAACTTCCAGATCCAGAGgtattccttc ... tgtgctgcagCTTGATGCAGGTATAAAAGAAGCATTTGATGTGGCATATGATAACATTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggcaaatttgtcaattccaatacctttaaaatttatatatgtctgtgctgcagCTTGATGCAGGTATAAAAGAAGCATTTGATGTGGCATATGATAACATTTTTGCATTTCATGCTGCTCAAAAGTCAGCTGAAAAAATTGTTGAGAACATGA
              aattccaataccttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctacttgtttgacctgaaaggttgatttgtgagctgtaacttctattggcaaatttgtcaattccaatacctttaaaatttatatatgtctgtgctgcagCTTGATGCAGGTATAAAAGAAGCATTTGATGTGGCATATGATAACATTTTTGCATTTCATGCTGCTCAAAAGTCAGCTGAAAAAATTGTTGAGAACATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
ctacttg
- - - - - -acctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - caattcc