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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgtgatttgaattttgtgtcttgacattcatgattcataatcctgacattcctaccatctatggcatctgatattcatcaagttttttcttaatttagATCCGGGTTTTCTTTTCTGTGCCTGAGAGCGTAGCAGCAAAAATTGAGCTGCCAGATTCTTTTTTCAACCTCTCGATTGGAGAGCTGAAAAGAGAAGCCG

Basic information

species Vitis vinifera
transcript Vv01s0011g05570.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g05570.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G04760.3 (Glycine max), 3'ss of exon 2
----tatgtgatttgaattttgtgtcttgacattcatgattcataatcctgacattcctaccatctatggcatctgatattc---atcaagttttttcttaatttagATCCGGGTTTTCTTTTCTGTGCCTGAGAGCGTAGCAGCAAAAATTGAGCTGCCAGATTCTTTTTTCAACCTCTCGATTGGAGAGCTGAAAAGAGAAGCCG
    ||| |  ||||  | ||   | ||||  ||||  | | | ||  |    | || |   ||  |     |||| | ||     | ||  ||  |||||    || |   ||| |||||| |||| ||||| || || ||||| |||||||||||||||||||| || |  || || ||   || |||| | | ||||||||| |
tagttat-tagtttggctctt---tattgattttcaaaaataagaaatcaactaatctttagattgaatatgtctgttttttccatttaaaattgctctta---cagGTGAAGGTCTTCTTTGCTGTCCCTGAAAGTGTTGCAGCTAAAATTGAGCTGCCAGATTCCTTCTATAAACTTTCAGCTGAAGAGGTCAGAAGAGAAGCTG
















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|110383250|gb|EC947609.1|EC947609
EST:     CTGAGGCTGATGTAGAAGAGCCCGTTGAGCTGAAAAAGGTCGACAGGCAG                         ATCCGGGTTTTCTTTTCTGTGCCTGAGAGCGTAGCAGCAAAAATTGAGCTG
genomic: CTGCGGCTGATGTAGAAGAGCCCGTTGAGCTGAAAAAGGTCGACAGGCAGgtagggtaat ... cttaatttagATCCGGGTTTTCTTTTCTGTGCCTGAGAGCGTAGCAGCAAAAATTGAGCTG
EST: gi|110687439|gb|EE064851.1|EE064851
EST:     CTGAGGCTGATGTAGAAGAGCCCGTTGAGCTGAAAAAGGTCGACAGGCAG                         ATCCGGGTTTTCTTTTCTGTGCCTGAGAGCGTAGCAGCAAAAATTGAGCTG
genomic: CTGCGGCTGATGTAGAAGAGCCCGTTGAGCTGAAAAAGGTCGACAGGCAGgtagggtaat ... cttaatttagATCCGGGTTTTCTTTTCTGTGCCTGAGAGCGTAGCAGCAAAAATTGAGCTG
EST: gi|110363232|gb|EC926808.1|EC926808
EST:     GATGTAGAAGAGCCCGTTGAGCTGAAAAAGGTCGACAGGCAG                         ATCCGGGTTTTCTTTTCTGTGCCTGAGAGCGTAGCAGCAAAAATTGAGCTG
genomic: GATGTAGAAGAGCCCGTTGAGCTGAAAAAGGTCGACAGGCAGgtagggtaat ... cttaatttagATCCGGGTTTTCTTTTCTGTGCCTGAGAGCGTAGCAGCAAAAATTGAGCTG
EST: gi|18458159|gb|BM436437.1|BM436437
EST:     CTGAGGCTGATGTAGAAGAGCCCGTTGAGCTGAAAAAGGTCGACAGGCAG                         ATCCGGGTTTTCTTTTCTGTGCCTGAGAGCGTAGCAGCAAAAATTGAGCTG
genomic: CTGCGGCTGATGTAGAAGAGCCCGTTGAGCTGAAAAAGGTCGACAGGCAGgtagggtaat ... cttaatttagATCCGGGTTTTCTTTTCTGTGCCTGAGAGCGTAGCAGCAAAAATTGAGCTG
EST: gi|110363231|gb|EC926807.1|EC926807
EST:     AAGAGCCCGTTGAGCTGAAAAAAGGTCGACAGGCAG                         ATCCGGGTTTTCTTTTCTGTGCCTGAGAGCGTAGCAGCAAAAATTGAGCTG
genomic: AAGAGCCCGTTGAGCTG-AAAAAGGTCGACAGGCAGgtagggtaat ... cttaatttagATCCGGGTTTTCTTTTCTGTGCCTGAGAGCGTAGCAGCAAAAATTGAGCTG
EST: gi|110386741|gb|EC951362.1|EC951362
EST:     CTGAGGCTGATGTAGAAGAGCCCGTTGAGCTGAAAAAGGTCGACAGGCAG                         ATCCGGGTTTTCTTTTCTGTGCCTGAGAGCGTAGCAGCAAAAATTGAGCTG
genomic: CTGCGGCTGATGTAGAAGAGCCCGTTGAGCTGAAAAAGGTCGACAGGCAGgtagggtaat ... cttaatttagATCCGGGTTTTCTTTTCTGTGCCTGAGAGCGTAGCAGCAAAAATTGAGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacattcctaccatctatggcatctgatattcatcaagttttttcttaatttagATCCGGGTTTTCTTTTCTGTGCCTGAGAGCGTAGCAGCAAAAATTGAGCTGCCAGATTCTTTTTTCAACCTCTCGATTGGAGAGCTGAAAAGAGAAGCCG
                                       ttttttcttaattt  CT-rich tract
                           atattcatcaagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgtgatttgaattttgtgtcttgacattcatgattcataatcctgacattcctaccatctatggcatctgatattcatcaagttttttcttaatttagATCCGGGTTTTCTTTTCTGTGCCTGAGAGCGTAGCAGCAAAAATTGAGCTGCCAGATTCTTTTTTCAACCTCTCGATTGGAGAGCTGAAAAGAGAAGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - tgtcttg
- - - - - - - - - - - - - cattcat
- - - - - - - - - - - - - - - - - - - - - -cctgaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatcaa