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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgcaatagaataaatctttcagatttgtttagttgttttttcttgaaacctcttcttgctttcttactagttctgattttgaatgatgataattgcagATATACTTCAAAGATGCTTTTGGCTGCAATTGATGAACGCCACCGGGGGACTTACGATTTCATTTACCTACCCATTGATTTCAAG

Basic information

species Vitis vinifera
transcript Vv01s0150g00090.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0150g00090.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G451716_T01 (Zea mays), 3'ss of exon 11
-actgcaatagaataaatctttcagatttgtttagttgttttttcttgaaacctcttcttgctttcttactagttctgattttgaatgatgataattgcagATATACTTCAAAGATGCTTTTGGCTGCAATTGATGAACGCCACCGGGGGACTTACGATTTCATTTACCTACCCATTGATTTCAAG
   |  |  |||  |  | ||  || ||| | |    | | ||   ||       |  |     | ||  |  |||  ||  |   |  || | || | || || || |||||||||||| |||| || ||||||||| | |||||||| ||||| ||||| || ||||| || ||||| || |||
gtatatatcagag-atttattctagttttctgtgaaggatcttctatgttttaagtcatacaaattttgatgtttcccataatcctttgtggtgat-gtagGTACACATCAAAGATGCTTCTGGCAGCTATTGATGAAAGTCACCGGGGAACTTATGATTTTATCTACCTGCCAATTGACTTTAAG
















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|110732197|gb|EE107275.1|EE107275
EST:     CGAGGGGACGACACCCGGACAACACTCATGATAAAGAACATTCCCAACAA                         ATATACTTCAAAGATGCTTTTGGCTGCAATTGATGAAACGCCACCGGGGGA
genomic: CGAGGGGAGGACACCCGGACAACACTCATGATAAAGAACATTCCCAACAAgtatgtggca ... ataattgcagATATACTTCAAAGATGCTTTTGGCTGCAATTGATG-AACGCCACCGGGGGA
EST: gi|110429936|gb|EC996451.1|EC996451
EST:     CCCGGACAACACTCATGATAAAGAACATTCCCTACAA                         ATATACTTCAAAGATGCTTTTGGCTGCAATTGATGAACGCCACCGGGGTAC
genomic: CCCGGACAACACTCATGATAAAGAACATTCCCAACAAgtatgtggca ... ataattgcagATATACTTCAAAGATGCTTTTGGCTGCAATTGATGAACGCCACCGGGGGAC
EST: gi|110389267|gb|EC954091.1|EC954091
EST:     CGAGGGGAGGACACCCGGACAACACTCATGATAAAGAACATTCCCAACAA                         ATATACTTCAAAGATGCTTTTGGCTGCAATTGATGAACGCCACCGGGGGAC
genomic: CGAGGGGAGGACACCCGGACAACACTCATGATAAAGAACATTCCCAACAAgtatgtggca ... ataattgcagATATACTTCAAAGATGCTTTTGGCTGCAATTGATGAACGCCACCGGGGGAC
EST: gi|32245389|gb|CD711208.1|CD711208
EST:     CGGACAACACTCATGATAAAGAACATTCCCAACAA                         ATATACTTCAAAGATGCTTTTGGCTGCAATTGATGAACGCCACCGGGGTAC
genomic: CGGACAACACTCATGATAAAGAACATTCCCAACAAgtatgtggca ... ataattgcagATATACTTCAAAGATGCTTTTGGCTGCAATTGATGAACGCCACCGGGGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaacctcttcttgctttcttactagttctgattttgaatgatgataattgcagATATACTTCAAAGATGCTTTTGGCTGCAATTGATGAACGCCACCGGGGGACTTACGATTTCATTTACCTACCCATTGATTTCAAG
                                attttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgcaatagaataaatctttcagatttgtttagttgttttttcttgaaacctcttcttgctttcttactagttctgattttgaatgatgataattgcagATATACTTCAAAGATGCTTTTGGCTGCAATTGATGAACGCCACCGGGGGACTTACGATTTCATTTACCTACCCATTGATTTCAAG

-ctgcaat
- - - - -gaataaa