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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaaaagtggtaggccttatctgttatacctttagaattaaatagttgacttttaaagggaaaataattgttaattttaaaattcttccttctgttacagGTTGGGTAAACCGGTTCGCCAATGCTGGTGATGCTGCCATGGAAGTAGCAGGAAATACAGCATTGCGG

Basic information

species Vitis vinifera
transcript Vv16s0050g01050.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g01050.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G24630.1 (Glycine max), 3'ss of exon 2
acaaaagtggtaggccttatctgttatacctttagaat-taaatagttgacttttaaagggaaaataattgttaatttta-aaattcttcc---ttctgttacagGTTGGGTAAACCGGTTCGCCAATGCTGGTGATGCTGCCATGGAAGTAGCAGGAAATACAGCATTGCGG
      |  | |||  | | |  | || | |  |   | | |||  ||| ||| |  |    |  |   ||||     |    |||||| |   |||  | ||||||||||| ||  |||| ||||||||||||||| |||| |||||||| || |||||||||||||| |||
----gtgaaggaggtttaagcattgatccatccaacttgtgaattattg-cttctgtacattacttttctgtttccactgtgtattcttacaacttccatgacagGTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGG

upper sequence: Vv16s0050g01050.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G29860.1 (Glycine max), 3'ss of exon 2
acaaaagtggtaggccttatctgttatacctttagaattaaatagttgacttttaaagggaaaataattgttaatttta-aaattcttcc---ttctgttacagGTTGGGTAAACCGGTTCGCCAATGCTGGTGATGCTGCCATGGAAGTAGCAGGAAATACAGCATTGCGG
   |  |  | |||    | |  | || | | | |   |||||  |||  || |  |  | |  |  ||| |     |  | |||||| |   |||  | ||||| ||||| ||  |||| ||||||||||||||| ||||||||||||| || |||||||||||||| |||
cttagtgaaggaggttaaagcattgatccatcttg---taaattattg-tttctgtacagtacttttttgcttccactgtatattcttacggcttccatgacagGCTGGGTGAATAGGTTTGCCAATGCTGGTGATACTGCCATGGAAGTGGCTGGAAATACAGCATTACGG
















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|161713166|gb|FC064316.1|FC064316
EST:     TCACTTCTGTGATGAGTTATGTGAAAAACTTGGTGTGCCGAAGCTTCCTG                         GTTGGGTAAACCGGTTCGCCAATGCTGGTGATGCTGCCATGGAAGTAGCAG
genomic: TCACTTCTGTGATGAGTTATGTGAAAAACTTGGTGTGCCGAAGCTTCCTGgtattattca ... tctgttacagGTTGGGTAAACCGGTTCGCCAATGCTGGTGATGCTGCCATGGAAGTAGCAG
EST: gi|110730010|gb|EE106598.1|EE106598
EST:     TCACTTCTGTGATGAGTTATGTGAAAAACTTGATGTGCCGAAGCTTCCTG                         GTTGGGTAAACCGGTTCGCCAATGCTGGTGGATGCTGC-ATGGAAGTAGCA
genomic: TCACTTCTGTGATGAGTTATGTGAAAAACTTGGTGTGCCGAAGCTTCCTGgtattattca ... tctgttacagGTTGGGTAAACCGGTTCGCCAATGCTGGTG-ATGCTGCCATGGAAGTAGCA
EST: gi|110712053|gb|EE089238.1|EE089238
EST:     TCACTTCTGTGATGAGTTATGTGAAAAACTTGATGTGCCGAAGCTTCCTG                         GTTGGGTAAACCGGTTCGCCAATGCTGGTGATGCTGCCATGGAAGTAGCAG
genomic: TCACTTCTGTGATGAGTTATGTGAAAAACTTGGTGTGCCGAAGCTTCCTGgtattattca ... tctgttacagGTTGGGTAAACCGGTTCGCCAATGCTGGTGATGCTGCCATGGAAGTAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgacttttaaagggaaaataattgttaattttaaaattcttccttctgttacagGTTGGGTAAACCGGTTCGCCAATGCTGGTGATGCTGCCATGGAAGTAGCAGGAAATACAGCATTGCGG
                       tgttaat  putative branch site (score: 3)
                                     ttcttccttctgttac  putative PPT
     ttttaaagggaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaaaagtggtaggccttatctgttatacctttagaattaaatagttgacttttaaagggaaaataattgttaattttaaaattcttccttctgttacagGTTGGGTAAACCGGTTCGCCAATGCTGGTGATGCTGCCATGGAAGTAGCAGGAAATACAGCATTGCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
acaaaag
- - - - ggtaggc
- - - - - - - - - - - - - - - - - -aattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa