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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttttttttttgcattcagcatattctgttttagttttctagctgttctttgattcacttgcatctccctgaacgtgctttatttggtattttgctctatttttacagCACAAAGTCAGGTGGCAAATTGGCTTCACTTGATCAATATATCTCAAGAATGAAACCAGGACAGAAGGATATCTTCTACATCACGGGTAACAGCAAGGAG

Basic information

species Vitis vinifera
transcript Vv18s0001g14500.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: PP1S126_38V6.1 (Physcomitrella patens), 3'ss of exon 12
gtactttttttttttgcattcagcatattctgttttagttttctagctgttctttgattcacttgcatctccctgaacgtgctttatttggtattttgctctatttttacagCACAAAGTCAGGTGGCAAATTGGCTTCACTTGATCAATATATCTCAAGAATGAAACCAGGACAGAAGGATATCTTCTACATCACGGGTAACAGCAAGGAG
                || | |     |  |    |   |||     ||    ||||  || || |     | |  | || | |  |   || || |  ||    | | |||  | ||||| || |  |||||| ||||||| |||||||| |||||| |||||||||||||||||||| | || | |||  |||| ||| |    | | | 
-----------gcggccagtaaaggcgtaatagaatgtatttacccttgcgtcttgaaacaattacgctgtcgtagaagtacat-gtaacgtcttcttatcgcggtgtgcagTTCTAAGTCTGGCGATAAATTGACTTCACTGGATCAATACATCTCACGAATGAAACCAGGACAGAAGCAAATTTACTATCTCACTGGTCAAGATAGGAAA
















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|161715138|gb|FC064271.1|FC064271
EST:     GAAGATGCATCCAACAGATACCGCTTGGCCAAGCTTCTCAGATTTGAAAG                         CACAAAGTCAGGTGGCAAATTGGCTTCACTTGATCAATATATCTCAAGAAT
genomic: GAAGATGCATCCAACAGAAACCGCTTGGCCAAGCTTCTCAGATTTGAAAGgtactttttt ... atttttacagCACAAAGTCAGGTGGCAAATTGGCTTCACTTGATCAATATATCTCAAGAAT
EST: gi|22008983|gb|BQ794017.1|BQ794017
EST:     GAAGATGCATCCAACAGAAACCGCTTGGCCAAGCTTCTCAGATTTGAAAG                         CACAAAGTCAGGTGGCAAATTGGCTTCACTTGATCAATATATCTCAAGAAT
genomic: GAAGATGCATCCAACAGAAACCGCTTGGCCAAGCTTCTCAGATTTGAAAGgtactttttt ... atttttacagCACAAAGTCAGGTGGCAAATTGGCTTCACTTGATCAATATATCTCAAGAAT
EST: gi|110719823|gb|EE095290.1|EE095290
EST:     GAAGATGCATCCAACAGAAACCGCTTGGCCAAGCTTCTCAGATTTGAAAG                         CACAAAGTCAGGTGGCAAATTGGCTTCACTTGATCAATATATCTCAAGAAT
genomic: GAAGATGCATCCAACAGAAACCGCTTGGCCAAGCTTCTCAGATTTGAAAGgtactttttt ... atttttacagCACAAAGTCAGGTGGCAAATTGGCTTCACTTGATCAATATATCTCAAGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcacttgcatctccctgaacgtgctttatttggtattttgctctatttttacagCACAAAGTCAGGTGGCAAATTGGCTTCACTTGATCAATATATCTCAAGAATGAAACCAGGACAGAAGGATATCTTCTACATCACGGGTAACAGCAAGGAG
                                    ttttgctctattttt  CT-rich tract
                         tttatttggtatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactttttttttttgcattcagcatattctgttttagttttctagctgttctttgattcacttgcatctccctgaacgtgctttatttggtattttgctctatttttacagCACAAAGTCAGGTGGCAAATTGGCTTCACTTGATCAATATATCTCAAGAATGAAACCAGGACAGAAGGATATCTTCTACATCACGGGTAACAGCAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG