DreEX6035645 @ danRer10
Exon Skipping
Gene
ENSDARG00000019815 | fn1a
Description
fibronectin 1a [Source:ZFIN;Acc:ZDB-GENE-000426-1]
Coordinates
chr9:15405061-15409134:-
Coord C1 exon
chr9:15409018-15409134
Coord A exon
chr9:15406510-15406674
Coord C2 exon
chr9:15405061-15405216
Length
165 bp
Sequences
Splice sites
3' ss Seq
GATTTTTTTTTTCAATGCAGGTG
3' ss Score
9.65
5' ss Seq
CCGGTAAAC
5' ss Score
4.81
Exon sequences
Seq C1 exon
TCTCTGATGCTCCTACTGACCTGGAAGTGATTTCCTCAACGCCGACCAGCATCACCGTTCGCTGGGATGCCCCCTCTGTCACTGTGCGGTACTACAGGATTACACATGGAGAGTCGG
Seq A exon
GTGGTTCTGATGCCCCTCTGGAATTTATGGTTCCCGGCTCCCAGTCTACAGCCACTATTGAAGATCTACGTCCAGGCACTGATTATACCATTACTGTTTATGCTGTGACCGGTAGAGGGGACAGCCCTGCATCCAGCACTCCCATCCATGTTAAACATAGAACCG
Seq C2 exon
ATATTGACTCTCCATCACAGATGGAGGTGACTGACGTGAAGGACAACACTATTACTGTACGCTGGACCCCAGCAGCCGGCCCCATCTCAAGATACAGAGTCAATGCAACTCCTCTTACTGGAGAAGGACCTGTGTTACATGCAGAAACGACTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000019815-'36-38,'36-37,37-38=AN
Average complexity
A_S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.275 A=0.750 C2=0.623
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(45.1=92.5)
A:
PF0004116=fn3=PD(53.7=78.6)
C2:
PF0004116=fn3=PU(61.7=94.3)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTGATTTCCTCAACGCCGAC
R:
TCGTTTCTGCATGTAACACAGGT
Band lengths:
242-407
Functional annotations
There are 4 annotated functions for this event
PMID: 6325925
Encodes an experimentally validated Eukaryotic Linear Motif (ELM). Method: cross linking study, overlapping binding peptide, x-ray crystallography. ELM ID: ELMI000104; ELM sequence: RGD; Overlap: FULL
PMID: 19738201
Encodes an experimentally validated Eukaryotic Linear Motif (ELM). Method: cross linking study, overlapping binding peptide, x-ray crystallography. ELM ID: ELMI000104; ELM sequence: RGD; Overlap: FULL
PMID: 22451694
Encodes an experimentally validated Eukaryotic Linear Motif (ELM). Method: cross linking study, overlapping binding peptide, x-ray crystallography. ELM ID: ELMI000104; ELM sequence: RGD; Overlap: FULL
PMID: 9533887
Encodes an experimentally validated Eukaryotic Linear Motif (ELM). Method: structure based prediction. ELM ID: ELMI000105; ELM sequence: RGD; Overlap: FULL
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]