RnoINT0060311 @ rn6
Intron Retention
Gene
ENSRNOG00000017063 | Fcna
Description
ficolin A [Source:RGD Symbol;Acc:621221]
Coordinates
chr3:2852556-2852827:-
Coord C1 exon
chr3:2852714-2852827
Coord A exon
chr3:2852610-2852713
Coord C2 exon
chr3:2852556-2852609
Length
104 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGCA
5' ss Score
4.75
3' ss Seq
TTTCATCCTTGTGTTTACAGGGG
3' ss Score
9.66
Exon sequences
Seq C1 exon
ATGTTAAGATCGTAGGTCTGGGGGCCCAGGACAAGGTGGCTGTCATCCAAAGTTGCCCTAGCTTTCCTGGCCCACCTGGACCCAAAGGGGAGCCTGGAAGTCCTGCTGGGAGAG
Seq A exon
GTAGCAATCTGGATGGGAAAGGGATCCCCCTTCACCTCCCCTTGGTCAGTCTTTCTCCAATCCTACCTAGGAGATGGGATCCAGTTTCATCCTTGTGTTTACAG
Seq C2 exon
GGGAACGGGGCTTACAGGGCAGCCCAGGGAAGATGGGACCCGCCGGCAGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017063:ENSRNOT00000023022:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.564 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(27.9=43.6)
A:
NA
C2:
PF0139113=Collagen=FE(29.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTAAGATCGTAGGTCTGGGGGC
R:
GCGGGTCCCATCTTCCCT
Band lengths:
154-258
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]