RnoINT0060310 @ rn6
Intron Retention
Gene
ENSRNOG00000017063 | Fcna
Description
ficolin A [Source:RGD Symbol;Acc:621221]
Coordinates
chr3:2852714-2853272:-
Coord C1 exon
chr3:2853027-2853272
Coord A exon
chr3:2852828-2853026
Coord C2 exon
chr3:2852714-2852827
Length
199 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
TTTTTTTTTTGTCTATGCAGATG
3' ss Score
11.44
Exon sequences
Seq C1 exon
ACAGGAAGTGCGCCTGGTTTTATAACTTGGGCTCCTTCTCAGGAGAAAAGCTGAGCTGGTGAGGAGTCCAGGCAGCGAGGGTCTTTGCTTCATACATCATTCACCAGCCTCTCAGCCCAGAGCCAGGGCGCCAAGGAGTGACCGCTGTGTCCAGAGCAATGTGGTGGCCTATGCTGTGGGCCTTTCCAGTACTGCTCTGTCTCTGTTCCTCCCAGGCCCTGGGTCAGGAGAGTGGTGCCTGTCCAG
Seq A exon
GTGAGAGGGTCCACTCGGGAAGGTGGACAAACACATTCTGTGTGTGTCTGCACATGTGGCAGCAGTGAACAGGACACTTCAGGAGGGCAGCCTAAGGCCACATCCGAGGCTGCTTGAGTGTTCGTGGGTACAGAAAGCTGTGGGTTTTTTAATGCTACTCAAAGCCACCCCTCTTTTTTTTTTTTTTTTGTCTATGCAG
Seq C2 exon
ATGTTAAGATCGTAGGTCTGGGGGCCCAGGACAAGGTGGCTGTCATCCAAAGTTGCCCTAGCTTTCCTGGCCCACCTGGACCCAAAGGGGAGCCTGGAAGTCCTGCTGGGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017063:ENSRNOT00000023022:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.564
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0139113=Collagen=PU(27.9=43.6)
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:
AAAGCTGAGCTGGTGAGGAGT
R:
GATGACAGCCACCTTGTCCTG
Band lengths:
247-446
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]