RnoINT0060318 @ rn6
Intron Retention
Gene
ENSRNOG00000017063 | Fcna
Description
ficolin A [Source:RGD Symbol;Acc:621221]
Coordinates
chr3:2849984-2850691:-
Coord C1 exon
chr3:2850557-2850691
Coord A exon
chr3:2850416-2850556
Coord C2 exon
chr3:2849984-2850415
Length
141 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAT
5' ss Score
8.76
3' ss Seq
GGGCTGACAGGTCTTTGCAGGAG
3' ss Score
-0.64
Exon sequences
Seq C1 exon
GGAACCAAGAGCTCCGGGTTGACTTAAGAGAGTTCCAAGGTCAAACCTCCTTTGCCAAATACAGCTCATTCCAGGTATCTGGAGAACAGGAGAAATACAAGCTGACCTTGGGGCAGTTTCTGGAGGGCACTGCAG
Seq A exon
GTAAATCACACAGAAAGCTTGAGGCTGTTGGTGGGGATGTGAAAGGGGGCCCACAAGCCGTCCCTGCCCATCTGAGCTGGGCTCCGCCTCGTCCTGAGGGCTGGGCTCTGCCTCGTCCTGAGGGCTGACAGGTCTTTGCAG
Seq C2 exon
GAGACTCCCTGACAAAGCACAACAACATGGCATTCTCAACTCATGACCAAGATAATGATACGAATGGCGGGAAGAACTGTGCAGCTTTGTTCCACGGAGCCTGGTGGTACCACGACTGTCACCAGTCCAACCTCAACGGGCGCTACTTGCCTGGCTCCCATGAAAGTTATGCGGATGGCATCAACTGGCTAAGTGGCCGAGGCCACCGCTACTCCTACAAGGTTGCTGAGATGAAAATCCGGGCATCATAAGGTGCCCCAGCCTCCACCCACCCCTGCAGCCATGCCCAGGCCATGTGGGGACACTGAAGGAAGGGGTCACGAGAAGATGGGGTCTGTGGCTGTATGTCGTGTGCTCTGGACACTGTCCAGCACTGACCAGTATGCACTAATAAAGGTCAGAGAAGCAGAGGTGAAAGCCTGTTCGCTGAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017063:ENSRNOT00000023022:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.169
Domain overlap (PFAM):
C1:
PF0014713=Fibrinogen_C=FE(21.0=100)
A:
NA
C2:
PF0014713=Fibrinogen_C=PD(38.3=97.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGACCTTGGGGCAGTTTCTG
R:
ACCTTGTAGGAGTAGCGGTGG
Band lengths:
257-398
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]