RnoINT0058133 @ rn6
Intron Retention
Gene
ENSRNOG00000010019 | Fam166a
Description
family with sequence similarity 166, member A [Source:RGD Symbol;Acc:1562762]
Coordinates
chr3:2438439-2439749:+
Coord C1 exon
chr3:2438439-2438564
Coord A exon
chr3:2438565-2439534
Coord C2 exon
chr3:2439535-2439749
Length
970 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGA
5' ss Score
8.91
3' ss Seq
TCCCCTGCTTCTCTCCACAGCTA
3' ss Score
12.4
Exon sequences
Seq C1 exon
GCAACAGGTCTCTTCAGGGAAGGAAGGCGGACACAGAAAGGGCTGAACCAGCAAGGACAGAGTCAAGCAAATGACAGCTACTCAGAAACACAACCTCTTCACTCCAGAACCCCACTACATCCCTGG
Seq A exon
GTAAGAGCTGGGAGCTCTACAGAAAGGATGGGGTATATGCAGTAAGGCTGGGGCTTCCTGGACTCTAAGAGGATAAGGACCAGTGCGAAGAGGCCCAAGGCCAGGGTTACCAAATGGAATAGAGACCACTGGGGATGAAGAGCTCTGGGACAGGAAAACTCTGAGGCAGAACTCCTTTCCCCTCCCTGTGGCCTCAACCTGAATGCAGTACTAGATGGCCTGCATGTCTGTCAAGGGCAAAAACTATGGCAGCCACATAGCTGGCAGAGACTGGATGAGCAAAGCTAGACGATCTCTCCGTAGGAAGTAGTGGTTTAGAGATGGGGTAAGTGTAAACCAATTAAATGCAAAAAACAGACATGTGCAAAATCTCCAGCACTGCACAATAAAAGAAAAACCCTACACAGACTGTGTGTGCACACCTACAGAGACTTACGTGCAACACTGGAGCACATAAGGTAGGGCATAACTGAAGGATCTATATACCTTTCAAAATGGGTCTCTATTTGAGCTGTCCCTGGGGTGAGGGATGGAGAGTGTCGAAAATGGTTGAGTGCTGGGCTGGAGAGATGGTCCAGCTGTTAAAGGCATTTGCAAGTCTTCTAGATAATGTAGGTTCAATTCCCAGCATCCACACGGTAGCTTTCTTAACCATCTATAACTCCAGTTCCAGGGGCTCCGTGCCCCTCTTCTGACTTCCACAGGCCCTAAATGCATATGTGGATCACAGACACACATGCAGGCAAAACCCCTCTGCACAGAAACCAAGAGGATTGCTGGGTATGGGTCTGCTGTGGAGGGCAGTCTGAGGGCAGTGCTGTCATAGAGATGTGGCATATGCTAACCCTGCGTCCCAGGAGGCACAGAAATCAGGTGTTTCCATGACTTTCATCTGAAGTGAGCAGGGGCAGGGTGACCTGCAATGGCTGATGACTGGCAGGAGTGCTTTCTCCCCTGCTTCTCTCCACAG
Seq C2 exon
CTATGCTGGTTTCTATCCTCAACTGCGCTACCAGGTGGGAAACACCTATGGCCGCACTACTGCACAGTTGCTCACAGATCCCAGTGTACAGAAGAGCCCCTGCTCTGTTCTGTCACCTATGTCCAAGCCCAAGTTCATTGAGGACTTCAGCAAATCCAAGCCACCATGGATGCCCTGCAGGGACCTGACAGAGCCTTACATCCCCCACTATACCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010019:ENSRNOT00000013335:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.404 A=NA C2=0.164
Domain overlap (PFAM):
C1:
PF106294=DUF2475=PU(9.0=31.6)
A:
NA
C2:
PF106294=DUF2475=PD(89.6=82.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAACAGGTCTCTTCAGGGAA
R:
AGTGGGGGATGTAAGGCTCTG
Band lengths:
335-1305
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]