MmuINT0061082 @ mm9
Intron Retention
Gene
ENSMUSG00000042788 | Fam166b
Description
family with sequence similarity 166, member B [Source:MGI Symbol;Acc:MGI:2445194]
Coordinates
chr4:43441115-43442006:-
Coord C1 exon
chr4:43441900-43442006
Coord A exon
chr4:43441339-43441899
Coord C2 exon
chr4:43441115-43441338
Length
561 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGA
5' ss Score
9.21
3' ss Seq
GGATGGATCCTGTGCTGCAGGTA
3' ss Score
5.18
Exon sequences
Seq C1 exon
AGAGTCCCTCCTGGAAGGGAAATAAAAGGAACTGCGCCAGTTCCCATGGCTGTGGTCAACACTTCCATCCCAGGGCTCAGCGGCGAGAATCCGCATTATATTCCAGG
Seq A exon
GTAAGACTCCTCCCAGAGCACTCCCCTGCTTGCTTCTGGGAATGGGGATTGGGATCTAGGAGCCAGTTCACAGACACTGGGGTCAAGATGAGAACTGGGGTGTGTCAATGGTATGGTATGGAAAGGGGAATCTAGCGGCTGTGAGAGCCAGGTCTAACAAAGCTTTGTGTTGTGGTCCCCACGGAAACAGGGTAAAAGCAGGAAGGACTGGACACCCAGGCAGAGGGCTGGGGATGTAGTCGCTTCAGTGATTTAATGATTGCCTAGAACACAAGGCACTAGGTCCTGTCCCCAGTAGGTAAAAGAGACAAAGAACAGAAATAAAGACCTCCAGACTCAAGCTGGGGCAGGAGTGGTTGGACCCGTGTGAGCCAAGCATGGGGCGGGGATGTAGAAGGATCAAAGGTGTTTGGTCAGCCTAGGCTAGAGAGTGAGACCCCGTGTAAAAATAAACACACAAGCACTTGCTGCAAGTGCACACCAAAGCGGGGCTTTCCTGCCTGTGTCAGGATGGTGGTGTAGGGTCCAACTCAGAGCTATGGGATGGATCCTGTGCTGCAG
Seq C2 exon
GTACACCGGACACTGCCCGCTACTTCGGTTCAGCATGGGCCAGACCTATGGGCAGGTGACTGGTCAGCTACTCCGAGGCCCTCCTGGTCTAGCCTGGCCTCCTGCCCACCGCACACTTCTGCCTCCCATCCAGTCTCCAAGATCTCCTGTGATCTCCAAGGGGAGGCTGCCTCCCAGGCGCGGGCATGAAAGGCTCAGCTCCAGCATAATCCCTGGGTATACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000042788-Fam166b:NM_001162381:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.039 A=NA C2=0.482
Domain overlap (PFAM):
C1:
PF106294=DUF2475=PU(9.7=28.6)
A:
NA
C2:
PF106294=DUF2475=PD(88.7=72.4),PF106294=DUF2475=PU(15.0=11.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCCTCCTGGAAGGGAAATAA
R:
TGTATACCCAGGGATTATGCTGGA
Band lengths:
326-887
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: