MmuINT1009971 @ mm10
Intron Retention
Gene
ENSMUSG00000042788 | Fam166b
Description
family with sequence similarity 166, member B [Source:MGI Symbol;Acc:MGI:2445194]
Coordinates
chr4:43427140-43427710:-
Coord C1 exon
chr4:43427513-43427710
Coord A exon
chr4:43427272-43427512
Coord C2 exon
chr4:43427140-43427271
Length
241 bp
Sequences
Splice sites
5' ss Seq
CAGGTTAGA
5' ss Score
5.94
3' ss Seq
TCAGACTCTTGGCCACGCAGGAT
3' ss Score
4.89
Exon sequences
Seq C1 exon
GTTTCACGGGCTATGTGCCCCGTGCCCGCTTCCTCTTTGGCTCCAGCTTCCCTGTGCTTACCAACCAGGCATTGCAGGAATTTGGGCAGATGTGCTCACGGGGCCGGGCGCACAAGGACCCCAAACCTCTCTCCCCACTTCCCAGGCCCACGTTTCAGAATCTGGGTCTCCTACCTCACTACGGAGGCTACGTGCCAG
Seq A exon
GTTAGAAGAGCCCGTGAGGGGCTCCGGGAACTGCGGTGTGTGTGCGGGTGGGGGGTGCTTTGGCAACGGGAATTAACAGACACGGAGAGATGTCCGACCCTGGGATTTAGCTTTAGAGAGGAAACTCTGAGGCAGTTCAGTGGGGAGTTGGGAGCAGATTTTAAAGGGCAGTTTGGAGGGTCGACGCAACTGGCTTTTTCATGCCTCTGGCTATATACATGTCAGACTCTTGGCCACGCAG
Seq C2 exon
GATATAAGTTCCAGTTTGGCGGTACATTTGGGCATCTTACCCATGATGCTCTGGGCCTCAGCATTACTCAGAAACAGCTCCCGGCCTAAGTACCTGGATTCCAAGTTCTCCCTTCTCATCCTAACCCAGTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000042788:ENSMUST00000107929:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.295 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF106294=DUF2475=PD(85.2=77.6),PF106294=DUF2475=PU(32.5=19.4)
A:
NA
C2:
PF106294=DUF2475=PD(65.0=86.7)
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTCCTCTTTGGCTCCAGCTT
R:
ACTGGGTTAGGATGAGAAGGGA
Band lengths:
300-541
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types