MmuINT0036509 @ mm10
Intron Retention
Gene
ENSMUSG00000045193 | Cirbp
Description
cold inducible RNA binding protein [Source:MGI Symbol;Acc:MGI:893588]
Coordinates
chr10:80169808-80170122:+
Coord C1 exon
chr10:80169808-80169916
Coord A exon
chr10:80169917-80170015
Coord C2 exon
chr10:80170016-80170122
Length
99 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
CTAATGTCTCTCTCCTGCAGTGG
3' ss Score
10.09
Exon sequences
Seq C1 exon
GCTGCCATGGCATCAGATGAAGGCAAGCTTTTCGTGGGAGGACTCAGCTTCGACACCAACGAGCAGGCGCTGGAGCAGGTCTTCTCCAAGTATGGGCAGATCTCCGAAG
Seq A exon
GTGAGTCTTGGGTCAGGATCATTGTTCTCGGCTTCTACTTGGGGGTGGGGGTGGGGGGCAGAGGGCTGACTGGGCACATCTAATGTCTCTCTCCTGCAG
Seq C2 exon
TGGTGGTGGTAAAGGACAGGGAGACCCAGCGATCCCGAGGCTTTGGGTTTGTCACCTTTGAAAATATCGATGACGCTAAGGACGCCATGATGGCTATGAATGGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000045193:ENSMUST00000105365:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.083
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PU(38.0=77.1)
A:
NA
C2:
PF0007617=RRM_1=FE(49.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTTTCGTGGGAGGACTCAGC
R:
CATGGCGTCCTTAGCGTCATC
Band lengths:
171-270
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- 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