MmuINT0029981 @ mm10
Intron Retention
Gene
ENSMUSG00000046318 | Ccbe1
Description
collagen and calcium binding EGF domains 1 [Source:MGI Symbol;Acc:MGI:2445053]
Coordinates
chr18:66066583-66066868:-
Coord C1 exon
chr18:66066729-66066868
Coord A exon
chr18:66066619-66066728
Coord C2 exon
chr18:66066583-66066618
Length
110 bp
Sequences
Splice sites
5' ss Seq
GTGGTCAGT
5' ss Score
4.85
3' ss Seq
CATATGCTTGCGTCTTCTAGGGC
3' ss Score
8.33
Exon sequences
Seq C1 exon
GCTCACCAGGACCCAAGGGGAGCCCTGGATTCCCCGGTATGCCAGGCCCTCCTGGACAGCCAGGCCCACGGGGCTCAATGGGACCTATGGGACCTTCCCCTGACCTGTCTCATATTAAGCAAGGCCGGAGGGGCCCCGTG
Seq A exon
GTCAGTATTTTCTCTGAGATCTGTGTAATATTGGCGGGGGCGGGGGGGACGACTGTGTTCTTGTCCCTTTTTTTTTTTCTTCAATTAAATCATATGCTTGCGTCTTCTAG
Seq C2 exon
GGCCCACCAGGAGCACCAGGAAGACACGGCTCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000046318:ENSMUST00000130300:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(68.0=72.3),PF0139113=Collagen=PU(20.5=17.0)
A:
NA
C2:
PF0139113=Collagen=FE(28.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTCACCAGGACCCAAGGG
R:
CTTGGAGCCGTGTCTTCCTG
Band lengths:
176-286
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