MmuINT0029973 @ mm10
Intron Retention
Gene
ENSMUSG00000046318 | Ccbe1
Description
collagen and calcium binding EGF domains 1 [Source:MGI Symbol;Acc:MGI:2445053]
Coordinates
chr18:66291132-66291838:-
Coord C1 exon
chr18:66291621-66291838
Coord A exon
chr18:66291213-66291620
Coord C2 exon
chr18:66291132-66291212
Length
408 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
TGACATTTTTCCTCCCTTAGAGA
3' ss Score
9.07
Exon sequences
Seq C1 exon
GAAGGCGGCTGCGGCCGCGGAGCCTCCCTGGGCACAGCGCAGGGAGAGAGCTCGGGCGCCGAGAAGAAGCCGCGAGCTTCCCCGATGGTGCCGCCGCCTCTTCCGAGCCGGGGAGGAGCAGCCAAGAGGCAGCTGGGCAAGAGCCTGGGGCCGCTGCTGCTACTCCTGGCGCTGGGACACACGTGGACCTACCGAGAGGAACCCGAGGACCGCGACAG
Seq A exon
GTAAGGGCCACCTGCCCTAGAGGGAGGACGAGCTGGGTGCGATCAGGACTGGCTGGCGGGGTGCAGACGATCACATGTGGCGGATCCACAGATCTCTGTGCGCTGAGCCACTGGCGGAGAGGTTAGCTGATCCAGGTGACTTTCATCTCATGCGGGAACCGCCTCGGCGCTCCCAGTTGTGAGTTGGGACGCTGGATGCCCTCTGTCCTGCTTTCCCGCCGCGCTCGGGTGCAGACTTCTTTGATTTTTCTTGTCGCTTGGTAGTGGGATCGCTCTGTGCAGGGACACTGTCCTGTCTCCTCCCGGGACCAGTAGCAGCCCGTGCGTCTGGACGCAGCAGCGCGTTCTGCTCTTCACTCTCCCGCTGACCTTAACGGAGTTTCCTCTCTGACATTTTTCCTCCCTTAG
Seq C2 exon
AGAAGTGTGCTCTGAAAACAAGATCACCACGACCAAATACCCATGTCTGAAGTCTTCGGGCGAGCTCACCACGTGCTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000046318:ENSMUST00000130300:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.289 A=NA C2=0.093
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCGCAGGGAGAGAGCTC
R:
CTGAAGCACGTGGTGAGCTC
Band lengths:
264-672
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