MmuINT0005549 @ mm10
Intron Retention
Gene
ENSMUSG00000015488 | Cacfd1
Description
calcium channel flower domain containing 1 [Source:MGI Symbol;Acc:MGI:1924317]
Coordinates
chr2:27018373-27018979:+
Coord C1 exon
chr2:27018373-27018480
Coord A exon
chr2:27018481-27018887
Coord C2 exon
chr2:27018888-27018979
Length
407 bp
Sequences
Splice sites
5' ss Seq
AAAGTGCGT
5' ss Score
5.93
3' ss Seq
ACCTGCTTTTCTCTCTCCAGGGG
3' ss Score
12.6
Exon sequences
Seq C1 exon
GATGGCCATCGTCCCCATCGTCATGAGCCTCACCCTGACTACACTGCTGGGCAATGCCATCGCCTTTGCCACGGGGGTGCTGTATGGACTGTCTGCCCTGGGCAAAAA
Seq A exon
GTGCGTCTACAACCTAGTCCCGGGGTGGAGCCTCCTCTGCTGCCCCTGCTGCCCCATCTGAAGTGGGAAAGGCCTGAGTGGGACCCTTTGTCTAGTTATGCAGTGGCCACAGGTGACTTTATCTGTGCCCTCAGGAACAGAGGCAAGAAATGAGGGGACAGCCTAGGTGGTCCCTCTTGCCTAGTTTATACACAGTGAGGTATGCACCAGACATTGCAGCCAGTTGCAACCCCTTCCCTTCAGCTCAGTCAGTGCCAGGCAACGTGTATCTGTCTCAGAGTAACAGTGCTCTGCCCCCTTGACCAGGGCCTCTGGGGAGCACAGTCTACAGGTCATGCCTGGGGTGCAACCTGGGAGTGGGAGGTGGGAGGGCTAGGCCCATAGAACACCTGCTTTTCTCTCTCCAG
Seq C2 exon
GGGCGATGCCATTTCTTATGCTCGGATCCAGCAGCAGAGACAGCAGGCAGATGAGGAGAAGCTGGCGGAGACTTTCGAGGGGGAACTGTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015488:ENSMUST00000114006:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF102334=Cg6151-P=FE(45.0=100)
A:
NA
C2:
PF102334=Cg6151-P=PD(0.1=0.0)
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:
GATGGCCATCGTCCCCATC
R:
TCACAGTTCCCCCTCGAAAGT
Band lengths:
199-606
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