MmuINT0023266 @ mm9
Intron Retention
Gene
ENSMUSG00000047228 | BC048546
Description
cDNA sequence BC048546 [Source:MGI Symbol;Acc:MGI:3039594]
Coordinates
chr6:128489840-128490367:-
Coord C1 exon
chr6:128490280-128490367
Coord A exon
chr6:128490038-128490279
Coord C2 exon
chr6:128489840-128490037
Length
242 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGG
5' ss Score
6.6
3' ss Seq
AACTATGCTTTAAATTGCAGGTA
3' ss Score
8.72
Exon sequences
Seq C1 exon
GTGAATATGCTTTTGATTCTTACAACATCAATAGCATTTCGGATTCCCAATAAAACAAAGAAGCGCACAGAAAAAAAGAAAAAAAAAA
Seq A exon
GTAAGGACATTTTACAGAAGCCATGCATACGACTCTTCAAGCCTCTCATGTTTTTCTTAATACCTTGGCAGGTTAAAAATATATATGTACATGCACTTATATATCAGCATGCATGCTATGTTTATAGAGCTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGAGAGAGAGAGAGAGAGAGAGAAAGAGAGAGAGAGAGAGAGATACATGTGTATTTACTGTTTAAACTATGCTTTAAATTGCAG
Seq C2 exon
GTATGAGACTATTTCTTTGAATAAACTGTTCTCCTGGTCACCATCCTACCAAGAGCCTGATCAAGCACCTCCCATCCTGAAGACTCTCCCATCACAATGACTTCTTGTCAGCTTCACTTCCTTCCTTCCTTCTTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCATTAAATGGCATCATTTTAAGTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000047228-BC048546:NM_001001179:35
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
3' UTR
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=NA
Domain overlap (PFAM):
C1:
PF076779=A2M_recep=PD(8.0=38.9)
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTTACAACATCAATAGCATTTCGGA
R:
CATTTAATGGAAGGAAGGAAGGAAGG
Band lengths:
252-494
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: