MmuINT0133067 @ mm9
Intron Retention
Gene
ENSMUSG00000040423 | Rc3h1
Description
RING CCCH (C3H) domains 1 [Source:MGI Symbol;Acc:MGI:2685397]
Coordinates
chr1:162895081-162895919:+
Coord C1 exon
chr1:162895081-162895251
Coord A exon
chr1:162895252-162895803
Coord C2 exon
chr1:162895804-162895919
Length
552 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
TTATTTCCTCTTCTTTTAAGGAG
3' ss Score
8.54
Exon sequences
Seq C1 exon
GCTGTTAGTAACCGGCTGGTGTTACAGAGGGAGGTGAACACCCTGGCAAGCCAGCCACAGCCCCCTCAGCTGCCTCCAAAATGGCCTGGAATGATCTCAAGTGAGCAGCTCAGCTTGGAACTGCATCAGGTGGAAAGAGAAATTGGGAAGAGGACCCGGGAATTGAGTATG
Seq A exon
GTGAGTGCTGAAGGTGGGGAAGGTGGAATGAACTCTGTGACTCTAGAGCTGATTCCAGGTACCTTGAGGAATAAGTAATATTTAGGGTGATTCTAATAAAGATGAGTTGTCATCTGGTGGTATTATTATTTTAGGTTTGTCCTTTGTCAAAGACTTTGGGGAAAACAAGGGAATTAATTAGAAATTTTAAAGTTTCTGTTTAATGTACTCATTAGGGAAGCAGATGGGATGGTTGCTCTTTTGGACTCTGTAATATTAAGATATGTTTACACAATAAAATGTTACTTTTCATGGTCTTTTATAGAAGAGATATATAGTCTGTACACTGTTCTCTGTACTGCTTTTTCATGCTAGTTTGCAGCATTTTCAAAAGGTAGTGAGAAAAGGTGGGTTGTACTGTATACTTTAGTGTATACTCTCTCATCTACCTGTTTTTTATTGTTAATTCTTAGTGAAGTAGGAATGACTTTTTGTTTTTTTAATCCGTGTTGTGTGAATTTGGTCTAACCCATTACACCACAGATTACGGACTTTATTTCCTCTTCTTTTAAG
Seq C2 exon
GAGAACCAGTGTTCTGTAGACATGAAAAGCAAACTGGGTACAAGCAAGCAAGCAGAAAATGGCCAGCCCGAGCCCCAAAACAAGATCCGCACTGAGGACCTTACATTGACATTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040423-Rc3h1:NM_001024952:18
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.872 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
GCTGTTAGTAACCGGCTGG
R:
TGAATGTCAATGTAAGGTCCTCAGT
Band lengths:
286-838
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: