MmuINT0133076 @ mm10
Intron Retention
Gene
ENSMUSG00000040423 | Rc3h1
Description
RING CCCH (C3H) domains 1 [Source:MGI Symbol;Acc:MGI:2685397]
Coordinates
chr1:160950222-160951122:+
Coord C1 exon
chr1:160950222-160950334
Coord A exon
chr1:160950335-160950840
Coord C2 exon
chr1:160950841-160951122
Length
506 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
AACATTTGCTTTTCATACAGGTT
3' ss Score
8.07
Exon sequences
Seq C1 exon
CCTCCACAGCATAGCAAATACAAAACATACATGTGTCGAGATATGAAGCAAAGGGGAGGATGCCCTCGTGGTGCCAGCTGTACGTTTGCACATTCACAGGAAGAACTGGAAAA
Seq A exon
GTAAGTATGAAAACCATGAAACACAGACTTGGGAATAGGGAATGATTTGTTGGCTTTAAGAAACACAGTAAGAGGGGCTGGTGATGGAGAGATGGCTCAGTGATTAAGAGCACTGGCTGTTTTTCCAGAAATCCGAGTTCAATTCCCAGCAAGTGCATGGTGGCTCACAACCATCTGAATTTGGATCTGATGCCCTCTTCTGGTGCGTCTGAAGACAGAAATAGCAATAGCATATACACATACATAAAATAAATCTTTAAAAATATATATAAAAGGAATAATTGAATTCAACACTTAGGAAATATTTATGAATTAGTACATTTCTTAAAAGTTTTTTTTTTAGTTTTCATTATATTGTTCTTATAAATGGGAAGCTATATTTTATCAACTAGATGACATTAGTTATTTCCACACTCACAAAAAGTTCTAGTTCTTTTTAACAATTTTAATTGCTTCTTACCAATTGTGTGCTGTATTTGTAGTTGAAACATTTGCTTTTCATACAG
Seq C2 exon
GTTTCGTAAAATGAACAAACGTCTGGTTCCCAGAAGACCCTTGAGTGCCTCTTTGGGTCAACTTAATGAGGTGGGCCTGCCTTCAGCACCTATACTTTCTGATGAAAGTGCAGTGGACTTGTCCAACAGAAAACCTCCTGCACTCCCAAATGGAATTGCATCGTCAGGGAGCACAGTGACACAACTGATTCCACGTGGGACAGACCCCAGCTTTGATTCTTCTCTGAAACCAGTAAAGCTAGACCACCTGAGCAGTAGTGCTCCGGGGTCCCCTCCTGACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040423:ENSMUST00000161609:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.737 A=NA C2=0.979
Domain overlap (PFAM):
C1:
PF0064219=zf-CCCH=WD(100=71.1)
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:
ATGAAGCAAAGGGGAGGATGC
R:
GGACCCCGGAGCACTACTG
Band lengths:
342-848
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