MmuINT0078187 @ mm10
Intron Retention
Gene
ENSMUSG00000066842 | Hmcn1
Description
hemicentin 1 [Source:MGI Symbol;Acc:MGI:2685047]
Coordinates
chr1:150603791-150604266:-
Coord C1 exon
chr1:150604096-150604266
Coord A exon
chr1:150603962-150604095
Coord C2 exon
chr1:150603791-150603961
Length
134 bp
Sequences
Splice sites
5' ss Seq
CAGGTATAG
5' ss Score
8.73
3' ss Seq
ATGGTTTTACTTCCCTGTAGTGG
3' ss Score
6.54
Exon sequences
Seq C1 exon
TGCACGGTGGGTTTTCATTGTGGTCTGCCTGGAGGCCCTGCAGTGTCACCTGTGGAAAAGGCATCCAAAAGAGGAGCCGGCTGTGCGACAACCCACCTCCAGCCAATGGAGGGAGGCCATGCCAAGGGGCGGATTCAGAAGCGCGACACTGTCACAATAAGCTGTGTCCAG
Seq A exon
GTATAGTTCTGCATTCATTGTGGAGGCAGGTGTTTAAGAGATGCCAATTTATGTTCTCCACCTTTGGCCTGCCTTGGGATTAGTGCTTGCTATTTAACTTTAGCTAATGGTGTAATGGTTTTACTTCCCTGTAG
Seq C2 exon
TGGATGGTCACTGGTCAGAATGGAGTTTCTGGGAAGACTGCTCAAGAAGCTGTGGGCATGGCAACCAAACTAGGACGAGAACTTGCAGCAACCCGCCGGCTCAGCATGGCGGGCGGCCATGCGAGGGGCATGCTGTGGAAACCATTATGTGTAACATCAGGCCTTGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000066842:ENSMUST00000074783:88
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.069 A=NA C2=0.052
Domain overlap (PFAM):
C1:
PF0009014=TSP_1=WD(100=87.9)
A:
NA
C2:
PF0009014=TSP_1=WD(100=87.9)
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:
GCACGGTGGGTTTTCATTGTG
R:
TCCTAGTTTGGTTGCCATGCC
Band lengths:
245-379
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