MmuINT0078187 @ mm9
Intron Retention
Gene
ENSMUSG00000066842 | Hmcn1
Description
hemicentin 1 [Source:MGI Symbol;Acc:MGI:2685047]
Coordinates
chr1:152450921-152451396:-
Coord C1 exon
chr1:152451226-152451396
Coord A exon
chr1:152451092-152451225
Coord C2 exon
chr1:152450921-152451091
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-Hmcn1:NM_001024720:88
Average complexity
IR-S
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: