MmuINT0078097 @ mm10
Intron Retention
Gene
ENSMUSG00000066842 | Hmcn1
Description
hemicentin 1 [Source:MGI Symbol;Acc:MGI:2685047]
Coordinates
chr1:150582223-150583280:-
Coord C1 exon
chr1:150583167-150583280
Coord A exon
chr1:150582349-150583166
Coord C2 exon
chr1:150582223-150582348
Length
818 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGA
5' ss Score
8.51
3' ss Seq
GCCTTTGTTCTTTTATCAAGATG
3' ss Score
6.51
Exon sequences
Seq C1 exon
ATATTAATGAATGTCAGGAGTCCAGCCCCTGTCACCAGCGATGTTTCAACGTCATAGGAAGTTTCCATTGTGGATGTGAAGCTGGCTATCAACTCAAAGGCAGAAAATGCATCG
Seq A exon
GTGAGATACTTGCTCTGAATTTACAGTGATGATGTCACTTTAACTCCGTGTGTTGTGTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTACATGTGCAGAGTCCAGAGGAGGACATCAGATGACCAGCCTGGTTTATCGCTCTCTTCCTTAGTCCTCTGAGACAGAGTCTCTCACTGAAAATGGAGCTCACTGCTTTTCAGCTAGAAAAGGCAGCCAACCAGCCCTAGCAATCCTCCTGCCTCCACCTCCTTGTGGTAATGAGGCTGTAGAAACACATGCAGGCATGCCCAGGACTTTATGTGGGTTCTGAAAATTCAAACCCCACTTCAAATGCTTGTGCAGCAAGCACTCTTGCCCACTGAGCCATACATATATGTATGTATGTATGTATACATGTATATGTATGTATATATGATGTGTGTGTGTGTGTGTGTGTGTGTGTAATGTCACTTTGTATTTGTAGGGACAGTGACAAACATAGCTAACAGCTCTTTGAAACAGCAGTTTGTCATTCTGATTTAAAGTAAAGTGAGTTAGCATAGCTTATTAGACTTACACATTTTTACATGTGAAACAATTGTGCAATACACATATATATTGATGTATAATCGCCGTAAAATCCAAAAGGCAGAGACAGGCGGATTTCTGAGTTCGAGGCCAGCCTGATCTACAAAGTGAGTTCCAGGACAGCCAGGACTATACAGAGAACCCTGTCTTGAAGAAAAAAAAAAGAGTCTTTTCTCTGGAGAAAAAGTGGAATCAGCCCTTTACTTTGTCTGTATTGCCTTTGTTCTTTTATCAAG
Seq C2 exon
ATGTGAATGAATGTAGACAGAATGTGTGCAGACCAGACCAGCATTGTAAGAACACCCGCGGTGGCTACAAGTGCATTGATCTTTGTCCAAGTGGAATGACCAAGGCTGAAAATGGGACCTGCATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000066842:ENSMUST00000074783:101
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0764510=EGF_CA=WD(100=94.9),PF0764510=EGF_CA=PU(0.1=0.0)
A:
NA
C2:
PF0764510=EGF_CA=WD(100=95.3),PF0764510=EGF_CA=PU(0.1=0.0)
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:
ATTAATGAATGTCAGGAGTCCAGCC
R:
CAATGCAGGTCCCATTTTCAGC
Band lengths:
238-1056
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