MmuINT0078186 @ mm10
Intron Retention
Gene
ENSMUSG00000066842 | Hmcn1
Description
hemicentin 1 [Source:MGI Symbol;Acc:MGI:2685047]
Coordinates
chr1:150604096-150605114:-
Coord C1 exon
chr1:150604845-150605114
Coord A exon
chr1:150604267-150604844
Coord C2 exon
chr1:150604096-150604266
Length
578 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
3' ss Seq
ATGCAGTGTTTTGTTTGCAGTGC
3' ss Score
5.63
Exon sequences
Seq C1 exon
GTTCTCCTATTATCACTCTTGAGCCAGTGGAAACTGTTGTAGATGCTGGTGGCAGAGTCATACTGGATTGCCAAGCAGCTGGTGAACCGCAGCCAACCATCACATGGTCCCGCCAAGGGCAACCCATCTCCTGGGATAACCGACTTTCCATGCTGCCTAACAGCTCATTATACATCGCTGCTGCTCGTAAGGAAGATACTTCTGAATATGAATGCGTTGCCCGAAACTTGATGGGCTCTGTCCTGGTCAGAGTGCCTGTCATAGTCCAGG
Seq A exon
GTAAGTGGGAAAACGAATCCAAGAAAGCTCAGCTTCCCAGTCTCCTCCTGGTTTACCAACTAATGAGATTAAAACAATACAGTTTAGAGGATTCAAATACCATGCTAATCGTTCAGAATCCTAACATAAATTTTCCTTGAAAACTAAACAAAAATGTTCAGAAAGTGATGCATATTATATAGAGAAACATAGATGATAAATAGAGAGATAGAGAGATGATAGAAAGCTATACACATACATATATAGAAGTGCACGAGCATGCATGCGCATACACACACACACACACACACACACACACACACACACACACACGGTAAGCAGTATATAAACTTCTTCATCTCTATTCTTCCCATAGCCATAGCCACAACCACATGACTCAGCAGAGGATCTGAGAGGGGGTTTCATTGACTGAGTTATTGTCTCACTTCTAGATATGAGATTTACCCCTAAGGGAAGGTTTCCATAGCTGCTCTGCAGCTATCACACTCAGCTCTCTACTCAGTATGTCACTTTGATGAAATTACTCTTCGAAACTCTCACTTGCAAACCCGAAACAACATGCAGTGTTTTGTTTGCAG
Seq C2 exon
TGCACGGTGGGTTTTCATTGTGGTCTGCCTGGAGGCCCTGCAGTGTCACCTGTGGAAAAGGCATCCAAAAGAGGAGCCGGCTGTGCGACAACCCACCTCCAGCCAATGGAGGGAGGCCATGCCAAGGGGCGGATTCAGAAGCGCGACACTGTCACAATAAGCTGTGTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000066842:ENSMUST00000074783:87
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.099 A=NA C2=0.069
Domain overlap (PFAM):
C1:
PF0767911=I-set=WD(100=95.6)
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:
GATTGCCAAGCAGCTGGTGAA
R:
ACAGTGTCGCGCTTCTGAATC
Band lengths:
357-935
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