MmuINT0078199 @ mm10
Intron Retention
Gene
ENSMUSG00000066842 | Hmcn1
Description
hemicentin 1 [Source:MGI Symbol;Acc:MGI:2685047]
Coordinates
chr1:150586355-150587068:-
Coord C1 exon
chr1:150586949-150587068
Coord A exon
chr1:150586490-150586948
Coord C2 exon
chr1:150586355-150586489
Length
459 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGTA
5' ss Score
5.69
3' ss Seq
CATGGTTCCTTCTGTTGTAGACA
3' ss Score
8.97
Exon sequences
Seq C1 exon
ATGAAGATGAATGCACAGCTGGGAACCCCTGCTCTCATACCTGCCACAATGCCATAGGAGCCTATTACTGCTCCTGCCCCAAAGGCCTCACCATAGCTGCAGATGGGAGAACCTGTCAAG
Seq A exon
GTAGTATCAAAGCTATATCCAACGACCAAGACAACCTTACCTCGGAAAAACATGGGAGGGCAGTGTCCTCTGCCCACAGCTTCACCACAAACAGGGAAGTCCTCATTTGGGTGGAGAAAGTAAGGAAGAGAACCCTGGCCAGCCATTACCTTAAAAGGGGACCTCTGAAATTAGGGATGCCTGGGATAGCTCACTGAGGATCTGAGAGAACAACTGGCTTGTTAAAAGTTACCTAATTGATATGTTCTCTAATCCAGTGATTGGGTTTTAAATCCATCACACCATGCTGCTGCGAATTCGTCATCTCTCTAGCTCATTTTAAATGACTCGACCAAACAATTCCATCTTTCTTATTCTATAATATTTTCCTATCTCATATAGTTTCTAACCCATGCTTCACAGCAAGTTCTTAAGTTATAGTTTCAACTCACCTCAATTTCATGGTTCCTTCTGTTGTAG
Seq C2 exon
ACATTGATGAGTGTGCTTTGGGTGGACATACCTGTCGTGCTGGTCAGGACTGTGACAACACCATTGGATCCTATCGCTGTGTGGTCCATTGTGGAACAGGCTTCCGAAGAACCTCTGATGGGTTAAGCTGTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000066842:ENSMUST00000074783:99
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:
PF146701=FXa_inhibition=WD(100=90.2),PF0764510=EGF_CA=PU(0.1=0.0)
A:
NA
C2:
PF0764510=EGF_CA=WD(100=95.7),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:
TGAAGATGAATGCACAGCTGGG
R:
CTTGACAGCTTAACCCATCAGAGG
Band lengths:
254-713
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