MmuINT1020677 @ mm10
Intron Retention
Gene
ENSMUSG00000055632 | Hmcn2
Description
hemicentin 2 [Source:MGI Symbol;Acc:MGI:2677838]
Coordinates
chr2:31458684-31459207:+
Coord C1 exon
chr2:31458684-31458803
Coord A exon
chr2:31458804-31459080
Coord C2 exon
chr2:31459081-31459207
Length
277 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGC
5' ss Score
7.75
3' ss Seq
TACCGCACCCTACCGCCCAGACA
3' ss Score
1.92
Exon sequences
Seq C1 exon
ACCTTGATGAGTGCCGTGTTAGGAGCCTGTGTCAGCATGCCTGCCAAAACACAGAGGGTAGCTACTATTGCCTGTGCCCCTCTGGCTACCGCCTCCTTCCCAGCGGGAAGAACTGCCAGG
Seq A exon
GTGAGCCAGCCAGAGCCAATCCACACCTCTCCCAGGATTAGGGACACACAAGTTCTGCTGTGTGTCCCTGGGCTATTCCATCTGAACCTTACCCATGATAGGAGGAAGTCCCTCCAAGCCATCCCCTCCAAGACATGCCCCTGGGAGATGGAGAGGTGTTGGGGAGGGTCTCTCCTTGGGGCTCTGCCTCAGAAAGCTGGTCTCTTTCACACGGCCTCCTCTGGTCTCCCTCTCCCCTGTTCTATCTTCCCATCTCCTACCGCACCCTACCGCCCAG
Seq C2 exon
ACATCAACGAGTGTGAGGAAGATGGCATCGAGTGTGGGCCTGGCCAGATGTGCTTCAACACCCGAGGCAGCTTCCAGTGTGTAGACACGCCCTGTCCTACCACCTACCGGCAGGGCTCCAGCCCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000055632:ENSMUST00000113532:96
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:
PF126622=cEGF=PU(83.3=48.8)
A:
NA
C2:
PF126622=cEGF=PD(12.5=7.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATGAGTGCCGTGTTAGGAGC
R:
CTGGAGCCCTGCCGGTAG
Band lengths:
236-513
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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