MmuINT1020672 @ mm10
Intron Retention
Gene
ENSMUSG00000055632 | Hmcn2
Description
hemicentin 2 [Source:MGI Symbol;Acc:MGI:2677838]
Coordinates
chr2:31454628-31454927:+
Coord C1 exon
chr2:31454628-31454690
Coord A exon
chr2:31454691-31454804
Coord C2 exon
chr2:31454805-31454927
Length
114 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
GTCTCATGTCTCCCACCCAGACA
3' ss Score
7.18
Exon sequences
Seq C1 exon
AGGAAAATGAAGTTGGCTGTCCCGAGGGCTTTGAGCCGGATGTGCAGGGAGCATTTTGTGTGG
Seq A exon
GTGAGTTATTCCCAGCCAGTAGGAACAAAGGTGACCTCTCCTTCTGGGATGTACAACCCACCCCAGCCAGCTGGCAGGAGAGCCTGTGAACAGAGTCTCATGTCTCCCACCCAG
Seq C2 exon
ACAAGGACGAATGCTCAGGAGGTCCCAGCCCCTGCTCTCATACCTGCCGCAATGCTCCTGGTCATTTCTCCTGCTCCTGCCCCACTGGCTTCTCCCTGGCTTGGGACCACAGGAATTGTAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000055632:ENSMUST00000113532:91
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.182 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF146701=FXa_inhibition=WD(100=85.7),PF0764510=EGF_CA=PU(0.1=0.0)
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:
AGGAAAATGAAGTTGGCTGTCCC
R:
CTCTACAATTCCTGTGGTCCCA
Band lengths:
186-300
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