MmuINT1020676 @ mm10
Intron Retention
Gene
ENSMUSG00000055632 | Hmcn2
Description
hemicentin 2 [Source:MGI Symbol;Acc:MGI:2677838]
Coordinates
chr2:31457733-31458803:+
Coord C1 exon
chr2:31457733-31458053
Coord A exon
chr2:31458054-31458683
Coord C2 exon
chr2:31458684-31458803
Length
630 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
TCTGTCCCCACCTGGACCAGACC
3' ss Score
4.41
Exon sequences
Seq C1 exon
ACATCAACGAGTGCCTACAGCTGCCCACACCCTGTGTCTACCAGTGTCAGAACCTCCAGGGCAGCTACCGATGCCTGTGCCCACCAGGCCAGACTCTCCTACGGGATGGCAGGACCTGTATCCCCCTGGAACGGAACCGTCAAAACATTACCATTGTCAGCCACCGGAGCCCATTTGGGCCCTGGCTGCGGTCTCGGGTACCCAGGCCCAGTAGTTCCTACCACACCTGGGTCTCCCTCCGGCCTGGTTCTGGGGCCCTGAATAGTGTGGGCCGGGCCTGGTGCCCACCTGGCTTCATAAGGCAGGATGGCGTGTGTGCAG
Seq A exon
GTAAGGCAGGCCTTAGGCACACACACTGTGGTCCTGGGCTCTTAGGCTGGGCGTGGATCTGGGCAAACTCAGAAACCCAGCACTCACGGGCAAAGTGGGGTGGAGGCAGGGGAAATTCTGCAAGTGAGGGGCAGCACTGTGGCTGTGCGGATGGACAAAGGGGATCCCAAGAGAGAGACTGGGGTGATATTCAAACCGTTTGTCTTTGGGATGTTTTTAGGAGGCCCTCCTAAAATGATGCCTGAGGAACCTCCTGCCCCCCACTCCATTAAGAAACACTGCTCTTGAGGGAGGGAAGTTTGCGGGGCTGTGAAAGAATATTCCAGTTAGGCACAAAGCTATAAAGAGGGACTGTAGGAGCAGAGGGTACAGGTCTGTAACCTGTGGACCCTGTGGAAGCTGGGCTGGCTGCAGAGGGGATGGACTCTGTCAGTAGAGTGGCCCCTGTTCTTGCCTTGGTGATGGCTCCCACTCTTCACCAGCCAGAGACTCCTCCTGCAGCAGGCCTGGGTGAAGCAGGCAGGGGAGGGGTTGCCTGGAGCAGAGAGCTTCCCTGACCGGTCTCAGAGCACATGGCCATCCGGCAATCTGACTCAGCATCTCTCTGCCCTCTGTCCCCACCTGGACCAG
Seq C2 exon
ACCTTGATGAGTGCCGTGTTAGGAGCCTGTGTCAGCATGCCTGCCAAAACACAGAGGGTAGCTACTATTGCCTGTGCCCCTCTGGCTACCGCCTCCTTCCCAGCGGGAAGAACTGCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000055632:ENSMUST00000113532:95
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=37.0)
A:
NA
C2:
PF126622=cEGF=PU(83.3=48.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACATCAACGAGTGCCTACAGC
R:
GCTGACACAGGCTCCTAACAC
Band lengths:
357-987
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