MmuINT1020675 @ mm10
Intron Retention
Gene
ENSMUSG00000055632 | Hmcn2
Description
hemicentin 2 [Source:MGI Symbol;Acc:MGI:2677838]
Coordinates
chr2:31457060-31458053:+
Coord C1 exon
chr2:31457060-31457188
Coord A exon
chr2:31457189-31457732
Coord C2 exon
chr2:31457733-31458053
Length
544 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAAG
5' ss Score
6.93
3' ss Seq
CTGCCGCTCTCCCTCTATAGACA
3' ss Score
10.97
Exon sequences
Seq C1 exon
ATGTGGATGAATGTCTAGAACAGCTGGATGAGTGTCACTACAATCAACTCTGTGAGAACACTCCAGGTGGCCACCACTGTGGTTGTCCCAGAGGGTACCGCCAACAGGGTCACAGCCTGCCTTGCCTAG
Seq A exon
GTAAAGGGGACAGCAGAACCCCCTCTGGGCCCTGGGTCTCACTCAGCTCTGGCTCAGGACAAGGAGTGTTTATGGTCTGGAGATTCTGAAAATGACTAAAGCAGTAGCCAAGACCTCTCACTAGATCCTGCACAGGGCACTTCTGTGGATGTCAGAAGGGGAGGAGGTGACAACCAAGGCAGGAGAGGTATGGGGTAGAATGAATGACTGTCACTAAGGATTGGGACTCCACCGCCTGGGAGTTAGGCCCTAACTGCAGACCTAGGGTCAGAGACTATGCAGGTACCAGAATCCTCATGAGGCCAGCTTGAAGGGAAACCCTGTGTATAGTGTATAAGGCATTGAATTCTGGGAGGATGACAGGGAGAGGCAGCTGAGCCAGGCATAGAGGGACACAGCTCTCATTTCAGTATTCAGGAGACAGAGGCACATTCCAAGCAAGACTGCCTCAAAGTAAAAAGAAAAAGAAGCCAAAGGGCAGCTGGAGCACCTGCAGGCCACAGAGCACCTACCCTCCTCACACCCTGCCGCTCTCCCTCTATAG
Seq C2 exon
ACATCAACGAGTGCCTACAGCTGCCCACACCCTGTGTCTACCAGTGTCAGAACCTCCAGGGCAGCTACCGATGCCTGTGCCCACCAGGCCAGACTCTCCTACGGGATGGCAGGACCTGTATCCCCCTGGAACGGAACCGTCAAAACATTACCATTGTCAGCCACCGGAGCCCATTTGGGCCCTGGCTGCGGTCTCGGGTACCCAGGCCCAGTAGTTCCTACCACACCTGGGTCTCCCTCCGGCCTGGTTCTGGGGCCCTGAATAGTGTGGGCCGGGCCTGGTGCCCACCTGGCTTCATAAGGCAGGATGGCGTGTGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000055632:ENSMUST00000113532:94
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=95.5),PF0764510=EGF_CA=PU(0.1=0.0)
A:
NA
C2:
PF0764510=EGF_CA=WD(100=37.0)
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:
TGTGGTTGTCCCAGAGGGTAC
R:
CTGCCTTATGAAGCCAGGTGG
Band lengths:
357-901
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