MmuINT0078168 @ mm9
Intron Retention
Gene
ENSMUSG00000066842 | Hmcn1
Description
hemicentin 1 [Source:MGI Symbol;Acc:MGI:2685047]
Coordinates
chr1:152480740-152482333:-
Coord C1 exon
chr1:152482252-152482333
Coord A exon
chr1:152480877-152482251
Coord C2 exon
chr1:152480740-152480876
Length
1375 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAAT
5' ss Score
7.76
3' ss Seq
TACTGTGTTCTCATGTTTAGTGC
3' ss Score
8.22
Exon sequences
Seq C1 exon
GTGGAGGATACAGGAAGATACACCTGCCTGGCATCCAGTCCTGCAGGGGATGATGATAAAGAATATTTAGTGAGAGTACACG
Seq A exon
GTAAATTTGGTGGCTTATGTTTGATCCACACACAACCCTAGTTAAAAACTGTACTAGAGAAAACTTGACATTTCACAACACATCATATGTTGATAAGTTGAAAAATACATACATATTTTACAAATTTTATTCTTAGTGTTAATAACATATGCGCTCTTTGGGATGTAGTTCATTGAAGTTTTGAGTTATTAGTCTCATTTTCACACAAAGAATTCAAATTTGATGTTTTAAAAATACCAGAACATAAATTACAATAATGATTAGAATAAAAACAATCCTTAGTCTTACCACATAACAATACAATGGTTTTTTTTATGTGAACATTAGATGGAAAAAAAAATGTGATCATAGTTGGGCATAGCAGCATATATCTGTAGTCCCAGCTTCTAGGGAAGTTGAGATAGGAAGATTGCCTAAGCTTAGAGTTTGCAACTGACTAGGGAATCAAGAAGATCCTTAATATCAAGAAAGTGACAATTCAGAACACAGAACTTAAGTTGCTTTATGTCTCACTTAATGGCGTGACAAACATTCTTATGTTAACAAATATATTCTATGGCATCATCTTTAAGATTGTATGTTGCCATATATCTTACTCCCTGTTTAGAGTTATTTAGGCAAATTAGGATATTCTGCCTTTTTATCTATATTAACAATATGTTAGCAACTCCCTTTATTTTTAAATTTTACTGAACTACACTTACTTGTTTATACATGCATGAATGTGCACATATATCCTTTTAAAGATATATGCCTTTTACTTGCCAGAAAGTTTGAATTAACTAGGCCCTTTCGAATAATATATATATATATATATATATATATATACTTAAACTGCTCTTCATGGAGAGAATTGTTTGAAAACTAAACAGATCTTTATCTAATTTTCAGAGCCTGACTGACTAGGCAATGCAGATTGTCTGGTATGAAGTTTCCCTGATATCTCTACTCAAAATTTAGCCTACCTAAGTAAACCCTAAAATATGATTTACTGAGAAATATATCTGTATTAATCAGGAAAAATGGACATAGTTCTTCGTACTGTGATGAGCAGTTCCTAATTCAGTAATTTTTTTGATAGTCAGGGAAAAGTATTGCCTATATGTCTCCATTTCCTTACCACCTGTCAAATGGTGGTGGTGATGTGGTTGTCGTATTATTTACATCATTGTTGGAAAGATTCCATTATTAAGCAACATGAAAGTGCTAAACAATAAAGATGCAATTTGTTAATAATCTAGACCATACATTGAATGGCAAACTGTTGAGGATCACGCCTCTTTTATCATACAATAAGCTTAACCCTTGCTGGATACTGATGGATCATTTACATCCCATTTATCAAACCCACTTGATACTGTGTTCTCATGTTTAG
Seq C2 exon
TGCCTCCTAATATTGCTGGCATGGATGAAGCCCAGGACTTCACTGTGTTAAGGAACAGGCAGGTGACACTGGAATGCAAATCCGATGCGGTGCCTCCACCTGTGATCATGTGGCTCAAAAACAGGGAGCAGTTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000066842-Hmcn1:NM_001024720:70
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.214 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0767911=I-set=PD(29.1=89.3)
A:
NA
C2:
PF0767911=I-set=PU(44.7=82.6)
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:
GGATACAGGAAGATACACCTGCC
R:
CTGTAACTGCTCCCTGTTTTTGA
Band lengths:
214-1589
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: