MmuINT0078347 @ mm9
Intron Retention
Gene
ENSMUSG00000035697 | Hmha1
Description
histocompatibility (minor) HA-1 [Source:MGI Symbol;Acc:MGI:1917969]
Coordinates
chr10:79484291-79484604:+
Coord C1 exon
chr10:79484291-79484428
Coord A exon
chr10:79484429-79484539
Coord C2 exon
chr10:79484540-79484604
Length
111 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGC
5' ss Score
7.23
3' ss Seq
TGCACCCCATTCTTTGGTAGAGA
3' ss Score
4.68
Exon sequences
Seq C1 exon
GTTGCCTGCCCCCCGAAGAGGTGGACATGCTTCTGCAGCGATGCGAAGGGGGTGTGGACGCTGCACTGCAGTATGCAAAAGACATGGCCAGGTACATGAAGGACCTCATCAGCTACCTGGAGAAGAGGACCACCCTGG
Seq A exon
GTGAGCGACTGAGACACCTGGGGTGGGGTGGATGGGAGGGGCAGGGTGGGGTGGGGGGGGTCTAGGGAAGGCTGTTTCCAAAGCCTCACTCTGCACCCCATTCTTTGGTAG
Seq C2 exon
AGATGGAATTCGCCAAAGGTCTCCAGAAGGTTGTCCACAACTGCAGACAGAGCGTCACACACGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035697-Hmha1:NM_027521:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.021 A=NA C2=0.182
Domain overlap (PFAM):
C1:
PF0061118=FCH=PU(40.0=76.6)
A:
NA
C2:
PF0061118=FCH=FE(23.3=100)
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:
CCGAAGAGGTGGACATGCTTC
R:
GCTCTGTCTGCAGTTGTGGAC
Band lengths:
179-290
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: