MmuINT0078334 @ mm9
Intron Retention
Gene
ENSMUSG00000035697 | Hmha1
Description
histocompatibility (minor) HA-1 [Source:MGI Symbol;Acc:MGI:1917969]
Coordinates
chr10:79489178-79489479:+
Coord C1 exon
chr10:79489178-79489302
Coord A exon
chr10:79489303-79489401
Coord C2 exon
chr10:79489402-79489479
Length
99 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGC
5' ss Score
5.97
3' ss Seq
ATCTCTCTCTCACCCTGCAGGGG
3' ss Score
11.97
Exon sequences
Seq C1 exon
GTCCCCAATCATGCGTACACGGAAGGGCAGCTTCAACCCTGGTGATGCTTCAGGACCCGAAGCTGCTGGTAGTCCCCCCGAGGAAGGTGGCACCTCTGAGGCAGCACCCAACAAGGACCACAGGG
Seq A exon
GTGAGCATATGCAAGCACACAGAGTGGATGCTGCATTCTGATGGCCGTTGCTGTTGGGGGGCGGGGGCACACTTTCTTCATCTCTCTCTCACCCTGCAG
Seq C2 exon
GGGGACGAGGTCACCAGGTTCATAAGTCCTGGCCCATCTCCATCTCAGACACCGAAGTTGGTCTGGACACCAGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035697-Hmha1:NM_027521:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.977 A=NA C2=0.963
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CCCAATCATGCGTACACGGAA
R:
TCTGAGATGGAGATGGGCCAG
Band lengths:
171-270
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: