MmuINT0078333 @ mm9
Intron Retention
Gene
ENSMUSG00000035697 | Hmha1
Description
histocompatibility (minor) HA-1 [Source:MGI Symbol;Acc:MGI:1917969]
Coordinates
chr10:79488901-79489302:+
Coord C1 exon
chr10:79488901-79489091
Coord A exon
chr10:79489092-79489177
Coord C2 exon
chr10:79489178-79489302
Length
86 bp
Sequences
Splice sites
5' ss Seq
CTGGTACCT
5' ss Score
4.11
3' ss Seq
TTACTGACCCCCACCACTAGGTC
3' ss Score
7.85
Exon sequences
Seq C1 exon
GCCACCATCTCCTACTACCAGCTGATGCACATGCAGACAGCACCGCTGCCCGTGAACTTCCAGATGCTGTGCGAGAGCAGCAAACTATATGACCCGGGCCAACAGTACGCATCTCACGTGCGTCAGCTGCAGAGAGGCGAGGAGCCGGACGTGCGCTACGACTTTGAGCCTTATGTCTCTAACAACTCCTG
Seq A exon
GTACCTTCACCCTGTGCAGCCACATGCATCTAGTGGGAGTGTGGGTGGTAGACCTGGGGAGGCCTCTTACTGACCCCCACCACTAG
Seq C2 exon
GTCCCCAATCATGCGTACACGGAAGGGCAGCTTCAACCCTGGTGATGCTTCAGGACCCGAAGCTGCTGGTAGTCCCCCCGAGGAAGGTGGCACCTCTGAGGCAGCACCCAACAAGGACCACAGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035697-Hmha1:NM_027521:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.469 A=NA C2=0.977
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:
ATATGACCCGGGCCAACAGTA
R:
CTTCGGGTCCTGAAGCATCAC
Band lengths:
167-253
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: