MmuINT0078348 @ mm9
Intron Retention
Gene
ENSMUSG00000035697 | Hmha1
Description
histocompatibility (minor) HA-1 [Source:MGI Symbol;Acc:MGI:1917969]
Coordinates
chr10:79484540-79484932:+
Coord C1 exon
chr10:79484540-79484604
Coord A exon
chr10:79484605-79484821
Coord C2 exon
chr10:79484822-79484932
Length
217 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGT
5' ss Score
7.07
3' ss Seq
CTGGCTGTCCTGCCCCACAGCCC
3' ss Score
9.96
Exon sequences
Seq C1 exon
AGATGGAATTCGCCAAAGGTCTCCAGAAGGTTGTCCACAACTGCAGACAGAGCGTCACACACGAG
Seq A exon
GTGGGTTGGGGGAAACAGGTGTGGGGAGAGGGATGCATAGGAGTTTGATAGGCGTGGCCGCTCCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCCAAGGGCTTCTGCTGGATGCCCTTGGGAGAAGGAGGATGCCCATCGGTTGCTAAGAGTGGCTGAAGGGTGCTGGGATCCCTCTGTCCTCATCCTGGTGACTGGCTGTCCTGCCCCACAG
Seq C2 exon
CCCCACATGCCTCTCTTGTCCATCTACTCACTGGCCCTGGAACAAGATTTGGAGTTTGGCCACGGCATGGTGCAGGCAGCGGGCACACTGCAGACCCAGACCTTCATGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035697-Hmha1:NM_027521:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.182 A=NA C2=0.108
Domain overlap (PFAM):
C1:
PF0061118=FCH=FE(23.3=100)
A:
NA
C2:
PF0061118=FCH=PD(34.4=83.8)
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:
GGAATTCGCCAAAGGTCTCCA
R:
CTGCATGAAGGTCTGGGTCTG
Band lengths:
172-389
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: