MmuINT0078340 @ mm9
Intron Retention
Gene
ENSMUSG00000035697 | Hmha1
Description
histocompatibility (minor) HA-1 [Source:MGI Symbol;Acc:MGI:1917969]
Coordinates
chr10:79491402-79491928:+
Coord C1 exon
chr10:79491402-79491628
Coord A exon
chr10:79491629-79491717
Coord C2 exon
chr10:79491718-79491928
Length
89 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
CCAACTCTGCCCCTCCCCAGGAT
3' ss Score
8.57
Exon sequences
Seq C1 exon
CTACCGGAGCCCCTTATCTCTTTTCGCTTCTACCATGAGCTGGTGGGACTAGCTAAGGACAGCCTAAAGGCCGAAGCCGAAGCTAAGGCAGCGAGCCGGGGTCGGCAGGGTGGGTCCGAGAGTGAGGCTGCAACCTTGGCTATGGTGGGCCGCCTGCGTGAGCTCATGCAGGATCTGCCAGCCGAAAACCGGGCCACACTCTTATACCTGCTGAAGCACTTGCGAAG
Seq A exon
GTGAGGGTCCCTGTGTGGTGCAAGAGCTGACTGGGGGTGGGGGTGTCCCGGAGCCACACCCACCTACACCCAACTCTGCCCCTCCCCAG
Seq C2 exon
GATCGTGGAAATGGAGCAGGATAACAAGATGACCCCTGGGAACCTGGGCATCGTTTTCGGGCCCACACTGTTGCGGCCTCGACCCACTGACGCCACCGTGTCCCTCTCTTCTCTGGTGGATTATCCCCACCAGGCCCGAGTTATTGAGACTCTGATTGTCCACTACGGCCTGGTCTTTGAGGAGGAGCCAGAGGAGGCGCCTGGCAGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035697-Hmha1:NM_027521:19
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.158 A=NA C2=0.310
Domain overlap (PFAM):
C1:
PF0062022=RhoGAP=FE(43.4=100)
A:
NA
C2:
PF0062022=RhoGAP=PD(18.5=45.1)
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:
CAGGATCTGCCAGCCGAAAAC
R:
AGAGAAGAGAGGGACACGGTG
Band lengths:
173-262
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: