MmuINT0078332 @ mm9
Intron Retention
Gene
ENSMUSG00000035697 | Hmha1
Description
histocompatibility (minor) HA-1 [Source:MGI Symbol;Acc:MGI:1917969]
Coordinates
chr10:79488154-79489091:+
Coord C1 exon
chr10:79488154-79488291
Coord A exon
chr10:79488292-79488900
Coord C2 exon
chr10:79488901-79489091
Length
609 bp
Sequences
Splice sites
5' ss Seq
TCGGTGTGT
5' ss Score
5.93
3' ss Seq
GACGAGCACATCTCCTCCAGGCC
3' ss Score
4.44
Exon sequences
Seq C1 exon
GCCGAGGAGGCCATGGCCACTTACCGCACATGCGTGGCAGACGCAAAGACACAGAAGCAGGAGCTGGAGGACACAAAGGTGACTGCGCTGCGGCAGATTCAGGAGGTCATCAGGCAGAGTGATCAGACCATTAAGTCG
Seq A exon
GTGTGTTATGGGCACTGGGTGGGCTGAACTTGGAGGGGTGGGGGCAATGAGCGGGATTTGGTGTATTTGCTAAATGGGCGGGGCATAATGTGGGCAGGGTTTGGTTTGGCACGGTGATTCTAGTGGCATAGAACAGTGGATAGATGGAGCGGGGCAGGGCAAAACCCTTTCACAGCAGCAGAGGTCACCGGGAGGGATTGGTCTGGTCTGTTACAAGCTGGATAATGCAGCAGGGTCCCAGCAAGGGTAGCGTGGCCACGGGAGGGTGTCCTGAAGCTGAAGGTGAACTGTGCAAGGGGCAGTGTTTGAAGGAGCAGTGATGGGACTTTGGGCAGAGTGCAGGGGCTGGGTGTTAGTTTTTTCAAAGTTGAAGGGTGTGGCTTAGTAGATGGGTTGGGGCAACAGGCAAAGTGCCACGAGACGGTCCTTGTCTAGTGTGAACTCTATGGGAGTAGAGGGTTTGGGCAGCAGACAGGAGGAGGGTCTGGTGGGTGCTATACAATGGGTGTGGTTTGGGATGGAGTGCTATAGGGGCTGGACTGTGGGAGGGACTTGATGTGGGCGTGGCTGTGGGCGTGGTCTAGCCCTTGACGAGCACATCTCCTCCAG
Seq C2 exon
GCCACCATCTCCTACTACCAGCTGATGCACATGCAGACAGCACCGCTGCCCGTGAACTTCCAGATGCTGTGCGAGAGCAGCAAACTATATGACCCGGGCCAACAGTACGCATCTCACGTGCGTCAGCTGCAGAGAGGCGAGGAGCCGGACGTGCGCTACGACTTTGAGCCTTATGTCTCTAACAACTCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035697-Hmha1:NM_027521:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.500 A=NA C2=0.469
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:
CATGGCCACTTACCGCACAT
R:
CAGGAGTTGTTAGAGACATAAGGCT
Band lengths:
318-927
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: