MmuINT0078339 @ mm9
Intron Retention
Gene
ENSMUSG00000035697 | Hmha1
Description
histocompatibility (minor) HA-1 [Source:MGI Symbol;Acc:MGI:1917969]
Coordinates
chr10:79490566-79491628:+
Coord C1 exon
chr10:79490566-79490703
Coord A exon
chr10:79490704-79491401
Coord C2 exon
chr10:79491402-79491628
Length
698 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CTAAATGTGTCACCCTGCAGCTA
3' ss Score
7.32
Exon sequences
Seq C1 exon
GGGATCTACCGGGTCAATGGCGTGAAAACGCGTGTGGAGAAGCTGTGCCAGGCTTTTGAGAATGGCAAAGAGTTGGTGGAGTTGTCACAGGCCTCACCCCACGACATCAGCAACGTCCTAAAGCTATACCTGCGGCAG
Seq A exon
GTGAGGCCAACCTGGATGAACTGTGGGAAGGGCGTGGCCAGGGTGGAGCAGGGGCGGGGCATTAGCATGGTAGGGGACAGTTAGAGGCTGGGCTGGATGGGCCTCTACTGTGAGTTTGCTAGAGACTATTGGGGGGGGGGGGCAGGTGTGTGCATGGGGACGGGTGGGGTGGTATTGTAAATGGGAGAGGGTCACATTCTATGCTAATAGGCGTGGCAATTGCTGGGTGGGTATGGCTATGGAGCCTGAGCAGCGGCATGGTGATGGGCTTCAGTCACTCTGTATTGGTGGAGCTAAAACTAGGTTGGATCAGCCACCAGGCATTGCTAGGACTAGTGAAGGTTTGAAGCATGGATGAGGTGGACCCAGACACTGCAGTGGGTGGGACCCAAGCACGATGGGCGTGGTCAGAGCTGGGCTGGAGCCAGAAAGGTTCTGAGCTGGTGGGCGTGCCTAGAGGTGGATAGGCAGGGGGTGACTGGTACAGGAATGGATGGGGAATTGTGAGTGTAGTACAGTGGGGCTCTTGCAGTGGTGGGCGTGGCTAACGTTGATGGACAAGCCTCTAGCAGGTCTGAGGCCAGACCGGACTTAAGGTGGTAGGCTTGACCAGGACCTGGCAGGGGGAGGGGCTCGTCAGGTACTCAAGTTGGCTAGGCCAGGCCCAGTGACCTCTCTCTAAATGTGTCACCCTGCAG
Seq C2 exon
CTACCGGAGCCCCTTATCTCTTTTCGCTTCTACCATGAGCTGGTGGGACTAGCTAAGGACAGCCTAAAGGCCGAAGCCGAAGCTAAGGCAGCGAGCCGGGGTCGGCAGGGTGGGTCCGAGAGTGAGGCTGCAACCTTGGCTATGGTGGGCCGCCTGCGTGAGCTCATGCAGGATCTGCCAGCCGAAAACCGGGCCACACTCTTATACCTGCTGAAGCACTTGCGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035697-Hmha1:NM_027521:18
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.158
Domain overlap (PFAM):
C1:
PF0062022=RhoGAP=FE(26.0=100)
A:
NA
C2:
PF0062022=RhoGAP=FE(43.4=100)
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:
GATCTACCGGGTCAATGGCGT
R:
AGGTATAAGAGTGTGGCCCGG
Band lengths:
345-1043
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: