Nova1 MGI Mouse Gene Detail - MGI:104297 - NOVA alternative splicing regulator 1

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_104297	protein coding gene	Chr12:46741300-46866143 (-)
129S1/SvImJ	ENSMUSG00200011463	protein coding gene	Chr12:38671378-38795908 (-)
A/J	ENSMUSG00195016041	protein coding gene	Chr12:41256869-41383620 (-)
AKR/J	ENSMUSG00220005043	protein coding gene	Chr12:39269457-39396220 (-)
BALB/cJ	ENSMUSG00180003572	protein coding gene	Chr12:40243864-40370613 (-)
C3H/HeJ	ENSMUSG00175011094	protein coding gene	Chr12:43311314-43438070 (-)
C57BL/6NJ	ENSMUSG00215011117	protein coding gene	Chr12:39682576-39808743 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0017728	protein coding gene	Chr12:42550580-42671944 (-)
CAST/EiJ	ENSTCUG00005003489	protein coding gene	Chr12:39942240-40066414 (-)
CBA/J	ENSMUSG00210016030	protein coding gene	Chr12:39785864-39912615 (-)
DBA/2J	ENSMUSG00185014046	protein coding gene	Chr12:41781311-41905835 (-)
FVB/NJ	ENSMUSG00205001347	protein coding gene	Chr12:39636918-39761437 (-)
JF1/MsJ	ENSUMUG00000002427	protein coding gene	Chr12:45951583-46076320 (-)
LP/J	ENSMUSG00230009933	protein coding gene	Chr12:48812248-48936759 (-)
NOD/ShiLtJ	ENSMUSG00190003526	protein coding gene	Chr12:38792323-38916791 (-)
NZO/HlLtJ	ENSMUSG00225031034	protein coding gene	Chr12:50952760-51077274 (-)
PWK/PhJ	ENSLUMG00010011835	protein coding gene	Chr12:40033633-40158359 (-)
SPRET/EiJ	ENSMSPG00010015651	protein coding gene	Chr12:41201225-41325819 (-)
WSB/EiJ	ENSIUOG00005001200	protein coding gene	Chr12:39600045-39726171 (-)

Length	Strain/Species	Flank
genomic	664883	NCBI Gene Model \| MGI Sequence Detail	121466	C57BL/6J	± kb
transcript	NM_001364637	RefSeq \| MGI Sequence Detail	3861	ZRU/MplStud
polypeptide	Q9JKN6	UniProt \| EBI \| MGI Sequence Detail	507	Not Applicable

TSS for Nova1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr116228	Chr12:46866282-46866300 (-)	-148 bp
Tssr116227	Chr12:46866252-46866281 (-)	-124 bp
Tssr116226	Chr12:46866136-46866154 (-)	-2 bp
Tssr116225	Chr12:46866027-46866032 (-)	113 bp
Tssr116224	Chr12:46865971-46865987 (-)	164 bp
Tssr116223	Chr12:46865870-46865879 (-)	268 bp
Tssr116222	Chr12:46865826-46865841 (-)	309 bp
Tssr116221	Chr12:46865803-46865809 (-)	337 bp
Tssr116220	Chr12:46865765-46865787 (-)	367 bp
Tssr116219	Chr12:46865709-46865720 (-)	428 bp
Tssr116218	Chr12:46865532-46865571 (-)	591 bp
Tssr116217	Chr12:46865279-46865300 (-)	853 bp
Tssr116216	Chr12:46865124-46865140 (-)	1,011 bp
Tssr116215	Chr12:46864918-46864938 (-)	1,215 bp
Tssr116214	Chr12:46864891-46864912 (-)	1,241 bp
Tssr116213	Chr12:46864861-46864879 (-)	1,273 bp
Tssr116212	Chr12:46863706-46863744 (-)	2,418 bp
Tssr116211	Chr12:46832052-46832055 (-)	34,089 bp
Tssr116210	Chr12:46831097-46831101 (-)	35,044 bp
Tssr116209	Chr12:46767619-46767627 (-)	98,520 bp
Tssr116208	Chr12:46745403-46745406 (-)	120,738 bp

Nova1 is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Fl1sa	Chr12, 13.69 cM		J:244215	Nonalcoholic fatty liver disease (NAFLD) is a multifactorial disease caused by interactions between environmental and genetic factors. It was previously determined that SMXA-5 mice develop severe fatty liver on a high fat diet, although parental SM/J and A/J mice were resistant to fatty liver. Quantitative trait analysis using (SM/J x SMxA-5)F2 intercrossed mice identified a significant QTL, Fl1sa (fatty liver 1 in SMXA), for liver weight, liver triglyceride and total lipid content on centromere-53.06 Mb of mouse Chromosome 12. The A/J allele at Fl1sa was associated with the fatty liver. [J:124974] In a subsequent study using the livers from A/J-Chr 12 consomic and A/J mice that were fed a high fat diet three candidate genes were identified, Iah1, Rrm2 and Prkd1 using DNA microarray analysis. [J: 240255] The goal of the current study was to narrow the previously identified Fl1sa region by genetic dissection using novel congenic mice to identify candidate genes within the narrowed Fl1sa region. Two strains of congenic mice, A.SM-(centromere - D12Mit85)/J (R2) and A.SM-(D12Mit85-D12Mit112)/J (R3), were constructed from parental A/J and A/JChr 12 . Microsatellite markers and SNPs were used for the genotyping of R2 and R3 genomic DNA. Physical positions were taken from GRCm38.P4. The lipid accumulation in the respective livers was analyzed. As the liver triglyceride content in R2 and R3 congenic mice was significantly lower than in A/J mice. Male A/J, A/J-Chr12, R2 and R3 mice were fed standard chow until 6 weeks of age and thereafter fed a high fat diet from 6 to 13 weeks of age. At 13 weeks of age all mice were sacrificed after a 4 hour fast. The liver and white adipose tissue (subcutaneous fat, epididymal fat, mesenteric fat and retroperitoneal fat) were harvested and weighed. Blood sample were collected to measure serum lipids. Serum triglyceride, cholesterol and hepatic triglyceride content were measured. Whole transcripts from epididymal fats were measured using a Mouse Genome ST 2.0 array. Liver triglyceride content was significantly lower in A/J-Chr 12, R2 and R3 mice compared with that of A/J mice. Liver triglyceride and liver total lipid in R2 and R3 mice showed intermediate values between those of A/J and A/J-Chr 12 mice. The results suggested that the genes responsible for fatty liver existed in the SM/J region in strain R2 (centromere-29.20 Mb) and in the SM/J region in strain R3 (29.20-46.75 Mb) of Chromosome 12, Fig 1. Subsequently, in both of the narrowed Fl1sa regions microarray analysis of liver and epididymal fat from A/J and A/J-Chr 12 mice was performed in an attempt to identify candidate genes. Significant differences in gene expression levels in epididymal fat analysis were confirmed in 6 candidate genes: Ntsr2, Zfp125, Gdap10, Nrcam, Stxbp6 and Nova1 between the two strains.

*cM position of peak correlated region/marker

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early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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