Nova1 Gene Detail

Summary

• Symbol
  Nova1
• Name
  NOVA alternative splicing regulator 1
• Synonyms
  9430099M15Rik, Nova-1

• Feature Type
  protein coding gene
• IDs
  MGI:104297
  NCBI Gene: 664883
• Alliance
  gene page
• Transcription Start Sites
  21 TSS
• Candidate for QTL
  1 QTL

Location &
Maps

• Sequence Map
  Chr12:46744678-46866143 bp, - strand

  From NCBI annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 12, 21.46 cM
• Mapping Data
  4 experiments

Strain
Comparison

• SNPs within 2kb
  3584 from dbSNP Build 142
• Strain Annotations
  18
• RFLP
  1

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_104297	protein coding gene	Chr12:46741300-46866143 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0019714	protein coding gene	Chr12:45352718-45487129 (-)
A/J	MGP_AJ_G0019678	protein coding gene	Chr12:43708739-43837473 (-)
AKR/J	MGP_AKRJ_G0019649	protein coding gene	Chr12:45095432-45225565 (-)
BALB/cJ	MGP_BALBcJ_G0019656	protein coding gene	Chr12:44005926-44132218 (-)
C3H/HeJ	MGP_C3HHeJ_G0019460	protein coding gene	Chr12:45100761-45232947 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0020103	protein coding gene	Chr12:46648176-46785951 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0017728	protein coding gene	Chr12:42550580-42671944 (-)
CAST/EiJ	MGP_CASTEiJ_G0019013	protein coding gene	Chr12:40224766-40365969 (-)
CBA/J	MGP_CBAJ_G0019432	protein coding gene	Chr12:48214532-48358948 (-)
DBA/2J	MGP_DBA2J_G0019545	protein coding gene	Chr12:43545937-43678289 (-)
FVB/NJ	MGP_FVBNJ_G0019534	protein coding gene	Chr12:43098612-43220613 (-)
LP/J	MGP_LPJ_G0019615	protein coding gene	Chr12:45332558-45453062 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0019570	protein coding gene	Chr12:49167835-49322706 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0020143	protein coding gene	Chr12:44616532-44746295 (-)
PWK/PhJ	MGP_PWKPhJ_G0018780	protein coding gene	Chr12:38199463-38328259 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0018570	protein coding gene	Chr12:39251622-39388149 (-)
WSB/EiJ	MGP_WSBEiJ_G0019063	protein coding gene	Chr12:44980946-45112560 (-)

Homology

• Human Ortholog
  NOVA1, NOVA alternative splicing regulator 1

• Vertebrate Orthologs
  4

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  NOVA1, NOVA alternative splicing regulator 1
  
• Synonyms
  Nova-1
• Links
  HGNC:7886

  NCBI Gene ID: 4857

  neXtProt AC: NX_P51513

  UniProt: P51513

  
  
• Chr Location
  14q12; chr14:26443090-26598033 (-)  GRCh38

---

• MGI Vertebrate Homology
  Nova1 stringent orthology
  1 human;1 mouse;1 rat;2 zebrafish
  
• HCOP
  vertebrate homology predictions: NOVA1
• Gene Tree
  Nova1
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  7 phenotypes from 1 allele in 1 genetic background
  18 phenotype references
  

• All Mutations and Alleles
  12
• Endonuclease-mediated
  6
• Gene trapped
  1
• Targeted
  5
• Incidental Mutations
  APF , CvDC
• Find Mice (IMSR)
  24 strains or lines available
• Comparison Matrix
  Gene Expression + Phenotype

Mice homozygous for a null allele are born small, develop motor dysfunction associated with neuron apoptosis, and die within 10 days of birth.

Gene Ontology
(GO)
Classifications

• All GO Annotations
  26
• GO References
  15

Expression

• Assay Results
  834
• Tissues
  101
• cDNA Data
  39
• Literature Summary
  13

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

• Other Mouse Links
  Allen Institute
  GENSAT
  GEO
  Expression Atlas
• Other Vertebrate Links
  Xenbase nova1

Sequences &
Gene Models

• All Sequences
  117
• RefSeq
  73
• UniProt
  5
• CCDS
  CCDS49058.1

• Ensembl
  ENSMUSG00000021047 (Evidence)
• NCBI Gene
  664883

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

Protein
Information

• UniProt
  5 Sequences
• Protein Ontology
  PR:000011339 RNA-binding protein Nova-1
  (term hierarchy)
• InterPro Domains
  IPR004087 K Homology domain
  IPR004088 K Homology domain, type 1
  IPR036612 K Homology domain, type 1 superfamily
  IPR047275 RNA-binding protein Nova-1/2, type I K Homology domain 1
  IPR047276 RNA-binding protein Nova-1/2, type I K Homology domain 2
  IPR047274 RNA-binding protein Nova-1/2, type I K Homology domain 3

Molecular
Reagents

• All nucleic 41

  cDNA 39

  Primer pair 2

  
  

  Microarray probesets 3

Other
Accession IDs

MGD-MRK-25624, MGI:2442886

References

• Summaries
  All 62

  Developmental Gene Expression 13

  Gene Ontology 15

  Phenotypes 18
• Earliest
  J:306713 Buckanovich RJ, et al., The onconeural antigen Nova-1 is a neuron-specific RNA-binding protein, the activity of which is inhibited by paraneoplastic antibodies. J Neurosci. 1996 Feb 1;16(3):1114-22
• Latest
  J:359186 Ibrahim LA, et al., Nova proteins direct synaptic integration of somatostatin interneurons through activity-dependent alternative splicing. Elife. 2023 Jun 22;12

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