NOVA1 NOVA alternative splicing regulator 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NOVA1provided by HGNC
Official Full Name: NOVA alternative splicing regulator 1provided by HGNC
Primary source: HGNC:HGNC:7886
See related: Ensembl:ENSG00000139910 MIM:602157; AllianceGenome:HGNC:7886
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: Nova-1
Summary: This gene encodes a neuron-specific RNA-binding protein, a member of the Nova family of paraneoplastic disease antigens, that is recognized and inhibited by paraneoplastic antibodies. These antibodies are found in the sera of patients with paraneoplastic opsoclonus-ataxia, breast cancer, and small cell lung cancer. Alternatively spliced transcripts encoding distinct isoforms have been described. [provided by RefSeq, Jul 2008]
Expression: Biased expression in brain (RPKM 10.5), fat (RPKM 4.3) and 12 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 14q12

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (26443090..26598033, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (20640973..20795930, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (26912296..27067239, complement)

Chromosome 14 - NC_000014.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Upregulation of FGF9 and NOVA1 in cancer-associated fibroblasts promotes cell proliferation, invasion and migration of triple negative breast cancer.
Title: Upregulation of FGF9 and NOVA1 in cancer-associated fibroblasts promotes cell proliferation, invasion and migration of triple negative breast cancer.
NOVA1 acts as an oncogenic RNA-binding protein to regulate cholesterol homeostasis in human glioblastoma cells.
Title: NOVA1 acts as an oncogenic RNA-binding protein to regulate cholesterol homeostasis in human glioblastoma cells.
RNA-binding protein NOVA1 promotes acute T-lymphocyte leukemia progression by stabilizing USP44 mRNA.
Title: RNA-binding protein NOVA1 promotes acute T-lymphocyte leukemia progression by stabilizing USP44 mRNA.
Pattern of Brain Parenchymal Damage Related to Cerebral Small Vessel Disease in Carriers of Rare NOTCH3 Variants.
Title: Pattern of Brain Parenchymal Damage Related to Cerebral Small Vessel Disease in Carriers of Rare NOTCH3 Variants.
Interaction of the C9orf72-Amyotrophic Lateral Sclerosis-Related Proline-Arginine Dipeptide Repeat Protein with the RNA-Binding Protein NOVA1 Causes Decreased Expression of UNC13A Due to Enhanced Inclusion of Cryptic Exons, Which Is Reversed by Betulin Treatment.
Title: Interaction of the C9orf72-Amyotrophic Lateral Sclerosis-Related Proline-Arginine Dipeptide Repeat Protein with the RNA-Binding Protein NOVA1 Causes Decreased Expression of UNC13A Due to Enhanced Inclusion of Cryptic Exons, Which Is Reversed by Betulin Treatment.
NOVA1 prevents overactivation of the unfolded protein response and facilitates chromatin access during human white adipogenesis.
Title: NOVA1 prevents overactivation of the unfolded protein response and facilitates chromatin access during human white adipogenesis.
Spliceosomic dysregulation unveils NOVA1 as a candidate actionable therapeutic target in pancreatic neuroendocrine tumors.
Title: Spliceosomic dysregulation unveils NOVA1 as a candidate actionable therapeutic target in pancreatic neuroendocrine tumors.
Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis.
Title: Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis.
MiR-146a functions as a potential tumor suppressor in retinoblastoma by negatively regulate neuro-oncological ventral antigen-1.
Title: MiR-146a functions as a potential tumor suppressor in retinoblastoma by negatively regulate neuro-oncological ventral antigen-1.
Knockdown of NOVA1 inhibits inflammation and migration of asthmatic airway smooth muscle cells to regulate PTEN/Akt pathway by targeting PTBP1.
Title: Knockdown of NOVA1 inhibits inflammation and migration of asthmatic airway smooth muscle cells to regulate PTEN/Akt pathway by targeting PTBP1.

Submit: New GeneRIF Correction See all GeneRIFs (39)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association studies and heritability estimates of body mass index related phenotypes in bangladeshi adults. EBI GWAS Catalog EBI GWAS CatalogPubMed
GWAS identifies four novel eosinophilic esophagitis loci. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:482308

NOVA1__6065 (e-PCR)
- UniSTS:463641

G59267 (e-PCR)
- UniSTS:136582

Nova1 (e-PCR), detects polymorphism
- UniSTS:479181

RH66321 (e-PCR)
- UniSTS:21231

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables mRNA 3'-UTR binding	IEA Inferred from Electronic Annotation more info
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables mRNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific mRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific mRNA binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in RNA processing	TAS Traceable Author Statement more info	PubMed
involved_in RNA splicing	TAS Traceable Author Statement more info	PubMed
involved_in mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of cold-induced thermogenesis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in nervous system development	IEA Inferred from Electronic Annotation more info
involved_in regulation of alternative mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of alternative mRNA splicing, via spliceosome	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in nucleolus	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: RNA-binding protein Nova-1

Names: neuro-oncological ventral antigen 1; onconeural ventral antigen 1; paraneoplastic Ri antigen; ventral neuron-specific protein 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001366390.2 → NP_001353319.1 RNA-binding protein Nova-1 isoform 4

Status: REVIEWED

Source sequence(s)

AL079343, AL132716

Conserved Domains (2) summary

cd00105
Location:277 → 342

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

cd02396
Location:27 → 92

PCBP_like_KH; K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are ...
NM_001366391.2 → NP_001353320.1 RNA-binding protein Nova-1 isoform 5

Status: REVIEWED

Source sequence(s)

AL079343, AL132716

UniProtKB/TrEMBL

B7Z770

Conserved Domains (2) summary

cd00105
Location:301 → 366

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

cd02396
Location:51 → 116

PCBP_like_KH; K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are ...
NM_001366392.2 → NP_001353321.1 RNA-binding protein Nova-1 isoform 6

Status: REVIEWED

Source sequence(s)

AL079343, AL132716

UniProtKB/TrEMBL

A8K603

Conserved Domains (2) summary

cd00105
Location:422 → 487

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

cd02396
Location:172 → 237

PCBP_like_KH; K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are ...
NM_001366393.2 → NP_001353322.1 RNA-binding protein Nova-1 isoform 7

Status: REVIEWED

Source sequence(s)

AL079343, AL132716

UniProtKB/TrEMBL

A8K603

Conserved Domains (2) summary

cd00105
Location:386 → 451

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

cd02396
Location:136 → 201

PCBP_like_KH; K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are ...
NM_001366394.2 → NP_001353323.1 RNA-binding protein Nova-1 isoform 8

Status: REVIEWED

Source sequence(s)

AL079343, AL132716

UniProtKB/TrEMBL

A8K603

Conserved Domains (2) summary

cd00105
Location:362 → 427

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

cd02396
Location:112 → 177

PCBP_like_KH; K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are ...
NM_001366395.2 → NP_001353324.1 RNA-binding protein Nova-1 isoform 5

Status: REVIEWED

Source sequence(s)

AL079343, AL132716

UniProtKB/TrEMBL

B7Z770

Conserved Domains (2) summary

cd00105
Location:301 → 366

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

cd02396
Location:51 → 116

PCBP_like_KH; K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are ...
NM_001366396.2 → NP_001353325.1 RNA-binding protein Nova-1 isoform 5

Status: REVIEWED

Source sequence(s)

AL079343, AL132716

UniProtKB/TrEMBL

B7Z770

Conserved Domains (2) summary

cd00105
Location:301 → 366

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

cd02396
Location:51 → 116

PCBP_like_KH; K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are ...
NM_001366397.2 → NP_001353326.1 RNA-binding protein Nova-1 isoform 4

Status: REVIEWED

Source sequence(s)

AL079343, AL132716

Conserved Domains (2) summary

cd00105
Location:277 → 342

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

cd02396
Location:27 → 92

PCBP_like_KH; K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are ...
NM_001366398.2 → NP_001353327.1 RNA-binding protein Nova-1 isoform 5

Status: REVIEWED

Source sequence(s)

AL132716

UniProtKB/TrEMBL

B7Z770

Conserved Domains (2) summary

cd00105
Location:301 → 366

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

cd02396
Location:51 → 116

PCBP_like_KH; K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are ...
NM_002515.3 → NP_002506.2 RNA-binding protein Nova-1 isoform 1

See identical proteins and their annotated locations for NP_002506.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AI569678, AL079343, AL132716, BE762927, BX431656, CN409914, R60636, U04840

Consensus CDS

CCDS32061.1

UniProtKB/Swiss-Prot

A8K0S4, A8K4Q7, D3DS81, D3DS82, P51513, Q6B004

UniProtKB/TrEMBL

A8K603

Related

ENSP00000438875.2, ENST00000539517.7

Conserved Domains (2) summary

cd00105
Location:423 → 488

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

cd02396
Location:173 → 238

PCBP_like_KH; K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are ...
NM_006489.3 → NP_006480.2 RNA-binding protein Nova-1 isoform 2

See identical proteins and their annotated locations for NP_006480.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The resulting protein (isoform 2) is shorter, compared to isoform 1.

Source sequence(s)

AI569678, AL079343, AL132716, BE762927, BX431656, CN409914, R60636, U04840

Consensus CDS

CCDS32060.1

UniProtKB/TrEMBL

A8K603

Related

ENSP00000447391.1, ENST00000465357.6

Conserved Domains (2) summary

cd00105
Location:399 → 464

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

cd02396
Location:149 → 214

PCBP_like_KH; K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are ...
NM_006491.3 → NP_006482.1 RNA-binding protein Nova-1 isoform 3

See identical proteins and their annotated locations for NP_006482.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 3' coding region, and differs in the 3' UTR, compared to variant 1. The resulting protein (isoform 3) is shorter and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

AI569678, AL079343, AL132716, BE644739, CN409914, U04840

Consensus CDS

CCDS9635.1

UniProtKB/TrEMBL

I3L2B5

Related

ENSP00000342387.5, ENST00000344429.9

Conserved Domains (1) summary

cd22435
Location:49 → 121

KH-I_NOVA_rpt1; first type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000014.9 Reference GRCh38.p14 Primary Assembly

Range

26443090..26598033 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017021345.2 → XP_016876834.1 RNA-binding protein Nova-1 isoform X1

UniProtKB/TrEMBL

B7Z770

Conserved Domains (2) summary

cd00105
Location:301 → 366

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

cd02396
Location:51 → 116

PCBP_like_KH; K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are ...