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NVL nuclear VCP-like [ Homo sapiens (human) ]

Gene ID: 4931, updated on 4-Nov-2018

Summary

Official Symbol
NVLprovided by HGNC
Official Full Name
nuclear VCP-likeprovided by HGNC
Primary source
HGNC:HGNC:8070
See related
Ensembl:ENSG00000143748 MIM:602426; Vega:OTTHUMG00000037536
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
NVL2
Summary
This gene encodes a member of the AAA (ATPases associated with diverse cellular activities) superfamily. Multiple transcript variants encoding different isoforms have been found for this gene. Two encoded proteins, described as major and minor isoforms, have been localized to distinct regions of the nucleus. The largest encoded protein (major isoform) has been localized to the nucleolus and shown to participate in ribosome biosynthesis (PMID: 15469983, 16782053), while the minor isoform has been localized to the nucleoplasmin. [provided by RefSeq, Aug 2011]
Expression
Ubiquitous expression in skin (RPKM 7.5), lymph node (RPKM 5.1) and 25 other tissues See more
Orthologs

Genomic context

See NVL in Genome Data Viewer
Location:
1q42.11
Exon count:
28
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (224227334..224330189, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (224415036..224517891, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene delta 4-desaturase, sphingolipid 1 Neighboring gene uncharacterized LOC101927143 Neighboring gene uncharacterized LOC101927164 Neighboring gene microRNA 320b-2 Neighboring gene RNA, U6 small nuclear 1008, pseudogene Neighboring gene cornichon family AMPA receptor auxiliary protein 4 Neighboring gene WD repeat domain 26 Neighboring gene microRNA 4742

Genomic regions, transcripts, and products

Expression

  • 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association study of major depressive disorder: new results, meta-analysis, and lessons learned.
NHGRI GWA Catalog

Pathways from BioSystems

  • Ribosome biogenesis in eukaryotes, organism-specific biosystem (from KEGG)
    Ribosome biogenesis in eukaryotes, organism-specific biosystemRibosomes are the cellular factories responsible for making proteins. In eukaryotes, ribosome biogenesis involves the production and correct assembly of four rRNAs and about 80 ribosomal proteins. It...
  • Ribosome biogenesis in eukaryotes, conserved biosystem (from KEGG)
    Ribosome biogenesis in eukaryotes, conserved biosystemRibosomes are the cellular factories responsible for making proteins. In eukaryotes, ribosome biogenesis involves the production and correct assembly of four rRNAs and about 80 ribosomal proteins. It...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
ATPase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA binding HDA PubMed 
preribosome binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
preribosome binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
positive regulation of protein binding IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of telomerase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of telomerase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
rRNA processing IDA
Inferred from Direct Assay
more info
PubMed 
regulation of protein localization to nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
ribosomal large subunit biogenesis IDA
Inferred from Direct Assay
more info
PubMed 
ribosomal large subunit biogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
ribosome biogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ribosome biogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
membrane HDA PubMed 
colocalizes_with nuclear exosome (RNase complex) IDA
Inferred from Direct Assay
more info
PubMed 
nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
telomerase holoenzyme complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
nuclear valosin-containing protein-like
Names
NVLp

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_029641.1 RefSeqGene

    Range
    5001..107856
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001243146.1NP_001230075.1  nuclear valosin-containing protein-like isoform 3

    See identical proteins and their annotated locations for NP_001230075.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks three alternate coding exons in the 5' coding region, uses a downstream initiation codon, and contains an alternate in-frame exon, compared to variant 1. The resulting protein (isoform 3) is shorter and has a distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AC092809, AK297396, BP284587, BU683548
    Consensus CDS
    CCDS58062.1
    UniProtKB/Swiss-Prot
    O15381
    Related
    ENSP00000341362.4, OTTHUMP00000274660, ENST00000340871.8, OTTHUMT00000357506
    Conserved Domains (3) summary
    COG0464
    Location:68663
    SpoVK; AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]
    pfam00004
    Location:429559
    AAA; ATPase family associated with various cellular activities (AAA)
    cl21455
    Location:409445
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
  2. NM_001243147.1NP_001230076.1  nuclear valosin-containing protein-like isoform 4

    See identical proteins and their annotated locations for NP_001230076.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC092809, AK298244, BP284587, BU683548
    Consensus CDS
    CCDS58063.1
    UniProtKB/Swiss-Prot
    O15381
    Related
    ENSP00000417826.1, OTTHUMP00000216594, ENST00000469075.5, OTTHUMT00000357507
    Conserved Domains (5) summary
    COG0464
    Location:193761
    SpoVK; AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]
    pfam00004
    Location:527657
    AAA; ATPase family associated with various cellular activities (AAA)
    pfam16725
    Location:272
    Nucleolin_bd; Nucleolin binding domain
    cl11522
    Location:75125
    Tom22; Mitochondrial import receptor subunit Tom22
    cl21455
    Location:507543
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
  3. NM_002533.3NP_002524.2  nuclear valosin-containing protein-like isoform 1

    See identical proteins and their annotated locations for NP_002524.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest protein (isoform 1, also known as NVL.2 or the major isoform).
    Source sequence(s)
    AC092809, AK293923, BP284587, BU683548, U68140
    Consensus CDS
    CCDS1541.1
    UniProtKB/Swiss-Prot
    O15381
    UniProtKB/TrEMBL
    B4DF43
    Related
    ENSP00000281701.6, OTTHUMP00000035641, ENST00000281701.10, OTTHUMT00000091453
    Conserved Domains (4) summary
    COG0464
    Location:284852
    SpoVK; AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]
    pfam00004
    Location:618748
    AAA; ATPase family associated with various cellular activities (AAA)
    pfam16725
    Location:272
    Nucleolin_bd; Nucleolin binding domain
    cl21455
    Location:598634
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
  4. NM_206840.2NP_996671.1  nuclear valosin-containing protein-like isoform 2

    See identical proteins and their annotated locations for NP_996671.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon and uses a downstream start codon compared to variant 1. The resulting protein (isoform 2, also known as NVL.1 or the minor isoform) is shorter and has a distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AC092809, AK293923, BP284587, BU683548, U78772
    Consensus CDS
    CCDS1542.1
    UniProtKB/Swiss-Prot
    O15381
    UniProtKB/TrEMBL
    B4DF43
    Related
    ENSP00000375747.2, OTTHUMP00000216599, ENST00000391875.6, OTTHUMT00000091454
    Conserved Domains (1) summary
    cl27568
    Location:137750
    TIP49; TIP49 C-terminus

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    224227334..224330189 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011544200.1XP_011542502.1  nuclear valosin-containing protein-like isoform X9

    See identical proteins and their annotated locations for XP_011542502.1

    Conserved Domains (3) summary
    COG0464
    Location:166761
    SpoVK; AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]
    pfam00004
    Location:527657
    AAA; ATPase family associated with various cellular activities (AAA)
    cl21455
    Location:507543
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
  2. XM_017001383.1XP_016856872.1  nuclear valosin-containing protein-like isoform X6

  3. XM_017001382.1XP_016856871.1  nuclear valosin-containing protein-like isoform X5

  4. XM_017001379.1XP_016856868.1  nuclear valosin-containing protein-like isoform X2

  5. XM_017001378.1XP_016856867.1  nuclear valosin-containing protein-like isoform X1

  6. XM_011544198.2XP_011542500.1  nuclear valosin-containing protein-like isoform X8

    Conserved Domains (3) summary
    COG0464
    Location:178773
    SpoVK; AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]
    pfam00004
    Location:539669
    AAA; ATPase family associated with various cellular activities (AAA)
    cl21455
    Location:519555
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
  7. XM_011544196.1XP_011542498.1  nuclear valosin-containing protein-like isoform X4

    Conserved Domains (4) summary
    COG0464
    Location:284879
    SpoVK; AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]
    pfam00004
    Location:645775
    AAA; ATPase family associated with various cellular activities (AAA)
    pfam16725
    Location:272
    Nucleolin_bd; Nucleolin binding domain
    cl21455
    Location:625661
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
  8. XM_017001381.1XP_016856870.1  nuclear valosin-containing protein-like isoform X5

  9. XM_024447367.1XP_024303135.1  nuclear valosin-containing protein-like isoform X11

    Conserved Domains (1) summary
    cl27568
    Location:137750
    TIP49; TIP49 C-terminus
  10. XM_011544199.1XP_011542501.1  nuclear valosin-containing protein-like isoform X9

    See identical proteins and their annotated locations for XP_011542501.1

    Conserved Domains (3) summary
    COG0464
    Location:166761
    SpoVK; AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]
    pfam00004
    Location:527657
    AAA; ATPase family associated with various cellular activities (AAA)
    cl21455
    Location:507543
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
  11. XM_017001386.2XP_016856875.1  nuclear valosin-containing protein-like isoform X12

  12. XM_017001380.2XP_016856869.1  nuclear valosin-containing protein-like isoform X3

  13. XM_017001384.1XP_016856873.1  nuclear valosin-containing protein-like isoform X7

  14. XM_017001385.2XP_016856874.1  nuclear valosin-containing protein-like isoform X10

RNA

  1. XR_001737205.1 RNA Sequence

  2. XR_001737204.1 RNA Sequence

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