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VCF2 VCP nuclear cofactor family member 2 [ Homo sapiens (human) ]

Gene ID: 90736, updated on 5-Mar-2024

Summary

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Official Symbol
VCF2provided by HGNC
Official Full Name
VCP nuclear cofactor family member 2provided by HGNC
Primary source
HGNC:HGNC:25085
See related
Ensembl:ENSG00000182518 AllianceGenome:HGNC:25085
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CXorf44; FAM104B
Expression
Ubiquitous expression in kidney (RPKM 4.5), brain (RPKM 4.0) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
Xp11.21
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (55143102..55161185, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (54436245..54454327, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (55169535..55187618, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene PAGE family member 2 Neighboring gene CRISPRi-validated cis-regulatory element chrX.1184 Neighboring gene component of oligomeric golgi complex 1 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:55187406-55187906 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:55187907-55188407 Neighboring gene X antigen family member 3-like Neighboring gene MT-CO1 pseudogene 52 Neighboring gene MT-ND2 pseudogene 24

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. The DNA sequence of the human X chromosome. Ross MT, et al. Nature, 2005 Mar 17. PMID 15772651, Free PMC Article
  2. Ubiquitin-mediated proteolysis of HuR by heat shock. Abdelmohsen K, et al. EMBO J, 2009 May 6. PMID 19322201, Free PMC Article
  3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
  4. A reference map of the human binary protein interactome. Luck K, et al. Nature, 2020 Apr. PMID 32296183, Free PMC Article
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Gerhard DS, et al. Genome Res, 2004 Oct. PMID 15489334, Free PMC Article

See all (6) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The FAM104 proteins VCF1/2 promote the nuclear localization of p97/VCP.
    Title: The FAM104 proteins VCF1/2 promote the nuclear localization of p97/VCP.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ18375, FLJ20434

General protein information

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Preferred Names
protein VCF2; protein FAM104B
Names
family with sequence similarity 104 member B

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)

  1. NM_001166699.2 → NP_001160171.1  protein VCF2 isoform 2

    See identical proteins and their annotated locations for NP_001160171.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in an isoform (2) that is longer than isoform 1.
    Source sequence(s)
    BC017571, BI850888, DB216586
    Consensus CDS
    CCDS55426.1
    UniProtKB/Swiss-Prot
    Q5XKR9
    Related
    ENSP00000333394.4, ENST00000332132.8
    Conserved Domains (1) summary
    pfam15434
    Location:7 → 115
    FAM104; Family 104

  2. NM_001166700.2 → NP_001160172.1  protein VCF2 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the central coding region, and differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (3) has a distinct C-terminus and is longer than isoform 1.
    Source sequence(s)
    AK311333, AK311699, BC006406, DB216586
    Consensus CDS
    CCDS55425.1
    UniProtKB/Swiss-Prot
    Q5XKR9
    Related
    ENSP00000397188.2, ENST00000425133.2
    Conserved Domains (1) summary
    pfam15434
    Location:7 → 116
    FAM104; Family 104

  3. NM_001166701.4 → NP_001160173.1  protein VCF2 isoform 4

    See identical proteins and their annotated locations for NP_001160173.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (4) has a distinct C-terminus and is the same length as isoform 1.
    Source sequence(s)
    AL590240
    Consensus CDS
    CCDS94615.1
    UniProtKB/TrEMBL
    A0A8I5KUH0
    Related
    ENSP00000509111.1, ENST00000685693.1
    Conserved Domains (1) summary
    pfam15434
    Location:12 → 115
    FAM104; Family 104

  4. NM_001166702.2 → NP_001160174.1  protein VCF2 isoform 5

    See identical proteins and their annotated locations for NP_001160174.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in both UTRs and in the 5' and 3' coding regions, compared to variant 1. The encoded isoform (5) has distinct N- and C-termini and is shorter than isoform 1.
    Source sequence(s)
    AK299935, AK311333, AK311699, AL590240, BC006406, DC413808
    Consensus CDS
    CCDS55423.1
    UniProtKB/Swiss-Prot
    Q5XKR9
    Related
    ENSP00000421161.1, ENST00000477847.6
    Conserved Domains (1) summary
    pfam15434
    Location:4 → 112
    FAM104; Family 104

  5. NM_001166703.2 → NP_001160175.1  protein VCF2 isoform 6

    See identical proteins and their annotated locations for NP_001160175.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) differs in both UTRs and in the 5' and 3' coding regions, compared to variant 1. The encoded isoform (6) has distinct N- and C-termini and is shorter than isoform 1.
    Source sequence(s)
    AK311333, AK311699, AL590240, BX100076
    Consensus CDS
    CCDS55422.1
    UniProtKB/Swiss-Prot
    Q5XKR9
    Related
    ENSP00000423164.1, ENST00000489298.1
    Conserved Domains (1) summary
    pfam15434
    Location:7 → 114
    FAM104; Family 104

  6. NM_001166704.2 → NP_001160176.1  protein VCF2 isoform 7

    See identical proteins and their annotated locations for NP_001160176.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) uses an alternate splice site in the central coding region, and differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (7) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AK311333, AK311699, DB216586
    Consensus CDS
    CCDS55424.1
    UniProtKB/Swiss-Prot
    Q5XKR9
    Related
    ENSP00000420895.1, ENST00000472571.2
    Conserved Domains (1) summary
    pfam15434
    Location:7 → 40
    FAM104; Family 104

  7. NM_138362.4 → NP_612371.2  protein VCF2 isoform 1

    See identical proteins and their annotated locations for NP_612371.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    BC000919, BC017571, DB216586
    Consensus CDS
    CCDS35305.2
    UniProtKB/Swiss-Prot
    A6NEH1, B4DSV6, D6R9S5, D6RDJ5, E9PH40, Q5XKR9, Q8WVU5, Q9BRA1
    Related
    ENSP00000364101.3, ENST00000358460.8
    Conserved Domains (1) summary
    pfam15434
    Location:7 → 114
    FAM104; Family 104

RNA

  1. NR_030722.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (8) uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    BC000919, BC017571, CK004182, DB216586

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    55143102..55161185 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017029953.2 → XP_016885442.1  protein FAM104B isoform X4

    Conserved Domains (1) summary
    pfam15434
    Location:9 → 111
    FAM104; Family 104

  2. XM_024452476.2 → XP_024308244.1  protein FAM104B isoform X3

    Conserved Domains (1) summary
    pfam15434
    Location:4 → 112
    FAM104; Family 104

  3. XM_017029952.2 → XP_016885441.1  protein FAM104B isoform X2

    Conserved Domains (1) summary
    pfam15434
    Location:17 → 124
    FAM104; Family 104

  4. XM_024452475.2 → XP_024308243.1  protein FAM104B isoform X1

    Conserved Domains (1) summary
    pfam15434
    Location:23 → 130
    FAM104; Family 104

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    54436245..54454327 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054328083.1 → XP_054184058.1  protein FAM104B isoform X4

  2. XM_054328082.1 → XP_054184057.1  protein FAM104B isoform X3

  3. XM_054328081.1 → XP_054184056.1  protein FAM104B isoform X2

  4. XM_054328080.1 → XP_054184055.1  protein FAM104B isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5XKR9.1 GenPept UniProtKB/Swiss-Prot:Q5XKR9

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