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

    Gene ID: 90736, updated on 10-Dec-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
    mouse all
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    Genomic context

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    See VCF2 in Genome Data Viewer
    Location:
    Xp11.21
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (55143102..55161185, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (54436245..54454327, complement)
    RS_2024_09 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 FAM104 proteins VCF1/2 promote the nuclear localization of p97/VCP. Körner M, et al. Elife, 2023 Sep 15. PMID 37713320, Free PMC Article
    2. The DNA sequence of the human X chromosome. Ross MT, et al. Nature, 2005 Mar 17. PMID 15772651, Free PMC Article
    3. Ubiquitin-mediated proteolysis of HuR by heat shock. Abdelmohsen K, et al. EMBO J, 2009 May 6. PMID 19322201, Free PMC Article
    4. Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains. Haenig C, et al. Cell Rep, 2020 Aug 18. PMID 32814053
    5. 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

    See all (8) 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)

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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

    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_2024_08

    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 VCF2 isoform X4

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

    2. XM_024452476.2 → XP_024308244.1  protein VCF2 isoform X3

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

    3. XM_017029952.2 → XP_016885441.1  protein VCF2 isoform X2

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

    4. XM_024452475.2 → XP_024308243.1  protein VCF2 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 VCF2 isoform X4

    2. XM_054328082.1 → XP_054184057.1  protein VCF2 isoform X3

    3. XM_054328081.1 → XP_054184056.1  protein VCF2 isoform X2

    4. XM_054328080.1 → XP_054184055.1  protein VCF2 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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