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    KNOP1 lysine rich nucleolar protein 1 [ Homo sapiens (human) ]

    Gene ID: 400506, updated on 5-May-2024

    Summary

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    Official Symbol
    KNOP1provided by HGNC
    Official Full Name
    lysine rich nucleolar protein 1provided by HGNC
    Primary source
    HGNC:HGNC:34404
    See related
    Ensembl:ENSG00000103550 AllianceGenome:HGNC:34404
    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
    TSG118; FAM191A; 101F10.1; C16orf88
    Summary
    The protein encoded by this gene is a nucleolar protein that interacts with zinc finger 106 protein. The encoded protein has several of the same characteristics as nucleostemin and may be involved in testis development. [provided by RefSeq, Feb 2017]
    Expression
    Ubiquitous expression in testis (RPKM 5.4), placenta (RPKM 4.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See KNOP1 in Genome Data Viewer
    Location:
    16p12.3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (19701937..19718227, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (19632739..19649030, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (19713259..19729549, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene centriolar coiled-coil protein 110 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:19566659-19567621 Neighboring gene VPS35 endosomal protein sorting factor like Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:19620544-19621743 Neighboring gene NANOG hESC enhancer GRCh37_chr16:19673654-19674240 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:19698132-19698632 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:19710103-19710758 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:19710759-19711413 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:19721101-19721825 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:19721826-19722552 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:19723278-19724003 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10534 Neighboring gene IQ motif containing K Neighboring gene uncharacterized LOC105371115 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:19778410-19778910 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:19778911-19779411 Neighboring gene LARP7 pseudogene 2

    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. Subcellular recruitment by TSG118 and TSPYL implicates a role for zinc finger protein 106 in a novel developmental pathway. Grasberger H, et al. Int J Biochem Cell Biol, 2005 Jul. PMID 15833274
    2. Genome-wide association study in obsessive-compulsive disorder: results from the OCGAS. Mattheisen M, et al. Mol Psychiatry, 2015 Mar. PMID 24821223, Free PMC Article
    3. The OTUD6B-LIN28B-MYC axis determines the proliferative state in multiple myeloma. Paulmann C, et al. EMBO J, 2022 Oct 17. PMID 36059274, Free PMC Article
    4. Genome duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q. Loftus BJ, et al. Genomics, 1999 Sep 15. PMID 10493829
    5. KSHV episome tethering sites on host chromosomes and regulation of latency-lytic switch by CHD4. Kumar A, et al. Cell Rep, 2022 May 10. PMID 35545047, Free PMC Article

    See all (55) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Vif vif HIV-1 Vif downregulates the expression of lysine-rich nucleolar protein 1 (C16orf88, KNOP1) in Vif-expression T cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    lysine-rich nucleolar protein 1
    Names
    family with sequence similarity 191, member A
    protein C16orf88
    testis-specific gene 118 protein

    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_001012991.3 → NP_001013009.2  lysine-rich nucleolar protein 1 isoform b

      See identical proteins and their annotated locations for NP_001013009.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2-6 all encode the same isoform (b).
      Source sequence(s)
      AC002550, BC117562
      Consensus CDS
      CCDS42127.1
      UniProtKB/Swiss-Prot
      O43328, Q1ED39, Q5FWF3
      Related
      ENSP00000219837.7, ENST00000219837.12
      Conserved Domains (1) summary
      pfam15477
      Location:362 → 435
      SMAP; Small acidic protein family

    2. NM_001348527.2 → NP_001335456.1  lysine-rich nucleolar protein 1 isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AC002550
      Conserved Domains (1) summary
      pfam15477
      Location:422 → 495
      SMAP; Small acidic protein family

    3. NM_001348528.2 → NP_001335457.1  lysine-rich nucleolar protein 1 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2-6 all encode the same isoform (b).
      Source sequence(s)
      AC002550
      Consensus CDS
      CCDS42127.1
      UniProtKB/Swiss-Prot
      O43328, Q1ED39, Q5FWF3
      Conserved Domains (1) summary
      pfam15477
      Location:362 → 435
      SMAP; Small acidic protein family

    4. NM_001348529.2 → NP_001335458.1  lysine-rich nucleolar protein 1 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2-6 all encode the same isoform (b).
      Source sequence(s)
      AC002550
      Consensus CDS
      CCDS42127.1
      UniProtKB/Swiss-Prot
      O43328, Q1ED39, Q5FWF3
      Conserved Domains (1) summary
      pfam15477
      Location:362 → 435
      SMAP; Small acidic protein family

    5. NM_001348530.2 → NP_001335459.1  lysine-rich nucleolar protein 1 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2-6 all encode the same isoform (b).
      Source sequence(s)
      AC002550
      Consensus CDS
      CCDS42127.1
      UniProtKB/Swiss-Prot
      O43328, Q1ED39, Q5FWF3
      Conserved Domains (1) summary
      pfam15477
      Location:362 → 435
      SMAP; Small acidic protein family

    6. NM_001348531.2 → NP_001335460.1  lysine-rich nucleolar protein 1 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2-6 all encode the same isoform (b).
      Source sequence(s)
      AC002550
      Consensus CDS
      CCDS42127.1
      UniProtKB/Swiss-Prot
      O43328, Q1ED39, Q5FWF3
      Conserved Domains (1) summary
      pfam15477
      Location:362 → 435
      SMAP; Small acidic protein family

    7. NM_001348532.2 → NP_001335461.1  lysine-rich nucleolar protein 1 isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) differs in the 5' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (c) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform a. Variants 7-12 all encode the same isoform (c).
      Source sequence(s)
      AC002550
      Conserved Domains (1) summary
      pfam15477
      Location:339 → 412
      SMAP; Small acidic protein family

    8. NM_001348533.2 → NP_001335462.1  lysine-rich nucleolar protein 1 isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) differs in the 5' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (c) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform a. Variants 7-12 all encode the same isoform (c).
      Source sequence(s)
      AC002550
      Conserved Domains (1) summary
      pfam15477
      Location:339 → 412
      SMAP; Small acidic protein family

    9. NM_001348534.2 → NP_001335463.1  lysine-rich nucleolar protein 1 isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) differs in the 5' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (c) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform a. Variants 7-12 all encode the same isoform (c).
      Source sequence(s)
      AC002550
      Conserved Domains (1) summary
      pfam15477
      Location:339 → 412
      SMAP; Small acidic protein family

    10. NM_001348535.2 → NP_001335464.1  lysine-rich nucleolar protein 1 isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (10) differs in the 5' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (c) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform a. Variants 7-12 all encode the same isoform (c).
      Source sequence(s)
      AC002550
      Conserved Domains (1) summary
      pfam15477
      Location:339 → 412
      SMAP; Small acidic protein family

    11. NM_001348536.2 → NP_001335465.1  lysine-rich nucleolar protein 1 isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (11) differs in the 5' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (c) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform a. Variants 7-12 all encode the same isoform (c).
      Source sequence(s)
      AC002550
      Conserved Domains (1) summary
      pfam15477
      Location:339 → 412
      SMAP; Small acidic protein family

    12. NM_001348537.2 → NP_001335466.1  lysine-rich nucleolar protein 1 isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (12) differs in the 5' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (c) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform a. Variants 7-12 all encode the same isoform (c).
      Source sequence(s)
      AC002550
      Conserved Domains (1) summary
      pfam15477
      Location:339 → 412
      SMAP; Small acidic protein family

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      19701937..19718227 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      19632739..19649030 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q1ED39.1 GenPept UniProtKB/Swiss-Prot:Q1ED39

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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