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ZCCHC17 zinc finger CCHC-type containing 17 [ Homo sapiens (human) ]

Gene ID: 51538, updated on 21-Dec-2019

Summary

Official Symbol
ZCCHC17provided by HGNC
Official Full Name
zinc finger CCHC-type containing 17provided by HGNC
Primary source
HGNC:HGNC:30246
See related
Ensembl:ENSG00000121766
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
PS1D; pNO40; HSPC251
Expression
Ubiquitous expression in heart (RPKM 23.1), brain (RPKM 18.8) and 24 other tissues See more
Orthologs

Genomic context

See ZCCHC17 in Genome Data Viewer
Location:
1p35.2
Exon count:
9
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (31296982..31365722)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (31769832..31838569)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene sodium/potassium transporting ATPase interacting 1 Neighboring gene small nuclear ribonucleoprotein U5 subunit 40 Neighboring gene fatty acid binding protein 3 Neighboring gene uncharacterized LOC105378623 Neighboring gene uncharacterized LOC107985470

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 Apr 4 07:08:55 2018

Bibliography

Phenotypes

NHGRI GWAS Catalog

Description
NKAIN1-SERINC2 is a functional, replicable and genome-wide significant risk gene region specific for alcohol dependence in subjects of European descent.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of zinc finger, CCHC domain containing 17 (ZCCHC17) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

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

General protein information

Preferred Names
nucleolar protein of 40 kDa
Names
nucleolar protein 40
pnn-interacting nucleolar protein
putative S1 RNA binding domain protein
zinc finger CCHC domain-containing protein 17
zinc finger, CCHC domain containing 17

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.

mRNA and Protein(s)

  1. NM_001282566.1NP_001269495.1  nucleolar protein of 40 kDa isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AF247661, AK307478, BC050609, DC366453
    Consensus CDS
    CCDS72741.1
    UniProtKB/Swiss-Prot
    Q9NP64
    UniProtKB/TrEMBL
    A0A087WXF8
    Related
    ENSP00000480986.1, ENST00000615916.4
    Conserved Domains (1) summary
    cd05686
    Location:45108
    S1_pNO40; S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. ...
  2. NM_001282567.1NP_001269496.1  nucleolar protein of 40 kDa isoform b

    See identical proteins and their annotated locations for NP_001269496.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks a portion of the 5' UTR and 5' coding region, initiates translation at a downstream in-frame start codon, and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AF247661, AK302343, AK307478, BC050609, DC366453
    Consensus CDS
    CCDS60062.1
    UniProtKB/Swiss-Prot
    Q9NP64
    UniProtKB/TrEMBL
    A0A0D9SEW3, B4DYA9
    Related
    ENSP00000486079.1, ENST00000627541.1
    Conserved Domains (1) summary
    cl09927
    Location:162
    S1_like; S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. ...
  3. NM_001282568.1NP_001269497.1  nucleolar protein of 40 kDa isoform c

    See identical proteins and their annotated locations for NP_001269497.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and 5' coding region, and uses an alternate start codon, compared to variant 1. The encoded isoform (c) has a distinct and shorter N-terminus, compared to isoform a. Both variants 3 and 4 encode isoform c.
    Source sequence(s)
    AK302248, AK302343, AK307478, BC000685, BC050609, DC366453
    Consensus CDS
    CCDS341.1
    UniProtKB/Swiss-Prot
    Q9NP64
    UniProtKB/TrEMBL
    B4DYA9
    Related
    ENSP00000362819.1, ENST00000373714.5
    Conserved Domains (1) summary
    cd05686
    Location:1386
    S1_pNO40; S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. ...
  4. NM_001282569.1NP_001269498.1  nucleolar protein of 40 kDa isoform d

    See identical proteins and their annotated locations for NP_001269498.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and 5' coding region, and uses an alternate start codon, compared to variant 1. The encoded isoform (d) has a distinct and shorter N-terminus, compared to isoform a.
    Source sequence(s)
    AK302248, AK307478, BC050609, DC366453
    Consensus CDS
    CCDS60061.1
    UniProtKB/Swiss-Prot
    Q9NP64
    Related
    ENSP00000444742.1, ENST00000546109.5
    Conserved Domains (1) summary
    cl09927
    Location:1578
    S1_like; S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. ...
  5. NM_001282570.1NP_001269499.1  nucleolar protein of 40 kDa isoform e

    See identical proteins and their annotated locations for NP_001269499.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) lacks a portion of the 5' UTR and 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (e) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AK307478, BC050609, DC366453
    UniProtKB/Swiss-Prot
    Q9NP64
    Conserved Domains (1) summary
    cl09927
    Location:162
    S1_like; S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. ...
  6. NM_001282571.1NP_001269500.1  nucleolar protein of 40 kDa isoform f

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) differs in the 5' UTR and 5' coding region, and uses an alternate start codon, compared to variant 1. The encoded isoform (f) has a distinct and shorter N-terminus, compared to isoform a.
    Source sequence(s)
    AK001929, AK302343, AK307478, BC050609, BP309837, BP371153, DC366453
    Consensus CDS
    CCDS72744.1
    UniProtKB/Swiss-Prot
    Q9NP64
    UniProtKB/TrEMBL
    A0A087WYV3, B4DYA9
    Related
    ENSP00000482122.1, ENST00000616393.4
  7. NM_001282572.1NP_001269501.1  nucleolar protein of 40 kDa isoform g

    See identical proteins and their annotated locations for NP_001269501.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (8) differs in the 5' UTR and 5' coding region, uses an alternate start codon, and lacks two exons that result in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (g) has distinct N- and C-termini and is shorter than isoform a.
    Source sequence(s)
    AK001929, AK302343, AK307478, BC050609, BF309574, DC366453
    UniProtKB/Swiss-Prot
    Q9NP64
    UniProtKB/TrEMBL
    B4DYA9
    Conserved Domains (1) summary
    cd05686
    Location:1386
    S1_pNO40; S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. ...
  8. NM_001282573.1NP_001269502.1  nucleolar protein of 40 kDa isoform h

    See identical proteins and their annotated locations for NP_001269502.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (9) differs in the 5' UTR and 5' coding region, uses an alternate start codon, and lacks two exons that result in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (h) has distinct N- and C-termini and is shorter than isoform a.
    Source sequence(s)
    AK001929, AK302343, AK307478, BC050609, DA737244, DC366453
    Consensus CDS
    CCDS72743.1
    UniProtKB/Swiss-Prot
    Q9NP64
    UniProtKB/TrEMBL
    A0A087WYF0, B4DYA9
    Related
    ENSP00000481743.1, ENST00000616859.4
    Conserved Domains (1) summary
    cl09927
    Location:1578
    S1_like; S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. ...
  9. NM_001282574.1NP_001269503.1  nucleolar protein of 40 kDa isoform i

    See identical proteins and their annotated locations for NP_001269503.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (10) differs in the 5' UTR and 5' coding region, uses an alternate start codon, and lacks an exon that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (i) has distinct N- and C-termini and is shorter than isoform a.
    Source sequence(s)
    AK001929, AK302343, AK307478, BC050609, CN423139, DC366453
    Consensus CDS
    CCDS72742.1
    UniProtKB/Swiss-Prot
    Q9NP64
    UniProtKB/TrEMBL
    A0A087WXU5, B4DYA9
    Related
    ENSP00000481299.1, ENST00000618216.4
    Conserved Domains (1) summary
    cd05686
    Location:1386
    S1_pNO40; S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. ...
  10. NM_016505.3NP_057589.2  nucleolar protein of 40 kDa isoform c

    See identical proteins and their annotated locations for NP_057589.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and 5' coding region, and uses an alternate start codon, compared to variant 1. The encoded isoform (c) has a distinct and shorter N-terminus, compared to isoform a. Both variants 3 and 4 encode isoform c.
    Source sequence(s)
    AK001929, AK302343, AK307478, BC050609, DC366453
    Consensus CDS
    CCDS341.1
    UniProtKB/Swiss-Prot
    Q9NP64
    UniProtKB/TrEMBL
    B4DYA9
    Related
    ENSP00000343557.5, ENST00000344147.9
    Conserved Domains (1) summary
    cd05686
    Location:1386
    S1_pNO40; S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. ...

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    31296982..31365722
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006710681.4XP_006710744.1  nucleolar protein of 40 kDa isoform X1

    See identical proteins and their annotated locations for XP_006710744.1

    UniProtKB/Swiss-Prot
    Q9NP64
    Conserved Domains (1) summary
    cl09927
    Location:1578
    S1_like; S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. ...
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