ZNF638 zinc finger protein 638 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ZNF638provided by HGNC
Official Full Name: zinc finger protein 638provided by HGNC
Primary source: HGNC:HGNC:17894
See related: Ensembl:ENSG00000075292 MIM:614349; AllianceGenome:HGNC:17894
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: ZFML; NP220; Zfp638
Summary: The protein encoded by this gene is a nucleoplasmic protein. It binds cytidine-rich sequences in double-stranded DNA. This protein has three types of domains: MH1, MH2 (repeated three times) and MH3. It is associated with packaging, transferring, or processing transcripts. Multiple alternatively spliced transcript variants have been found for this gene, but the biological validity of some variants has not been determined. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in testis (RPKM 14.1), thyroid (RPKM 11.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2p13.2

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (71331782..71435061)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (71342787..71445995)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (71558912..71662191)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Epigenetic Silencing of Recombinant Adeno-associated Virus Genomes by NP220 and the HUSH Complex.
Title: Epigenetic Silencing of Recombinant Adeno-associated Virus Genomes by NP220 and the HUSH Complex.
USP7 mediates pathological hepatic de novo lipogenesis through promoting stabilization and transcription of ZNF638.
Title: USP7 mediates pathological hepatic de novo lipogenesis through promoting stabilization and transcription of ZNF638.
NP220 is the key protein that recruits the HUSH complex, SETDB1 and the histone deacetylases HDAC1 and HDAC4 to silence the unintegrated retroviral DNA; knockout of NP220 accelerates the replication of retroviruses; these experiments identify the molecular machinery that silences extrachromosomal retroviral DNA
Title: NP220 mediates silencing of unintegrated retroviral DNA.
ZNF638 is a novel and early regulator of adipogenesis that works as a transcription cofactor of C/EBPs.
Title: Regulation of adipocyte differentiation by the zinc finger protein ZNF638.
Observational study of gene-disease association. (HuGE Navigator)
Title: New genetic associations detected in a host response study to hepatitis B vaccine.
Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
Title: Human variation in alcohol response is influenced by variation in neuronal signaling genes.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study in Han Chinese identifies three novel loci for human height. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

RH80604 (e-PCR)
- UniSTS:92990

D1S1425 (e-PCR)
- UniSTS:149621

RH45151 (e-PCR)
- UniSTS:22169

RH68305 (e-PCR)
- UniSTS:37333

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables double-stranded DNA binding	TAS Traceable Author Statement more info	PubMed
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in RNA splicing	IEA Inferred from Electronic Annotation more info
involved_in regulation of RNA splicing	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in cytoplasm	TAS Traceable Author Statement more info	PubMed
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in nuclear speck	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: zinc finger protein 638

Names: CTCL tumor antigen se33-1; CTCL-associated antigen se33-1; NP220 nuclear protein; cutaneous T-cell lymphoma-associated antigen se33-1; nuclear protein 220; zinc finger matrin-like 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)

NM_001014972.3 → NP_001014972.1 zinc finger protein 638 isoform 1

See identical proteins and their annotated locations for NP_001014972.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same isoform (1).

Source sequence(s)

AI357871, BC143728, BP348645, DB130984

Consensus CDS

CCDS1917.1

UniProtKB/Swiss-Prot

A0A096LPH6, B5MDV1, B7ZLD1, Q14966, Q53R34, Q5XJ05, Q68DP3, Q6P2H2, Q7Z3T7, Q8NF92, Q8TCA1, Q9H2G1, Q9NP37

Conserved Domains (4) summary

PTZ00121
Location:1293 → 1907

PTZ00121; MAEBL; Provisional

smart00451
Location:1927 → 1959

ZnF_U1; U1-like zinc finger

cd12716
Location:905 → 979

RRM1_2_NP220; RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220)

cl17169
Location:676 → 751

RRM_SF; RNA recognition motif (RRM) superfamily
NM_001252612.2 → NP_001239541.1 zinc finger protein 638 isoform 1

See identical proteins and their annotated locations for NP_001239541.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate splice site in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same isoform (1).

Source sequence(s)

AI357871, BC024000, BC143728, BP348645, CR749322, DB094964

Consensus CDS

CCDS1917.1

UniProtKB/Swiss-Prot

A0A096LPH6, B5MDV1, B7ZLD1, Q14966, Q53R34, Q5XJ05, Q68DP3, Q6P2H2, Q7Z3T7, Q8NF92, Q8TCA1, Q9H2G1, Q9NP37

Related

ENSP00000386433.1, ENST00000409544.5

Conserved Domains (4) summary

PTZ00121
Location:1293 → 1907

PTZ00121; MAEBL; Provisional

smart00451
Location:1927 → 1959

ZnF_U1; U1-like zinc finger

cd12716
Location:905 → 979

RRM1_2_NP220; RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220)

cl17169
Location:676 → 751

RRM_SF; RNA recognition motif (RRM) superfamily
NM_001252613.2 → NP_001239542.1 zinc finger protein 638 isoform 2

See identical proteins and their annotated locations for NP_001239542.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses an alternate splice site in the 3' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AI357871, AK291198, BC010355, BC083513, BP348645, DB130984

UniProtKB/TrEMBL

A8K583

Conserved Domains (2) summary

cd12436
Location:1009 → 1082

RRM1_2_MATR3_like; RNA recognition motif 1 and 2 in the matrin 3 family of nuclear proteins

cd12716
Location:676 → 751

RRM1_2_NP220; RNA recognition motif 1 and 2 in vertebrate nuclear protein 220 (NP220)
NM_014497.5 → NP_055312.2 zinc finger protein 638 isoform 1

See identical proteins and their annotated locations for NP_055312.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes isoform 1. Variants 1, 2 and 3 encode the same isoform.

Source sequence(s)

AI357871, BC143728, BP348645, D83032, DB130984

Consensus CDS

CCDS1917.1

UniProtKB/Swiss-Prot

A0A096LPH6, B5MDV1, B7ZLD1, Q14966, Q53R34, Q5XJ05, Q68DP3, Q6P2H2, Q7Z3T7, Q8NF92, Q8TCA1, Q9H2G1, Q9NP37

Related

ENSP00000264447.4, ENST00000264447.9

Conserved Domains (4) summary

PTZ00121
Location:1293 → 1907

PTZ00121; MAEBL; Provisional

smart00451
Location:1927 → 1959

ZnF_U1; U1-like zinc finger

cd12716
Location:905 → 979

RRM1_2_NP220; RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220)

cl17169
Location:676 → 751

RRM_SF; RNA recognition motif (RRM) superfamily