ZNF556 zinc finger protein 556 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ZNF556provided by HGNC
Official Full Name: zinc finger protein 556provided by HGNC
Primary source: HGNC:HGNC:25669
See related: Ensembl:ENSG00000172000 AllianceGenome:HGNC:25669
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
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in ovary (RPKM 2.7), testis (RPKM 0.5) and 4 other tissues See more
Orthologs: all
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Genomic context

Location:: 19p13.3

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (2867335..2883445)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (2842602..2858723)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (2867333..2883443)

Chromosome 19 - NC_000019.10 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 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?

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)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of zinc finger protein 556 (ZNF556) by siRNA enhances the early stages of HIV-1 replication in HeLa-CD4 cells infected with viral pseudotypes HIV89.6R and HIV8.2N	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

D8S2279 (e-PCR)
- UniSTS:473907

D11S3114 (e-PCR)
- UniSTS:152207

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
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 556

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_001300843.2 → NP_001287772.1 zinc finger protein 556 isoform 2

See identical proteins and their annotated locations for NP_001287772.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. It encodes isoform 2, which is shorter by an amino-acid, compared to isoform 1.

Source sequence(s)

AK225297, BC009374

Consensus CDS

CCDS74254.1

UniProtKB/TrEMBL

A0A0C4DGQ3

Related

ENSP00000467366.1, ENST00000586426.5

Conserved Domains (3) summary

COG5048
Location:145 → 293

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:148 → 168

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam01352
Location:14 → 44

KRAB; KRAB box
NM_024967.3 → NP_079243.1 zinc finger protein 556 isoform 1

See identical proteins and their annotated locations for NP_079243.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC006130, AK021699, BC009374

Consensus CDS

CCDS12097.1

UniProtKB/Swiss-Prot

Q96GM3, Q9HAH1

Related

ENSP00000302603.2, ENST00000307635.3

Conserved Domains (5) summary

COG5048
Location:146 → 294

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:149 → 169

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:175 → 197

zf-C2H2; Zinc finger, C2H2 type

pfam01352
Location:14 → 43

KRAB; KRAB box

pfam13465
Location:217 → 242

zf-H2C2_2; Zinc-finger double domain