RCHY1 ring finger and CHY zinc finger domain containing 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: RCHY1provided by HGNC
Official Full Name: ring finger and CHY zinc finger domain containing 1provided by HGNC
Primary source: HGNC:HGNC:17479
See related: Ensembl:ENSG00000163743 MIM:607680; AllianceGenome:HGNC:17479
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: ZCHY; ARNIP; CHIMP; PIRH2; RNF199; ZNF363; PRO1996
Summary: The protein encoded by this gene has ubiquitin ligase activity. It mediates E3-dependent ubiquitination and proteasomal degradation of target proteins, including tumor protein 53, histone deacetylase 1, and cyclin-dependent kinase inhibitor 1B, thus regulating their levels and cell cycle progression. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jun 2013]
Expression: Ubiquitous expression in thyroid (RPKM 7.9), bone marrow (RPKM 6.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4q21.1

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (75479033..75514715, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (78819170..78854879, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (76404243..76439925, complement)

Chromosome 4 - NC_000004.12 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 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?

Mechanism and evolutionary origins of alanine-tail C-degron recognition by E3 ligases Pirh2 and CRL2-KLHDC10.
Title: Mechanism and evolutionary origins of alanine-tail C-degron recognition by E3 ligases Pirh2 and CRL2-KLHDC10.
PRPF8 controls alternative splicing of PIRH2 to modulate the p53 pathway and survival of human ESCs.
Title: PRPF8 controls alternative splicing of PIRH2 to modulate the p53 pathway and survival of human ESCs.
p53, Pirh2, and L1CAM as Promising Prognostic Biomarkers of Endometrial Carcinoma: An Immunohistochemical and Genetic Study.
Title: p53, Pirh2, and L1CAM as Promising Prognostic Biomarkers of Endometrial Carcinoma: An Immunohistochemical and Genetic Study.
Regulation of autophagy flux by E3 ubiquitin ligase Pirh2 in lung cancer.
Title: Regulation of autophagy flux by E3 ubiquitin ligase Pirh2 in lung cancer.
The RNA-binding protein HuR is a novel target of Pirh2 E3 ubiquitin ligase.
Title: The RNA-binding protein HuR is a novel target of Pirh2 E3 ubiquitin ligase.
Pirh2, an E3 ligase, regulates the AIP4-p73 regulatory pathway by modulating AIP4 expression and ubiquitination.
Title: Pirh2, an E3 ligase, regulates the AIP4-p73 regulatory pathway by modulating AIP4 expression and ubiquitination.
These data provide an evidence that RCHY1 negatively regulates HDAC2.
Title: E3 ligase RCHY1 negatively regulates HDAC2.
By forming a complex with Twist1 and the E3 ligase Pirh2, WT p53 promotes the ubiquitination and proteasomal degradation of Twist1, thus inhibiting EMT and maintaining the epithelial phenotype. The ability of p53 to induce Twist1 degradation is abrogated when p53 is mutated.
Title: p53-Pirh2 Complex Promotes Twist1 Degradation and Inhibits EMT.
higher expression level of Naa10 and lower expression level of Pirh2 in oral squamous cell carcinoma tissues than adjacent normal tissues; expression of Naa10p is negatively correlated with that of Pirh2
Title: Inverse correlation between Naa10p and Pirh2 expression and the combined prognostic value in oral squamous cell carcinoma patients.
High Pirh2 expression was positively correlated with high tumor grade in brain glioma specimens.
Title: High Expression of Pirh2 is Associated with Poor Prognosis in Glioma.

Submit: New GeneRIF Correction See all GeneRIFs (47)

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

EBI GWAS Catalog

Description
Genome-wide association analysis implicates the involvement of eight loci with response to tocilizumab for the treatment of rheumatoid arthritis. 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

SHGC-64844 (e-PCR)
- UniSTS:42002

RH91327 (e-PCR)
- UniSTS:86438

D15S1390 (e-PCR)
- UniSTS:474340

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables p53 binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info
NOT enables ubiquitin protein ligase activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin protein ligase activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin-protein transferase activity	TAS Traceable Author Statement more info
enables zinc ion binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in error-free translesion synthesis	TAS Traceable Author Statement more info
involved_in positive regulation of proteasomal ubiquitin-dependent protein catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of protein ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein autoubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein ubiquitination	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in rescue of stalled ribosome	IDA Inferred from Direct Assay more info	PubMed
involved_in ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in ubiquitin-dependent protein catabolic process	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
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
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of ubiquitin ligase complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: RING finger and CHY zinc finger domain-containing protein 1

Names: CH-rich interacting match with PLAG1; E3 ubiquitin-protein ligase Pirh2; RING finger protein 199; RING-type E3 ubiquitin transferase RCHY1; androgen-receptor N-terminal-interacting protein; p53-induced protein with a RING-H2 domain; ring finger and CHY zinc finger domain containing 1, E3 ubiquitin protein ligase; zinc finger protein 363; zinc finger, CHY-type

NP_001009922.1

EC 2.3.2.27

NP_001265465.1

EC 2.3.2.27

NP_001265466.1

EC 2.3.2.27

NP_001265467.1

EC 2.3.2.27

NP_001265468.1

EC 2.3.2.27

NP_001374065.1

EC 2.3.2.27

NP_001374066.1

EC 2.3.2.27

NP_056251.2

EC 2.3.2.27

XP_024309752.1

EC 2.3.2.27

XP_047305992.1

EC 2.3.2.27

XP_054205595.1

EC 2.3.2.27

XP_054205596.1

EC 2.3.2.27

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.

Genomic

NG_029152.1 RefSeqGene

Range

5028..40398

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001009922.3 → NP_001009922.1 RING finger and CHY zinc finger domain-containing protein 1 isoform 3

See identical proteins and their annotated locations for NP_001009922.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an in-frame exon in the internal coding region, compared to variant 1. The encoded isoform (3, also known as Pirh2B) is shorter, compared to isoform 1.

Source sequence(s)

AC096759, AF255666, AK091501, AK308754, AW236209, DB044826, DN919417, GQ250945

Consensus CDS

CCDS34012.1

UniProtKB/TrEMBL

G3FDP4

Related

ENSP00000421084.1, ENST00000513257.5

Conserved Domains (3) summary

pfam05495
Location:20 → 91

zf-CHY; CHY zinc finger

pfam14599
Location:182 → 240

zinc_ribbon_6; Zinc-ribbon

cl17238
Location:144 → 178

RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
NM_001278536.2 → NP_001265465.1 RING finger and CHY zinc finger domain-containing protein 1 isoform 4

See identical proteins and their annotated locations for NP_001265465.1

Status: REVIEWED

Description

Transcript Variant: This variant (6) lacks an in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (4) is shorter, compared to isoform 1.

Source sequence(s)

AC096759, AK308754, DA197338

Consensus CDS

CCDS63991.1

UniProtKB/TrEMBL

G3FDP4

Related

ENSP00000370220.2, ENST00000380840.6

Conserved Domains (2) summary

pfam14599
Location:151 → 209

zinc_ribbon_6; Zinc-ribbon

cd16464
Location:104 → 147

RING-H2_Pirh2; RING finger, H2 subclass, found in p53-induced RING-H2 protein (Pirh2) and similar proteins
NM_001278537.2 → NP_001265466.1 RING finger and CHY zinc finger domain-containing protein 1 isoform 5

See identical proteins and their annotated locations for NP_001265466.1

Status: REVIEWED

Description

Transcript Variant: This variant (7) lacks two in-frame coding exons, compared to variant 1. The encoded isoform (5) is shorter, compared to isoform 1.

Source sequence(s)

AC096759, BP314571, DA197338

Consensus CDS

CCDS63990.1

UniProtKB/Swiss-Prot

Q96PM5

Related

ENSP00000424472.1, ENST00000507014.1

Conserved Domains (2) summary

pfam14599
Location:142 → 200

zinc_ribbon_6; Zinc-ribbon

cl17238
Location:104 → 138

RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
NM_001278538.2 → NP_001265467.1 RING finger and CHY zinc finger domain-containing protein 1 isoform 6

See identical proteins and their annotated locations for NP_001265467.1

Status: REVIEWED

Description

Transcript Variant: This variant (8) uses an alternate splice site in the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (6) has a shorter and distinct N-terminus, compared to isoform 1.

Source sequence(s)

AC096759, BQ959587, DA197338

Consensus CDS

CCDS63992.1

UniProtKB/TrEMBL

G3FDP4

Related

ENSP00000423976.1, ENST00000512706.5

Conserved Domains (3) summary

cd16464
Location:122 → 165

RING-H2_Pirh2; RING finger, H2 subclass, found in p53-induced RING-H2 protein (Pirh2) and similar proteins

pfam05495
Location:4 → 71

zf-CHY; CHY zinc finger

pfam14599
Location:169 → 227

zinc_ribbon_6; Zinc-ribbon
NM_001278539.2 → NP_001265468.1 RING finger and CHY zinc finger domain-containing protein 1 isoform 7

See identical proteins and their annotated locations for NP_001265468.1

Status: REVIEWED

Description

Transcript Variant: This variant (9) uses an alternate splice site in the 5' terminal exon, and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (7) has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AC096759, BG703058, DA197338

UniProtKB/TrEMBL

Q96BL1

Conserved Domains (2) summary

cd16464
Location:17 → 60

RING-H2_Pirh2; RING finger, H2 subclass, found in p53-induced RING-H2 protein (Pirh2) and similar proteins

pfam14599
Location:64 → 122

zinc_ribbon_6; Zinc-ribbon
NM_001387136.1 → NP_001374065.1 RING finger and CHY zinc finger domain-containing protein 1 isoform 7

Status: REVIEWED

Source sequence(s)

AC096759

UniProtKB/TrEMBL

Q96BL1

Conserved Domains (2) summary

cd16464
Location:17 → 60

RING-H2_Pirh2; RING finger, H2 subclass, found in p53-induced RING-H2 protein (Pirh2) and similar proteins

pfam14599
Location:64 → 122

zinc_ribbon_6; Zinc-ribbon
NM_001387137.1 → NP_001374066.1 RING finger and CHY zinc finger domain-containing protein 1 isoform 7

Status: REVIEWED

Source sequence(s)

AC096759

UniProtKB/TrEMBL

Q96BL1

Conserved Domains (2) summary

cd16464
Location:17 → 60

RING-H2_Pirh2; RING finger, H2 subclass, found in p53-induced RING-H2 protein (Pirh2) and similar proteins

pfam14599
Location:64 → 122

zinc_ribbon_6; Zinc-ribbon
NM_015436.4 → NP_056251.2 RING finger and CHY zinc finger domain-containing protein 1 isoform 1

See identical proteins and their annotated locations for NP_056251.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1, also known as Pirh2A).

Source sequence(s)

AC096759, AF255666, AK091501, AK308754, AW236209, DB044826, DN919417, GQ250944

Consensus CDS

CCDS3567.1

UniProtKB/Swiss-Prot

B3KRG3, C7E541, C7E542, C7E543, D3YRV2, E7EMC8, E7ETW5, J3KPI0, Q2KN33, Q59GN7, Q86X26, Q96PM5, Q96PR5

UniProtKB/TrEMBL

G3FDP4

Related

ENSP00000321239.5, ENST00000324439.10

Conserved Domains (3) summary

cd16464
Location:144 → 187

RING-H2_Pirh2; RING finger, H2 subclass, found in p53-induced RING-H2 protein (Pirh2) and similar proteins

pfam05495
Location:20 → 93

zf-CHY; CHY zinc finger

pfam14599
Location:191 → 249

zinc_ribbon_6; Zinc-ribbon

RNA

NR_037913.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses an alternate donor splice site at an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon as used in variant 1, renders this transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC096759, AF255666, AK091501, AK308754, AK309555, AW236209, BQ024871, DB044826, DN919417, GQ250946
NR_037914.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) uses alternate donor splice sites at two internal exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon as used in variant 1, renders this transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC096759, AF255666, AK091501, AK308754, AK309555, AW236209, BQ024871, DB044826, DN919417
NR_103723.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC096759, AF247041, DA197338
NR_103724.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (10) 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 5'-most supported translational start codon, as used in variant 1, renders this transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC096759, AY888047, DA197338
NR_103725.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (11) uses an alternate 5'-terminal exon, and lacks an internal exon, compared to variant 1. This variant is represented as non-coding because it does not encode a supported protein.

Source sequence(s)

AC096759, BF102905, GQ250945

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

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

75479033..75514715 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_024453984.2 → XP_024309752.1 RING finger and CHY zinc finger domain-containing protein 1 isoform X2

UniProtKB/TrEMBL

Q96BL1

Conserved Domains (2) summary

pfam14599
Location:55 → 113

zinc_ribbon_6; Zinc-ribbon

cl17238
Location:17 → 51

RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
XM_047450036.1 → XP_047305992.1 RING finger and CHY zinc finger domain-containing protein 1 isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060928.1 Alternate T2T-CHM13v2.0

Range

78819170..78854879 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054349621.1 → XP_054205596.1 RING finger and CHY zinc finger domain-containing protein 1 isoform X2
XM_054349620.1 → XP_054205595.1 RING finger and CHY zinc finger domain-containing protein 1 isoform X1

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001008925.2: Suppressed sequence

Description

NM_001008925.2: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.