SHPRH SNF2 histone linker PHD RING helicase [Homo sapiens (human)] - Gene

Summary

Official Symbol: SHPRHprovided by HGNC
Official Full Name: SNF2 histone linker PHD RING helicaseprovided by HGNC
Primary source: HGNC:HGNC:19336
See related: Ensembl:ENSG00000146414 MIM:608048; AllianceGenome:HGNC:19336
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: RAD5; bA545I5.2
Summary: SHPRH is a ubiquitously expressed protein that contains motifs characteristics of several DNA repair proteins, transcription factors, and helicases. SHPRH is a functional homolog of S. cerevisiae RAD5 (Unk et al., 2006 [PubMed 17108083]).[supplied by OMIM, Mar 2008]
Expression: Ubiquitous expression in ovary (RPKM 1.7), thyroid (RPKM 1.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6q24.3

Exon count:: 35

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (145857838..145964358, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (147050896..147157428, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (146205943..146285494, complement)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

Integrative genomics identifies SHPRH as a tumor suppressor gene in lung adenocarcinoma that regulates DNA damage response.
Title: Integrative genomics identifies SHPRH as a tumor suppressor gene in lung adenocarcinoma that regulates DNA damage response.
A peptide encoded by the circular form of the SHPRH gene induces apoptosis in neuroblastoma cells.
Title: A peptide encoded by the circular form of the SHPRH gene induces apoptosis in neuroblastoma cells.
KMT2B promotes SHPRH expression to regulate (131)I sensitivity in thyroid carcinoma cells by affecting FYN protein stability.
Title: KMT2B promotes SHPRH expression to regulate (131)I sensitivity in thyroid carcinoma cells by affecting FYN protein stability.
The Human RAD5 Homologs, HLTF and SHPRH, Have Separate Functions in DNA Damage Tolerance Dependent on The DNA Lesion Type.
Title: The Human RAD5 Homologs, HLTF and SHPRH, Have Separate Functions in DNA Damage Tolerance Dependent on The DNA Lesion Type.
Helicase-Like Transcription Factor HLTF and E3 Ubiquitin Ligase SHPRH Confer DNA Damage Tolerance through Direct Interactions with Proliferating Cell Nuclear Antigen (PCNA).
Title: Helicase-Like Transcription Factor HLTF and E3 Ubiquitin Ligase SHPRH Confer DNA Damage Tolerance through Direct Interactions with Proliferating Cell Nuclear Antigen (PCNA).
circ-0001649 regulated behaviors of hepatocellular carcinoma cells by targeting SHPRH; circ-0001649 served as a ceRNA to sponge miR-127-5p, miR-612 and miR-4688, thus activating SHPRH
Title: Circular RNA hsa_circ_0001649 inhibits hepatocellular carcinoma progression via multiple miRNAs sponge.
A novel perspective regarding circRNA function in physiological and pathological processes: specifically, SHPRH-146aa generated from overlapping genetic codes of circ-SHPRH is a tumor suppressor in human glioblastoma.
Title: A novel protein encoded by the circular form of the SHPRH gene suppresses glioma tumorigenesis.
This study suggests that SHPRH could be a link between mTOR-mediated epigenetic regulations and rRNA transcription, while concomitantly affecting genomic integrity.
Title: SHPRH as a new player in ribosomal RNA transcription and its potential role in homeostasis of ribosomal DNA repeats.
evidence that SHPRH functions in rRNA transcription through its interaction with histone H3 in a mammalian target of rapamycin (mTOR)-dependent manner
Title: SHPRH regulates rRNA transcription by recognizing the histone code in an mTOR-dependent manner.
HLTF and SHPRH suppress mutagenesis in a damage-specific manner, preventing mutations induced by UV rays and methyl methanesulfonate.
Title: SHPRH and HLTF act in a damage-specific manner to coordinate different forms of postreplication repair and prevent mutagenesis.

Submit: New GeneRIF Correction See all GeneRIFs (15)

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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-17307 (e-PCR)
- UniSTS:45932

RH93573 (e-PCR)
- UniSTS:88438

SHGC-155911 (e-PCR)
- UniSTS:185232

STS-N20832 (e-PCR)
- UniSTS:37287

SHGC-64749 (e-PCR)
- UniSTS:95405

NoName (e-PCR)
- UniSTS:487373

Clone Names

FLJ27258, FLJ37625, FLJ45012, FLJ90837, KIAA2023, MGC134886

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables helicase activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin protein ligase activity	EXP Inferred from Experiment more info	PubMed
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin protein ligase binding	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin-protein transferase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA damage response	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within DNA damage response	IDA Inferred from Direct Assay more info	PubMed
involved_in DNA repair	IEA Inferred from Electronic Annotation more info
involved_in nucleosome assembly	IEA Inferred from Electronic Annotation more info
involved_in protein polyubiquitination	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein polyubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein ubiquitination	TAS Traceable Author Statement more info

Component	Evidence Code	Pubs
located_in nucleoplasm	TAS Traceable Author Statement more info
part_of nucleosome	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase SHPRH

Names: 2610103K11Rik; RING-type E3 ubiquitin transferase SHPRH; SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase; SNF2, histone-linker, PHD and RING finger domain-containing helicase

NP_001036148.2

EC 2.3.2.27

NP_001357256.1

EC 2.3.2.27

NP_001357257.1

EC 2.3.2.27

NP_775105.1

EC 2.3.2.27

XP_006715502.1

EC 2.3.2.27

XP_006715506.1

EC 2.3.2.27

XP_011534021.1

EC 2.3.2.27

XP_011534024.1

EC 2.3.2.27

XP_016866180.1

EC 2.3.2.27

XP_016866181.1

EC 2.3.2.27

XP_016866182.1

EC 2.3.2.27

XP_047274556.1

EC 2.3.2.27

XP_047274557.1

EC 2.3.2.27

XP_047274558.1

EC 2.3.2.27

XP_047274559.1

EC 2.3.2.27

XP_047274560.1

EC 2.3.2.27

XP_054211055.1

EC 2.3.2.27

XP_054211056.1

EC 2.3.2.27

XP_054211057.1

EC 2.3.2.27

XP_054211058.1

EC 2.3.2.27

XP_054211059.1

EC 2.3.2.27

XP_054211060.1

EC 2.3.2.27

XP_054211061.1

EC 2.3.2.27

XP_054211062.1

EC 2.3.2.27

XP_054211063.1

EC 2.3.2.27

XP_054211064.1

EC 2.3.2.27

XP_054211065.1

EC 2.3.2.27

XP_054211066.1

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.

mRNA and Protein(s)

NM_001042683.3 → NP_001036148.2 E3 ubiquitin-protein ligase SHPRH isoform a

See identical proteins and their annotated locations for NP_001036148.2

Status: VALIDATED

Description

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

Source sequence(s)

AA315737, AK126959, AL451145, AY161136, AY163808, BC117686, BX648322

Consensus CDS

CCDS43513.2

UniProtKB/Swiss-Prot

Q149N8, Q149N9, Q5VV79, Q68DS5, Q7Z5J5, Q8IVE8, Q8IWQ9, Q8N1S8, Q8NBR7

UniProtKB/TrEMBL

A0A0D9SFM0

Related

ENSP00000275233.7, ENST00000275233.12

Conserved Domains (7) summary

COG0553
Location:24 → 389

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd15547
Location:660 → 706

PHD_SHPRH; PHD finger found in E3 ubiquitin-protein ligase SHPRH

cd16569
Location:1429 → 1479

RING-HC_SHPRH; RING finger, HC subclass, found in SNF2 histone-linker PHD finger RING finger helicase (SHPRH) and similar proteins

pfam00538
Location:440 → 511

Linker_histone; linker histone H1 and H5 family

cd18793
Location:1508 → 1633

SF2_C_SNF; C-terminal helicase domain of the SNF family helicases

cd18070
Location:702 → 903

DEXQc_SHPRH; DEXQ-box helicase domain of SHPRH

cl28899
Location:304 → 409

DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
NM_001370327.1 → NP_001357256.1 E3 ubiquitin-protein ligase SHPRH isoform a

Status: VALIDATED

Source sequence(s)

AL356599, AL451145

Consensus CDS

CCDS43513.2

UniProtKB/Swiss-Prot

Q149N8, Q149N9, Q5VV79, Q68DS5, Q7Z5J5, Q8IVE8, Q8IWQ9, Q8N1S8, Q8NBR7

UniProtKB/TrEMBL

A0A0D9SFM0

Related

ENSP00000356475.2, ENST00000367505.6

Conserved Domains (7) summary

COG0553
Location:24 → 389

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd15547
Location:660 → 706

PHD_SHPRH; PHD finger found in E3 ubiquitin-protein ligase SHPRH

cd16569
Location:1429 → 1479

RING-HC_SHPRH; RING finger, HC subclass, found in SNF2 histone-linker PHD finger RING finger helicase (SHPRH) and similar proteins

pfam00538
Location:440 → 511

Linker_histone; linker histone H1 and H5 family

cd18793
Location:1508 → 1633

SF2_C_SNF; C-terminal helicase domain of the SNF family helicases

cd18070
Location:702 → 903

DEXQc_SHPRH; DEXQ-box helicase domain of SHPRH

cl28899
Location:304 → 409

DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
NM_001370328.1 → NP_001357257.1 E3 ubiquitin-protein ligase SHPRH isoform c

Status: VALIDATED

Source sequence(s)

AL356599, AL451145

Conserved Domains (4) summary

cd15547
Location:179 → 225

PHD_SHPRH; PHD finger found in E3 ubiquitin-protein ligase SHPRH

cd16569
Location:948 → 998

RING-HC_SHPRH; RING finger, HC subclass, found in SNF2 histone-linker PHD finger RING finger helicase (SHPRH) and similar proteins

cd18793
Location:1027 → 1152

SF2_C_SNF; C-terminal helicase domain of the SNF family helicases

cd18070
Location:221 → 422

DEXQc_SHPRH; DEXQ-box helicase domain of SHPRH
NM_173082.4 → NP_775105.1 E3 ubiquitin-protein ligase SHPRH isoform b

See identical proteins and their annotated locations for NP_775105.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses three alternate splice sites in the coding region, one of which results in a frameshift, compared to variant 1. It encodes isoform b, which is shorter and has a distinct C-terminus, compared to isoform a.

Source sequence(s)

AA315737, AL451145, AY161136, AY163808, BX648322

Consensus CDS

CCDS47496.1

UniProtKB/TrEMBL

A0A0D9SFM0

Related

ENSP00000412797.2, ENST00000438092.6

Conserved Domains (7) summary

COG0553
Location:1515 → 1652

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd00162
Location:1436 → 1486

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

cd15547
Location:660 → 706

PHD_SHPRH; PHD finger found in E3 ubiquitin-protein ligase SHPRH

pfam00176
Location:716 → 987

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:1517 → 1626

Helicase_C; Helicase conserved C-terminal domain

pfam00538
Location:440 → 511

Linker_histone; linker histone H1 and H5 family

pfam13424
Location:1029 → 1113

TPR_12; Tetratricopeptide repeat

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_000006.12 Reference GRCh38.p14 Primary Assembly

Range

145857838..145964358 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047418600.1 → XP_047274556.1 E3 ubiquitin-protein ligase SHPRH isoform X1
XM_006715439.5 → XP_006715502.1 E3 ubiquitin-protein ligase SHPRH isoform X3

See identical proteins and their annotated locations for XP_006715502.1

UniProtKB/TrEMBL

A0A0D9SFM0

Conserved Domains (7) summary

COG0553
Location:1511 → 1648

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd00162
Location:1432 → 1482

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

cd15547
Location:660 → 706

PHD_SHPRH; PHD finger found in E3 ubiquitin-protein ligase SHPRH

pfam00176
Location:716 → 987

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:1513 → 1622

Helicase_C; Helicase conserved C-terminal domain

pfam00538
Location:440 → 511

Linker_histone; linker histone H1 and H5 family

pfam13424
Location:1020 → 1104

TPR_12; Tetratricopeptide repeat
XM_047418601.1 → XP_047274557.1 E3 ubiquitin-protein ligase SHPRH isoform X1
XM_006715443.5 → XP_006715506.1 E3 ubiquitin-protein ligase SHPRH isoform X7

UniProtKB/TrEMBL

A0A0D9SFM0

Conserved Domains (5) summary

cd00162
Location:1432 → 1482

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

cd15547
Location:660 → 706

PHD_SHPRH; PHD finger found in E3 ubiquitin-protein ligase SHPRH

pfam00176
Location:716 → 987

SNF2_N; SNF2 family N-terminal domain

pfam00538
Location:440 → 511

Linker_histone; linker histone H1 and H5 family

pfam13424
Location:1020 → 1104

TPR_12; Tetratricopeptide repeat
XM_047418603.1 → XP_047274559.1 E3 ubiquitin-protein ligase SHPRH isoform X7
XM_017010693.3 → XP_016866182.1 E3 ubiquitin-protein ligase SHPRH isoform X4

UniProtKB/TrEMBL

A0A0D9SFM0
XM_017010691.3 → XP_016866180.1 E3 ubiquitin-protein ligase SHPRH isoform X2

UniProtKB/TrEMBL

A0A0D9SFM0
XM_017010692.2 → XP_016866181.1 E3 ubiquitin-protein ligase SHPRH isoform X2

UniProtKB/TrEMBL

A0A0D9SFM0
XM_011535719.4 → XP_011534021.1 E3 ubiquitin-protein ligase SHPRH isoform X5

UniProtKB/TrEMBL

A0A0D9SFM0

Conserved Domains (7) summary

COG0553
Location:1511 → 1658

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd00162
Location:1432 → 1482

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

cd15547
Location:660 → 706

PHD_SHPRH; PHD finger found in E3 ubiquitin-protein ligase SHPRH

pfam00176
Location:716 → 987

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:1513 → 1622

Helicase_C; Helicase conserved C-terminal domain

pfam00538
Location:440 → 511

Linker_histone; linker histone H1 and H5 family

pfam13424
Location:1020 → 1104

TPR_12; Tetratricopeptide repeat
XM_047418602.1 → XP_047274558.1 E3 ubiquitin-protein ligase SHPRH isoform X6
XM_047418604.1 → XP_047274560.1 E3 ubiquitin-protein ligase SHPRH isoform X8

Related

ENSP00000430528.1, ENST00000519632.5
XM_011535722.4 → XP_011534024.1 E3 ubiquitin-protein ligase SHPRH isoform X9

Conserved Domains (3) summary

COG0553
Location:24 → 389

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd15547
Location:660 → 706

PHD_SHPRH; PHD finger found in E3 ubiquitin-protein ligase SHPRH

pfam00538
Location:440 → 511

Linker_histone; linker histone H1 and H5 family