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] See more...

Aliases for SHPRH Gene

Aliases for SHPRH Gene

  • SNF2 Histone Linker PHD RING Helicase 2 3 5
  • SNF2, Histone-Linker, PHD And RING Finger Domain-Containing Helicase 3 4
  • SNF2 Histone Linker PHD RING Helicase, E3 Ubiquitin Protein Ligase 2 3
  • RING-Type E3 Ubiquitin Transferase SHPRH 3 4
  • E3 Ubiquitin-Protein Ligase SHPRH 3 4
  • BA545I5.2 2 3
  • KIAA2023 2 4
  • 2610103K11Rik 3
  • EC 2.3.2.27 4
  • EC 3.6.4.- 4
  • FLJ90837 2
  • SHPRH 5

External Ids for SHPRH Gene

Previous GeneCards Identifiers for SHPRH Gene

  • GC00U902638
  • GC06M146120
  • GC06M146186
  • GC06M146236
  • GC06M143769
  • GC06M146185

Summaries for SHPRH Gene

Entrez Gene Summary for SHPRH Gene

  • 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]

GeneCards Summary for SHPRH Gene

SHPRH (SNF2 Histone Linker PHD RING Helicase) is a Protein Coding gene. Diseases associated with SHPRH include Xeroderma Pigmentosum, Variant Type. Gene Ontology (GO) annotations related to this gene include ligase activity and helicase activity. An important paralog of this gene is CHD7.

UniProtKB/Swiss-Prot Summary for SHPRH Gene

  • E3 ubiquitin-protein ligase involved in DNA repair. Upon genotoxic stress, accepts ubiquitin from the UBE2N-UBE2V2 E2 complex and transfers it to 'Lys-164' of PCNA which had been monoubiquitinated by UBE2A/B-RAD18, promoting the formation of non-canonical poly-ubiquitin chains linked through 'Lys-63'.

Gene Wiki entry for SHPRH Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SHPRH Gene

Genomics for SHPRH Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SHPRH Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J145963 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 +0.4 423 3.6 ZSCAN16 CHD2 TBP SP1 MXD4 FEZF1 SIX5 NR2C1 MNT IKZF1 SHPRH FBXO30-DT GRM1 NONHSAG045082.2 FBXO30
GH06J145733 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas 34.6 +228.8 228825 4 CHD2 TBP SP1 ZBTB10 MXD4 NR2C1 MNT IKZF1 SMAD5 IRF2 FBXO30-DT EPM2A ENSG00000270638 ENSG00000270828 SHPRH
GH06J145812 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 28.1 +150.7 150707 5.4 TBP ZBTB10 NR2C1 MNT IKZF1 SMAD5 ZFP64 MBD2 POLR2A BHLHE40 FBXO30 FBXO30-DT SHPRH lnc-GRM1-10 ENSG00000280184 EPM2A
GH06J146912 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 19.7 -950.6 -950568 5 TBP FEZF1 MNT IKZF1 SMAD5 HES1 MBD2 BHLHE40 CEBPB ARNT STXBP5-AS1 SHPRH ADGB STXBP5 RAB32 HSALNG0054153 lnc-ADGB-4 ENSG00000272397 RF00017-5827
GH06J146887 Enhancer 1.1 Ensembl dbSUPER 35.8 -923.2 -923177 1.6 TBP CEBPA SIX5 SMAD5 IRF2 HES1 CEBPB ZNF395 REST GTF2E2 SHPRH STXBP5-AS1 STXBP5 lnc-ADGB-4 lnc-SHPRH-6 ENSG00000227748 RF00017-5827 ADGB
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SHPRH on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SHPRH

Top Transcription factor binding sites by QIAGEN in the SHPRH gene promoter:
  • c-Myc
  • CUTL1
  • Evi-1
  • HOXA9
  • HOXA9B
  • Max
  • Meis-1
  • Meis-1b
  • MRF-2
  • S8

Genomic Locations for SHPRH Gene

Latest Assembly
chr6:145,857,838-145,964,423
(GRCh38/hg38)
Size:
106,586 bases
Orientation:
Minus strand

Previous Assembly
chr6:146,205,943-146,285,494
(GRCh37/hg19 by Entrez Gene)
Size:
79,552 bases
Orientation:
Minus strand

chr6:146,185,381-146,285,559
(GRCh37/hg19 by Ensembl)
Size:
100,179 bases
Orientation:
Minus strand

Genomic View for SHPRH Gene

Genes around SHPRH on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SHPRH Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SHPRH Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SHPRH Gene

Proteins for SHPRH Gene

  • Protein details for SHPRH Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q149N8-SHPRH_HUMAN
    Recommended name:
    E3 ubiquitin-protein ligase SHPRH
    Protein Accession:
    Q149N8
    Secondary Accessions:
    • Q149N9
    • Q5VV79
    • Q68DS5
    • Q7Z5J5
    • Q8IVE8
    • Q8IWQ9
    • Q8N1S8
    • Q8NBR7

    Protein attributes for SHPRH Gene

    Size:
    1683 amino acids
    Molecular mass:
    193079 Da
    Quaternary structure:
    • Homodimer. Interacts with HLTF, PCNA, UBE2N and RAD18.
    SequenceCaution:
    • Sequence=AAI13090.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing.; Evidence={ECO:0000305}; Sequence=AAI17686.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing.; Evidence={ECO:0000305}; Sequence=BAC04459.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAC23119.1; Type=Erroneous translation; Note=Wrong choice of frame.; Evidence={ECO:0000305}; Sequence=CAH18145.1; Type=Frameshift; Evidence={ECO:0000305};
    Miscellaneous:
    • [Isoform 2]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.
    • [Isoform 4]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

    Three dimensional structures from OCA and Proteopedia for SHPRH Gene

    Alternative splice isoforms for SHPRH Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SHPRH Gene

Post-translational modifications for SHPRH Gene

  • Ubiquitination at Lys1256, Lys1562, and Lys1572
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SHPRH Gene

Domains & Families for SHPRH Gene

Gene Families for SHPRH Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for SHPRH Gene

Suggested Antigen Peptide Sequences for SHPRH Gene

GenScript: Design optimal peptide antigens:
  • SNF2 histone linker PHD RING helicase (Q5JT88_HUMAN)
  • SNF2, histone-linker, PHD and RING finger domain-containing helicase (SHPRH_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q149N8

UniProtKB/Swiss-Prot:

SHPRH_HUMAN :
  • The RING finger mediates E3 ubiquitin ligase activity.
  • Belongs to the SNF2/RAD54 helicase family.
Domain:
  • The RING finger mediates E3 ubiquitin ligase activity.
Family:
  • Belongs to the SNF2/RAD54 helicase family.
genes like me logo Genes that share domains with SHPRH: view

Function for SHPRH Gene

Molecular function for SHPRH Gene

UniProtKB/Swiss-Prot Function:
E3 ubiquitin-protein ligase involved in DNA repair. Upon genotoxic stress, accepts ubiquitin from the UBE2N-UBE2V2 E2 complex and transfers it to 'Lys-164' of PCNA which had been monoubiquitinated by UBE2A/B-RAD18, promoting the formation of non-canonical poly-ubiquitin chains linked through 'Lys-63'.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.; EC=2.3.2.27;.

Enzyme Numbers (IUBMB) for SHPRH Gene

Phenotypes From GWAS Catalog for SHPRH Gene

Gene Ontology (GO) - Molecular Function for SHPRH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003677 DNA binding IEA --
GO:0004386 helicase activity IEA --
GO:0004842 ubiquitin-protein transferase activity IDA 17108083
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with SHPRH: view
genes like me logo Genes that share phenotypes with SHPRH: view

Animal Models for SHPRH Gene

MGI Knock Outs for SHPRH:

miRNA for SHPRH Gene

miRTarBase miRNAs that target SHPRH

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SHPRH

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SHPRH Gene

Localization for SHPRH Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SHPRH gene
Compartment Confidence
nucleus 5
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nuclear membrane (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SHPRH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000786 nucleosome IEA --
GO:0005654 nucleoplasm TAS --
GO:0042025 host cell nucleus IEA --
genes like me logo Genes that share ontologies with SHPRH: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for SHPRH Gene

Pathways & Interactions for SHPRH Gene

PathCards logo

SuperPathways for SHPRH Gene

No Data Available

UniProtKB/Swiss-Prot Q149N8-SHPRH_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

SIGNOR curated interactions for SHPRH Gene

Activates:

Gene Ontology (GO) - Biological Process for SHPRH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000209 protein polyubiquitination IDA 17108083
GO:0006281 DNA repair IEA --
GO:0006334 nucleosome assembly IEA --
GO:0006974 cellular response to DNA damage stimulus IDA 25023518
GO:0016567 protein ubiquitination TAS --
genes like me logo Genes that share ontologies with SHPRH: view

No data available for Pathways by source for SHPRH Gene

Drugs & Compounds for SHPRH Gene

No Compound Related Data Available

Transcripts for SHPRH Gene

mRNA/cDNA for SHPRH Gene

4 REFSEQ mRNAs :
14 NCBI additional mRNA sequence :
11 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SHPRH

Alternative Splicing Database (ASD) splice patterns (SP) for SHPRH Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17a · 17b ^ 18 ^ 19 ^ 20 ^
SP1: -
SP2: - -
SP3:
SP4: - -
SP5: - -

ExUns: 21a · 21b ^ 22 ^ 23 ^ 24a · 24b ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32a · 32b · 32c
SP1: - - -
SP2: -
SP3:
SP4:
SP5:

Relevant External Links for SHPRH Gene

GeneLoc Exon Structure for
SHPRH

Expression for SHPRH Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SHPRH Gene

Protein differential expression in normal tissues from HIPED for SHPRH Gene

This gene is overexpressed in Breast (15.6), Plasma (15.2), Fetal ovary (10.2), Fetal testis (7.5), and Adrenal (6.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SHPRH Gene



Protein tissue co-expression partners for SHPRH Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SHPRH

SOURCE GeneReport for Unigene cluster for SHPRH Gene:

Hs.723297

mRNA Expression by UniProt/SwissProt for SHPRH Gene:

Q149N8-SHPRH_HUMAN
Tissue specificity: Broadly expressed.

Evidence on tissue expression from TISSUES for SHPRH Gene

  • Nervous system(4.8)
genes like me logo Genes that share expression patterns with SHPRH: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SHPRH Gene

Orthologs for SHPRH Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SHPRH Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SHPRH 30 31
  • 99.56 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SHPRH 30 31
  • 91.38 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SHPRH 30 31
  • 89.62 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Shprh 30 17 31
  • 85.5 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Shprh 30
  • 84.43 (n)
Oppossum
(Monodelphis domestica)
Mammalia SHPRH 31
  • 77 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SHPRH 31
  • 60 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SHPRH 30 31
  • 72.79 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SHPRH 31
  • 71 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia shprh 30
  • 67.99 (n)
Zebrafish
(Danio rerio)
Actinopterygii shprh 30 31
  • 63.63 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta CG7376 30 31
  • 45.39 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007417 30
  • 44.72 (n)
Worm
(Caenorhabditis elegans)
Secernentea T05A12.4 31
  • 16 (a)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes IRC20 31 33 33
  • 16 (a)
OneToOne
Species where no ortholog for SHPRH was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SHPRH Gene

ENSEMBL:
Gene Tree for SHPRH (if available)
TreeFam:
Gene Tree for SHPRH (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SHPRH: view image

Paralogs for SHPRH Gene

(5) SIMAP similar genes for SHPRH Gene using alignment to 5 proteins:

  • SHPRH_HUMAN
  • H0YBI0_HUMAN
  • H7C2W2_HUMAN
  • K4DI94_HUMAN
  • Q5JT88_HUMAN
genes like me logo Genes that share paralogs with SHPRH: view

Variants for SHPRH Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SHPRH Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
rs117008643 Benign: not provided 145,919,501(-) T/C
NM_001042683.3(SHPRH):c.4009-10A>G
INTRON
rs117586623 Benign: not provided 145,954,847(-) T/G
NM_001042683.3(SHPRH):c.476A>C (p.Asp159Ala)
MISSENSE_VARIANT,FIVE_PRIME_UTR
rs1411096648 An ovarian cancer cell line p.Gln438Arg
rs1582754487 Likely Benign: not provided 145,934,999(-) A/G
NM_001042683.3(SHPRH):c.2898T>C (p.Thr966=)
SYNONYMOUS
rs200336760 Likely Benign: not provided 145,922,843(-) C/G
NM_001042683.3(SHPRH):c.3546-7G>C
INTRON

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SHPRH Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SHPRH Gene

Variant ID Type Subtype PubMed ID
nsv437525 CNV loss 16327808
nsv830835 CNV loss 17160897

Variation tolerance for SHPRH Gene

Residual Variation Intolerance Score: 1.83% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.87; 59.00% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SHPRH Gene

Human Gene Mutation Database (HGMD)
SHPRH
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SHPRH

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SHPRH Gene

Disorders for SHPRH Gene

MalaCards: The human disease database

(1) MalaCards diseases for SHPRH Gene - From: COP

Disorder Aliases PubMed IDs
xeroderma pigmentosum, variant type
  • xpv
- elite association - COSMIC cancer census association via MalaCards
Search SHPRH in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SHPRH

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with SHPRH: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SHPRH Gene

Publications for SHPRH Gene

  1. Cloning and characterization of a novel gene, SHPRH, encoding a conserved putative protein with SNF2/helicase and PHD-finger domains from the 6q24 region. (PMID: 12837266) Sood R … Trent JM (Genomics 2003) 2 3 4 23
  2. Human SHPRH is a ubiquitin ligase for Mms2-Ubc13-dependent polyubiquitylation of proliferating cell nuclear antigen. (PMID: 17108083) Unk I … Haracska L (Proceedings of the National Academy of Sciences of the United States of America 2006) 3 4 23
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  4. Polyubiquitination of proliferating cell nuclear antigen by HLTF and SHPRH prevents genomic instability from stalled replication forks. (PMID: 18719106) Motegi A … Myung K (Proceedings of the National Academy of Sciences of the United States of America 2008) 3 4
  5. Human SHPRH suppresses genomic instability through proliferating cell nuclear antigen polyubiquitination. (PMID: 17130289) Motegi A … Myung K (The Journal of cell biology 2006) 3 4

Products for SHPRH Gene

Sources for SHPRH Gene