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

Gene ID: 257218, updated on 7-Apr-2024

Summary

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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

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See SHPRH in Genome Data Viewer
Location:
6q24.3
Exon count:
35
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (145857838..145964358, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (147050896..147157428, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (146205943..146285494, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene EPM2A divergent transcript Neighboring gene uncharacterized LOC124901419 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:146135340-146135894 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25227 Neighboring gene F-box protein 30 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25228 Neighboring gene uncharacterized LOC124901420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25229 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:146285382-146286369 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:146350016-146350516 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:146350517-146351017 Neighboring gene glutamate metabotropic receptor 1 Neighboring gene FUN14 domain containing 2 pseudogene 3 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:146578666-146579217 Neighboring gene RNA, 5S ribosomal pseudogene 222

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. SHPRH as a new player in ribosomal RNA transcription and its potential role in homeostasis of ribosomal DNA repeats. Lee D, et al. Transcription, 2018. PMID 29139335, Free PMC Article
  2. KMT2B promotes SHPRH expression to regulate (131)I sensitivity in thyroid carcinoma cells by affecting FYN protein stability. Chen W, et al. Cell Signal, 2021 Dec. PMID 34606908
  3. The Human RAD5 Homologs, HLTF and SHPRH, Have Separate Functions in DNA Damage Tolerance Dependent on The DNA Lesion Type. Seelinger M, et al. Biomolecules, 2020 Mar 17. PMID 32192191, Free PMC Article
  4. A novel protein encoded by the circular form of the SHPRH gene suppresses glioma tumorigenesis. Zhang M, et al. Oncogene, 2018 Mar. PMID 29343848
  5. Human SHPRH suppresses genomic instability through proliferating cell nuclear antigen polyubiquitination. Motegi A, et al. J Cell Biol, 2006 Dec 4. PMID 17130289, Free PMC Article

See all (44) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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).
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Submit: New GeneRIF Correction See all GeneRIFs (14)

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)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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 ATP-dependent chromatin remodeler activity 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
NP_001357256.1
NP_001357257.1
NP_775105.1
XP_006715502.1
XP_006715506.1
XP_011534021.1
XP_011534024.1
XP_016866180.1
XP_016866181.1
XP_016866182.1
XP_047274556.1
XP_047274557.1
XP_047274558.1
XP_047274559.1
XP_047274560.1
XP_054211055.1
XP_054211056.1
XP_054211057.1
XP_054211058.1
XP_054211059.1
XP_054211060.1
XP_054211061.1
XP_054211062.1
XP_054211063.1
XP_054211064.1
XP_054211065.1
XP_054211066.1

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)

  1. 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

  2. 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

  3. 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

  4. 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_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    145857838..145964358 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047418600.1 → XP_047274556.1  E3 ubiquitin-protein ligase SHPRH isoform X1

  2. 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

  3. XM_047418601.1 → XP_047274557.1  E3 ubiquitin-protein ligase SHPRH isoform X1

  4. 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

  5. XM_047418603.1 → XP_047274559.1  E3 ubiquitin-protein ligase SHPRH isoform X7

  6. XM_017010693.3 → XP_016866182.1  E3 ubiquitin-protein ligase SHPRH isoform X4

    UniProtKB/TrEMBL
    A0A0D9SFM0

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

    UniProtKB/TrEMBL
    A0A0D9SFM0

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

    UniProtKB/TrEMBL
    A0A0D9SFM0

  9. 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

  10. XM_047418602.1 → XP_047274558.1  E3 ubiquitin-protein ligase SHPRH isoform X6

  11. XM_047418604.1 → XP_047274560.1  E3 ubiquitin-protein ligase SHPRH isoform X8

    Related
    ENSP00000430528.1, ENST00000519632.5

  12. 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

RNA

  1. XR_942393.4 RNA Sequence

  2. XR_942390.4 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    147050896..147157428 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054355080.1 → XP_054211055.1  E3 ubiquitin-protein ligase SHPRH isoform X1

  2. XM_054355084.1 → XP_054211059.1  E3 ubiquitin-protein ligase SHPRH isoform X3

  3. XM_054355081.1 → XP_054211056.1  E3 ubiquitin-protein ligase SHPRH isoform X1

  4. XM_054355087.1 → XP_054211062.1  E3 ubiquitin-protein ligase SHPRH isoform X7

  5. XM_054355088.1 → XP_054211063.1  E3 ubiquitin-protein ligase SHPRH isoform X7

  6. XM_054355085.1 → XP_054211060.1  E3 ubiquitin-protein ligase SHPRH isoform X4

  7. XM_054355082.1 → XP_054211057.1  E3 ubiquitin-protein ligase SHPRH isoform X2

  8. XM_054355083.1 → XP_054211058.1  E3 ubiquitin-protein ligase SHPRH isoform X2

  9. XM_054355086.1 → XP_054211061.1  E3 ubiquitin-protein ligase SHPRH isoform X5

  10. XM_054355089.1 → XP_054211064.1  E3 ubiquitin-protein ligase SHPRH isoform X10

  11. XM_054355090.1 → XP_054211065.1  E3 ubiquitin-protein ligase SHPRH isoform X8

  12. XM_054355091.1 → XP_054211066.1  E3 ubiquitin-protein ligase SHPRH isoform X9

RNA

  1. XR_008487292.1 RNA Sequence

  2. XR_008487293.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q149N8.2 GenPept UniProtKB/Swiss-Prot:Q149N8

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