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

    Gene ID: 257218, updated on 5-May-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    NEW Try the new Transcript table

    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_001042683.3NP_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:24389
      HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
      cd15547
      Location:660706
      PHD_SHPRH; PHD finger found in E3 ubiquitin-protein ligase SHPRH
      cd16569
      Location:14291479
      RING-HC_SHPRH; RING finger, HC subclass, found in SNF2 histone-linker PHD finger RING finger helicase (SHPRH) and similar proteins
      pfam00538
      Location:440511
      Linker_histone; linker histone H1 and H5 family
      cd18793
      Location:15081633
      SF2_C_SNF; C-terminal helicase domain of the SNF family helicases
      cd18070
      Location:702903
      DEXQc_SHPRH; DEXQ-box helicase domain of SHPRH
      cl28899
      Location:304409
      DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
    2. NM_001370327.1NP_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:24389
      HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
      cd15547
      Location:660706
      PHD_SHPRH; PHD finger found in E3 ubiquitin-protein ligase SHPRH
      cd16569
      Location:14291479
      RING-HC_SHPRH; RING finger, HC subclass, found in SNF2 histone-linker PHD finger RING finger helicase (SHPRH) and similar proteins
      pfam00538
      Location:440511
      Linker_histone; linker histone H1 and H5 family
      cd18793
      Location:15081633
      SF2_C_SNF; C-terminal helicase domain of the SNF family helicases
      cd18070
      Location:702903
      DEXQc_SHPRH; DEXQ-box helicase domain of SHPRH
      cl28899
      Location:304409
      DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
    3. NM_001370328.1NP_001357257.1  E3 ubiquitin-protein ligase SHPRH isoform c

      Status: VALIDATED

      Source sequence(s)
      AL356599, AL451145
      Conserved Domains (4) summary
      cd15547
      Location:179225
      PHD_SHPRH; PHD finger found in E3 ubiquitin-protein ligase SHPRH
      cd16569
      Location:948998
      RING-HC_SHPRH; RING finger, HC subclass, found in SNF2 histone-linker PHD finger RING finger helicase (SHPRH) and similar proteins
      cd18793
      Location:10271152
      SF2_C_SNF; C-terminal helicase domain of the SNF family helicases
      cd18070
      Location:221422
      DEXQc_SHPRH; DEXQ-box helicase domain of SHPRH
    4. NM_173082.4NP_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:15151652
      HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
      cd00162
      Location:14361486
      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:660706
      PHD_SHPRH; PHD finger found in E3 ubiquitin-protein ligase SHPRH
      pfam00176
      Location:716987
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:15171626
      Helicase_C; Helicase conserved C-terminal domain
      pfam00538
      Location:440511
      Linker_histone; linker histone H1 and H5 family
      pfam13424
      Location:10291113
      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_047418600.1XP_047274556.1  E3 ubiquitin-protein ligase SHPRH isoform X1

    2. XM_006715439.5XP_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:15111648
      HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
      cd00162
      Location:14321482
      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:660706
      PHD_SHPRH; PHD finger found in E3 ubiquitin-protein ligase SHPRH
      pfam00176
      Location:716987
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:15131622
      Helicase_C; Helicase conserved C-terminal domain
      pfam00538
      Location:440511
      Linker_histone; linker histone H1 and H5 family
      pfam13424
      Location:10201104
      TPR_12; Tetratricopeptide repeat
    3. XM_047418601.1XP_047274557.1  E3 ubiquitin-protein ligase SHPRH isoform X1

    4. XM_006715443.5XP_006715506.1  E3 ubiquitin-protein ligase SHPRH isoform X7

      UniProtKB/TrEMBL
      A0A0D9SFM0
      Conserved Domains (5) summary
      cd00162
      Location:14321482
      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:660706
      PHD_SHPRH; PHD finger found in E3 ubiquitin-protein ligase SHPRH
      pfam00176
      Location:716987
      SNF2_N; SNF2 family N-terminal domain
      pfam00538
      Location:440511
      Linker_histone; linker histone H1 and H5 family
      pfam13424
      Location:10201104
      TPR_12; Tetratricopeptide repeat
    5. XM_047418603.1XP_047274559.1  E3 ubiquitin-protein ligase SHPRH isoform X7

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

      UniProtKB/TrEMBL
      A0A0D9SFM0
    7. XM_017010691.3XP_016866180.1  E3 ubiquitin-protein ligase SHPRH isoform X2

      UniProtKB/TrEMBL
      A0A0D9SFM0
    8. XM_017010692.2XP_016866181.1  E3 ubiquitin-protein ligase SHPRH isoform X2

      UniProtKB/TrEMBL
      A0A0D9SFM0
    9. XM_011535719.4XP_011534021.1  E3 ubiquitin-protein ligase SHPRH isoform X5

      UniProtKB/TrEMBL
      A0A0D9SFM0
      Conserved Domains (7) summary
      COG0553
      Location:15111658
      HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
      cd00162
      Location:14321482
      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:660706
      PHD_SHPRH; PHD finger found in E3 ubiquitin-protein ligase SHPRH
      pfam00176
      Location:716987
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:15131622
      Helicase_C; Helicase conserved C-terminal domain
      pfam00538
      Location:440511
      Linker_histone; linker histone H1 and H5 family
      pfam13424
      Location:10201104
      TPR_12; Tetratricopeptide repeat
    10. XM_047418602.1XP_047274558.1  E3 ubiquitin-protein ligase SHPRH isoform X6

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

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

      Conserved Domains (3) summary
      COG0553
      Location:24389
      HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
      cd15547
      Location:660706
      PHD_SHPRH; PHD finger found in E3 ubiquitin-protein ligase SHPRH
      pfam00538
      Location:440511
      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_054355080.1XP_054211055.1  E3 ubiquitin-protein ligase SHPRH isoform X1

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

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

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

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

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

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

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

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

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

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

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

    RNA

    1. XR_008487292.1 RNA Sequence

    2. XR_008487293.1 RNA Sequence