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    SHLD1 shieldin complex subunit 1 [ Homo sapiens (human) ]

    Gene ID: 149840, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SHLD1provided by HGNC
    Official Full Name
    shieldin complex subunit 1provided by HGNC
    Primary source
    HGNC:HGNC:26318
    See related
    Ensembl:ENSG00000171984 MIM:618028; AllianceGenome:HGNC:26318
    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
    RINN3; C20orf196
    Summary
    Involved in negative regulation of double-strand break repair via homologous recombination; positive regulation of double-strand break repair via nonhomologous end joining; and positive regulation of isotype switching. Located in site of double-strand break. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in lymph node (RPKM 1.6), adrenal (RPKM 1.1) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SHLD1 in Genome Data Viewer
    Location:
    20p12.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (5750193..5864395)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (5790559..5904751)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (5731047..5845041)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:5637190-5637690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:5637691-5638191 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:5668750-5669250 Neighboring gene Sharpr-MPRA regulatory region 5332 Neighboring gene uncharacterized LOC105372514 Neighboring gene Sharpr-MPRA regulatory region 14731 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17527 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17528 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17529 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17531 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:5807499-5808000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17532 Neighboring gene MPRA-validated peak4135 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr20:5872947-5873157 Neighboring gene RNA, U1 small nuclear 55, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12658 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12659 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr20:5904456-5905655 Neighboring gene chromogranin B

    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. MAD2L2 dimerization and TRIP13 control shieldin activity in DNA repair. de Krijger I, et al. Nat Commun, 2021 Sep 14. PMID 34521823, Free PMC Article
    2. Protein phosphatase 1 acts as a RIF1 effector to suppress DSB resection prior to Shieldin action. Isobe SY, et al. Cell Rep, 2021 Jul 13. PMID 34260925, Free PMC Article
    3. Shieldin complex promotes DNA end-joining and counters homologous recombination in BRCA1-null cells. Dev H, et al. Nat Cell Biol, 2018 Aug. PMID 30022119, Free PMC Article
    4. 53BP1-shieldin-dependent DSB processing in BRCA1-deficient cells requires CST-Polα-primase fill-in synthesis. Mirman Z, et al. Nat Cell Biol, 2022 Jan. PMID 35027730, Free PMC Article
    5. 53BP1 cooperation with the REV7-shieldin complex underpins DNA structure-specific NHEJ. Ghezraoui H, et al. Nature, 2018 Aug. PMID 30046110, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Protein phosphatase 1 acts as a RIF1 effector to suppress DSB resection prior to Shieldin action.
      Title: Protein phosphatase 1 acts as a RIF1 effector to suppress DSB resection prior to Shieldin action.
    2. MAD2L2 dimerization and TRIP13 control shieldin activity in DNA repair.
      Title: MAD2L2 dimerization and TRIP13 control shieldin activity in DNA repair.
    Submit: New GeneRIF Correction

    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
    Whole genome association scan for genetic polymorphisms influencing information processing speed.
    EBI GWAS Catalog

    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

    Homology

    Clone Names

    • FLJ25067

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of double-strand break repair via homologous recombination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of double-strand break repair via homologous recombination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of double-strand break repair via nonhomologous end joining IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of double-strand break repair via nonhomologous end joining IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of double-strand break repair via nonhomologous end joining NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of isotype switching IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of isotype switching IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in somatic diversification of immunoglobulins involved in immune response NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in telomere maintenance in response to DNA damage NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in chromosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in site of double-strand break IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in site of double-strand break IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in site of double-strand break NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    shieldin complex subunit 1
    Names
    RINN1-REV7-interacting novel NHEJ regulator 3
    shield complex subunit 1
    uncharacterized protein C20orf196

    NCBI Reference Sequences (RefSeq)

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    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_001303477.2 → NP_001290406.1  shieldin complex subunit 1 isoform 1

      See identical proteins and their annotated locations for NP_001290406.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). Variants 1 and 2 encode isoform 1.
      Source sequence(s)
      AK057796, AK292708, BU656896, HY270691
      Consensus CDS
      CCDS13091.1
      UniProtKB/Swiss-Prot
      A8K9J3, Q5TGA9, Q8IYI0, Q96LU1
      Conserved Domains (1) summary
      pfam15021
      Location:4 → 200
      DUF4521; Protein of unknown function (DUF4521)

    2. NM_001303478.2 → NP_001290407.1  shieldin complex subunit 1 isoform 2

      See identical proteins and their annotated locations for NP_001290407.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an exon in the 5' UTR, contains an alternate exon in the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct, shorter N-terminus than isoform 1.
      Source sequence(s)
      AK057796, AK292708, AL390028, HY080554, HY270691
      UniProtKB/Swiss-Prot
      Q8IYI0
      Conserved Domains (1) summary
      pfam15021
      Location:21 → 169
      DUF4521; Protein of unknown function (DUF4521)

    3. NM_001303479.2 → NP_001290408.1  shieldin complex subunit 1 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an exon in the 5' UTR and contains an alternate 3' terminal exon, resulting in a different 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (3) has a distinct, shorter C-terminus than isoform 1.
      Source sequence(s)
      AK057796, AV715251
      Consensus CDS
      CCDS77565.1
      UniProtKB/TrEMBL
      Q5TGA6
      Related
      ENSP00000368263.4, ENST00000378979.8
      Conserved Domains (1) summary
      pfam15021
      Location:3 → 59
      DUF4521; Protein of unknown function (DUF4521)

    4. NM_152504.4 → NP_689717.2  shieldin complex subunit 1 isoform 1

      See identical proteins and their annotated locations for NP_689717.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an exon in the 5' UTR compared to variant 1. Variants 1 and 2 encode isoform 1.
      Source sequence(s)
      AK057796, AK292708, AL390028, HY270691
      Consensus CDS
      CCDS13091.1
      UniProtKB/Swiss-Prot
      A8K9J3, Q5TGA9, Q8IYI0, Q96LU1
      Related
      ENSP00000305875.6, ENST00000303142.11
      Conserved Domains (1) summary
      pfam15021
      Location:4 → 200
      DUF4521; Protein of unknown function (DUF4521)

    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

    1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      5750193..5864395
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011529177.3 → XP_011527479.1  shieldin complex subunit 1 isoform X2

      Conserved Domains (1) summary
      pfam15021
      Location:17 → 213
      DUF4521; Protein of unknown function (DUF4521)

    2. XM_011529182.3 → XP_011527484.1  shieldin complex subunit 1 isoform X6

      Conserved Domains (1) summary
      pfam15021
      Location:17 → 74
      DUF4521; Protein of unknown function (DUF4521)

    3. XM_011529178.3 → XP_011527480.1  shieldin complex subunit 1 isoform X3

      Conserved Domains (1) summary
      pfam15021
      Location:17 → 76
      DUF4521; Protein of unknown function (DUF4521)

    4. XM_011529180.3 → XP_011527482.1  shieldin complex subunit 1 isoform X4

      Conserved Domains (1) summary
      pfam15021
      Location:17 → 72
      DUF4521; Protein of unknown function (DUF4521)

    5. XM_047439931.1 → XP_047295887.1  shieldin complex subunit 1 isoform X1

    6. XM_011529181.4 → XP_011527483.1  shieldin complex subunit 1 isoform X5

      Conserved Domains (1) summary
      pfam15021
      Location:4 → 63
      DUF4521; Protein of unknown function (DUF4521)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      5790559..5904751
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054323075.1 → XP_054179050.1  shieldin complex subunit 1 isoform X2

    2. XM_054323079.1 → XP_054179054.1  shieldin complex subunit 1 isoform X6

    3. XM_054323076.1 → XP_054179051.1  shieldin complex subunit 1 isoform X3

    4. XM_054323077.1 → XP_054179052.1  shieldin complex subunit 1 isoform X4

    5. XM_054323074.1 → XP_054179049.1  shieldin complex subunit 1 isoform X1

    6. XM_054323078.1 → XP_054179053.1  shieldin complex subunit 1 isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IYI0.1 GenPept UniProtKB/Swiss-Prot:Q8IYI0

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