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

Gene ID: 149840, updated on 2-Nov-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, Nov 2024]
Expression
Ubiquitous expression in lymph node (RPKM 1.6), adrenal (RPKM 1.1) and 24 other tissues See more
Orthologs
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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 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)

Genotypes

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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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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