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    SHLD2 shieldin complex subunit 2 [ Homo sapiens (human) ]

    Gene ID: 54537, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SHLD2provided by HGNC
    Official Full Name
    shieldin complex subunit 2provided by HGNC
    Primary source
    HGNC:HGNC:28773
    See related
    Ensembl:ENSG00000122376 MIM:618029; AllianceGenome:HGNC:28773
    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
    RINN2; FAM35A; FAM35A1; bA163M19.1
    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 actin cytoskeleton; nucleoplasm; and site of double-strand break. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in kidney (RPKM 20.9), thyroid (RPKM 14.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SHLD2 in Genome Data Viewer
    Location:
    10q23.2
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (87094473..87191465)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (87978839..88075088)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (88854963..88951222)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88779570-88780070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88780071-88780571 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:88784270-88785122 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:88785123-88785973 Neighboring gene family with sequence similarity 25 member A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3703 Neighboring gene RNA, U6 small nuclear 529, pseudogene Neighboring gene glutamate dehydrogenase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3704 Neighboring gene NANOG hESC enhancer GRCh37_chr10:88852612-88853149 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2576 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:88855254-88855511 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2577 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3705 Neighboring gene uncharacterized LOC124902475 Neighboring gene RNA, 7SL, cytoplasmic 733, pseudogene Neighboring gene uncharacterized LOC105378410 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3706 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2579 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88965395-88965896 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88987203-88987977 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88988752-88989526 Neighboring gene NUTM2A antisense RNA 1 Neighboring gene NUT family member 2A Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:89102067-89102674 Neighboring gene long intergenic non-protein coding RNA 863

    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. Genetic association and functional analysis of rs7903456 in FAM35A gene and hyperuricemia: a population based study. Yan F, et al. Sci Rep, 2018 Jun 25. PMID 29942023, Free PMC Article
    2. Molecular basis for assembly of the shieldin complex and its implications for NHEJ. Liang L, et al. Nat Commun, 2020 Apr 24. PMID 32332881, 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. GWAS of clinically defined gout and subtypes identifies multiple susceptibility loci that include urate transporter genes. Nakayama A, et al. Ann Rheum Dis, 2017 May. PMID 27899376, Free PMC Article
    5. FAM35A associates with REV7 and modulates DNA damage responses of normal and BRCA1-defective cells. Tomida J, et al. EMBO J, 2018 Jun 15. PMID 29789392, Free PMC Article

    See all (29) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Genetic association and functional analysis of rs7903456 in FAM35A gene and hyperuricemia
      Title: Genetic association and functional analysis of rs7903456 in FAM35A gene and hyperuricemia: a population based study.
    2. these results establish SHLD2 as a novel effector of REV7 in controlling the decision-making process during DSB repair.
      Title: SHLD2/FAM35A co-operates with REV7 to coordinate DNA double-strand break repair pathway choice.
    3. found FAM35A, a previously unstudied protein with an unstructured N-terminal region and a C-terminal region harboring three OB-fold domains similar to single-stranded DNA-binding protein RPA, as novel interactor of REV7/RIF1/53BP1.
      Title: FAM35A associates with REV7 and modulates DNA damage responses of normal and BRCA1-defective cells.
    4. the FAM35A locus showed an association with all gout by meta-analysis among the Japanese, Caucasian and NZ Polynesian sample sets at a genome-wide level of significance.
      Title: GWAS of clinically defined gout and subtypes identifies multiple susceptibility loci that include urate transporter genes.
    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

    Variation

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    See Variation Viewer (GRCh37.p13)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC5560

    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of double-strand break repair via homologous recombination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 actin cytoskeleton IDA
    Inferred from Direct Assay
    more info
    		  
    located_in chromatin NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in chromosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus 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 2
    Names
    RINN1-REV7-interacting novel NHEJ regulator 2
    family with sequence similarity 35 member A
    protein FAM35A
    shield complex subunit 2

    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_001330112.2 → NP_001317041.1  shieldin complex subunit 2 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AL136982, AL645992
      Consensus CDS
      CCDS81484.1
      UniProtKB/Swiss-Prot
      Q86V20
      Related
      ENSP00000298786.3, ENST00000298786.5
      Conserved Domains (1) summary
      pfam15793
      Location:720 → 892
      FAM35_C; Protein family FAM35, C-terminal

    2. NM_001377158.1 → NP_001364087.1  shieldin complex subunit 2 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3), as well as variants 2 and 4, encodes isoform 2.
      Source sequence(s)
      AL136982, AL645992
      Consensus CDS
      CCDS7383.1
      UniProtKB/Swiss-Prot
      O95885, Q86V20, Q9H991
      Conserved Domains (1) summary
      pfam15793
      Location:655 → 823
      FAM35_C; Protein family FAM35, C-terminal

    3. NM_001377159.1 → NP_001364088.1  shieldin complex subunit 2 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4), as well as variants 2 and 3, encodes isoform 2.
      Source sequence(s)
      AL136982, AL645992
      Consensus CDS
      CCDS7383.1
      UniProtKB/Swiss-Prot
      O95885, Q86V20, Q9H991
      Conserved Domains (1) summary
      pfam15793
      Location:655 → 823
      FAM35_C; Protein family FAM35, C-terminal

    4. NM_001377160.1 → NP_001364089.1  shieldin complex subunit 2 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL136982, AL645992
      Conserved Domains (1) summary
      pfam15793
      Location:703 → 871
      FAM35_C; Protein family FAM35, C-terminal

    5. NM_001377161.1 → NP_001364090.1  shieldin complex subunit 2 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL136982, AL645992
      Conserved Domains (1) summary
      pfam15793
      Location:722 → 875
      FAM35_C; Protein family FAM35, C-terminal

    6. NM_001377162.1 → NP_001364091.1  shieldin complex subunit 2 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AL136982, AL645992
      Conserved Domains (1) summary
      pfam15793
      Location:685 → 856
      FAM35_C; Protein family FAM35, C-terminal

    7. NM_001377163.1 → NP_001364092.1  shieldin complex subunit 2 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AL136982, AL645992
      Conserved Domains (1) summary
      pfam15793
      Location:721 → 840
      FAM35_C; Protein family FAM35, C-terminal

    8. NM_001377164.1 → NP_001364093.1  shieldin complex subunit 2 isoform 7

      Status: VALIDATED

      Description
      Transcript Variant: This variant (9), as well as variant 10, encodes isoform 7.
      Source sequence(s)
      AL136982, AL645992
      Conserved Domains (1) summary
      pfam15793
      Location:619 → 787
      FAM35_C; Protein family FAM35, C-terminal

    9. NM_001377165.1 → NP_001364094.1  shieldin complex subunit 2 isoform 7

      Status: VALIDATED

      Description
      Transcript Variant: This variant (10), as well as variant 9, encodes isoform 7.
      Source sequence(s)
      AL136982, AL645992
      Conserved Domains (1) summary
      pfam15793
      Location:619 → 787
      FAM35_C; Protein family FAM35, C-terminal

    10. NM_001377166.1 → NP_001364095.1  shieldin complex subunit 2 isoform 8

      Status: VALIDATED

      Description
      Transcript Variant: This variant (11), as well as variants 12 and 13, encodes isoform 8.
      Source sequence(s)
      AL136982, AL645992
      Conserved Domains (1) summary
      pfam15793
      Location:372 → 543
      FAM35_C; Protein family FAM35, C-terminal

    11. NM_001377167.1 → NP_001364096.1  shieldin complex subunit 2 isoform 8

      Status: VALIDATED

      Description
      Transcript Variant: This variant (12), as well as variants 11 and 13, encodes isoform 8.
      Source sequence(s)
      AL136982, AL645992
      Conserved Domains (1) summary
      pfam15793
      Location:372 → 543
      FAM35_C; Protein family FAM35, C-terminal

    12. NM_001377168.1 → NP_001364097.1  shieldin complex subunit 2 isoform 8

      Status: VALIDATED

      Description
      Transcript Variant: This variant (13), as well as variants 11 and 12, encodes isoform 8.
      Source sequence(s)
      AL136982, AL645992
      Conserved Domains (1) summary
      pfam15793
      Location:372 → 543
      FAM35_C; Protein family FAM35, C-terminal

    13. NM_001377169.1 → NP_001364098.1  shieldin complex subunit 2 isoform 9

      Status: VALIDATED

      Source sequence(s)
      AL136982, AL645992
      Conserved Domains (1) summary
      pfam15793
      Location:372 → 520
      FAM35_C; Protein family FAM35, C-terminal

    14. NM_001377170.1 → NP_001364099.1  shieldin complex subunit 2 isoform 10

      Status: VALIDATED

      Source sequence(s)
      AL136982, AL645992
      Conserved Domains (1) summary
      pfam15793
      Location:253 → 424
      FAM35_C; Protein family FAM35, C-terminal

    15. NM_001377171.1 → NP_001364100.1  shieldin complex subunit 2 isoform 11

      Status: VALIDATED

      Source sequence(s)
      AL136982, AL645992
      Conserved Domains (1) summary
      pfam15793
      Location:404 → 575
      FAM35_C; Protein family FAM35, C-terminal

    16. NM_001377172.1 → NP_001364101.1  shieldin complex subunit 2 isoform 12

      Status: VALIDATED

      Source sequence(s)
      AL136982, AL645992
      Conserved Domains (1) summary
      pfam15793
      Location:306 → 474
      FAM35_C; Protein family FAM35, C-terminal

    17. NM_019054.3 → NP_061927.2  shieldin complex subunit 2 isoform 2

      See identical proteins and their annotated locations for NP_061927.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region compared to variant 1. It encodes isoform 2, which is shorter than isoform 1. Variants 2-4 all encode the same isoform (2).
      Source sequence(s)
      AK022978, BC051863
      Consensus CDS
      CCDS7383.1
      UniProtKB/Swiss-Prot
      O95885, Q86V20, Q9H991
      Related
      ENSP00000298784.1, ENST00000298784.5
      Conserved Domains (1) summary
      pfam15793
      Location:655 → 823
      FAM35_C; Protein family FAM35, C-terminal

    RNA

    1. NR_165105.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL136982, AL645992

    2. NR_165106.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL136982, AL645992

    3. NR_165108.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL136982, AL645992

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      87094473..87191465
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047425370.1 → XP_047281326.1  shieldin complex subunit 2 isoform X1

    2. XM_047425371.1 → XP_047281327.1  shieldin complex subunit 2 isoform X2

    3. XM_047425374.1 → XP_047281330.1  shieldin complex subunit 2 isoform X5

    4. XM_047425375.1 → XP_047281331.1  shieldin complex subunit 2 isoform X6

    5. XM_047425372.1 → XP_047281328.1  shieldin complex subunit 2 isoform X3

    6. XM_047425373.1 → XP_047281329.1  shieldin complex subunit 2 isoform X4

    7. XM_047425376.1 → XP_047281332.1  shieldin complex subunit 2 isoform X7

      UniProtKB/Swiss-Prot
      O95885, Q86V20, Q9H991

    8. XM_047425377.1 → XP_047281333.1  shieldin complex subunit 2 isoform X8

    9. XM_047425378.1 → XP_047281334.1  shieldin complex subunit 2 isoform X9

    10. XM_047425379.1 → XP_047281335.1  shieldin complex subunit 2 isoform X10

    11. XM_047425380.1 → XP_047281336.1  shieldin complex subunit 2 isoform X11

    12. XM_011539877.3 → XP_011538179.1  shieldin complex subunit 2 isoform X1

      See identical proteins and their annotated locations for XP_011538179.1

      Conserved Domains (1) summary
      pfam15793
      Location:769 → 940
      FAM35_C; Protein family FAM35, C-terminal

    13. XM_011539879.3 → XP_011538181.1  shieldin complex subunit 2 isoform X1

      See identical proteins and their annotated locations for XP_011538181.1

      Conserved Domains (1) summary
      pfam15793
      Location:769 → 940
      FAM35_C; Protein family FAM35, C-terminal

    14. XM_006717905.4 → XP_006717968.1  shieldin complex subunit 2 isoform X1

      See identical proteins and their annotated locations for XP_006717968.1

      Conserved Domains (1) summary
      pfam15793
      Location:769 → 940
      FAM35_C; Protein family FAM35, C-terminal

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      87978839..88075088
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054366137.1 → XP_054222112.1  shieldin complex subunit 2 isoform X1

    2. XM_054366136.1 → XP_054222111.1  shieldin complex subunit 2 isoform X12

    3. XM_054366138.1 → XP_054222113.1  shieldin complex subunit 2 isoform X1

    4. XM_054366134.1 → XP_054222109.1  shieldin complex subunit 2 isoform X2

    5. XM_054366135.1 → XP_054222110.1  shieldin complex subunit 2 isoform X6

    6. XM_054366139.1 → XP_054222114.1  shieldin complex subunit 2 isoform X8

    7. XM_054366140.1 → XP_054222115.1  shieldin complex subunit 2 isoform X9

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86V20.1 GenPept UniProtKB/Swiss-Prot:Q86V20

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