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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
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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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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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