Aliases for SLF2 Gene

Aliases for SLF2 Gene

  • SMC5-SMC6 Complex Localization Factor 2 2 3 5
  • SMC5-SMC6 Complex Localization Factor Protein 2 3 4
  • Family With Sequence Similarity 178, Member A 2 3
  • Smc5/6 Localization Factor 1 3 4
  • C10orf6 3 4
  • FAM178A 3 4
  • Chromosome 10 Open Reading Frame 6 2
  • Protein FAM178A 3
  • FLJ10512 2
  • FLJ25012 2
  • SLF2 5

External Ids for SLF2 Gene

Previous HGNC Symbols for SLF2 Gene

  • C10orf6
  • FAM178A

Summaries for SLF2 Gene

GeneCards Summary for SLF2 Gene

SLF2 (SMC5-SMC6 Complex Localization Factor 2) is a Protein Coding gene. Diseases associated with SLF2 include Form Agnosia and Alveoli Adenoma. An important paralog of this gene is FAM178B.

UniProtKB/Swiss-Prot Summary for SLF2 Gene

  • Plays a role in the DNA damage response (DDR) pathway by regulating postreplication repair of UV-damaged DNA and genomic stability maintenance (PubMed:25931565). The SLF1-SLF2 complex acts to link RAD18 with the SMC5-SMC6 complex at replication-coupled interstrand cross-links (ICL) and DNA double-strand breaks (DSBs) sites on chromatin during DNA repair in response to stalled replication forks (PubMed:25931565). Promotes the recruitment of the SMC5-SMC6 complex to DNA lesions (PubMed:25931565).

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SLF2 Gene

Genomics for SLF2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SLF2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10J100909 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 605.2 +3.1 3107 6.6 SP1 HNRNPL CREB1 TEAD4 PRDM10 ZNF629 TFE3 SIX5 IKZF1 ZNF692 ENSG00000272572 SLF2 MRPL43 TWNK SEMA4G CHUK MIR608
GH10J100907 Enhancer 0.9 Ensembl CraniofacialAtlas 600.7 -1.6 -1616 0.8 GATAD2A RCOR2 RXRB IKZF2 SP1 PBX2 PKNOX1 CEBPA SCRT2 DPF2 ENSG00000222072 SLF2 SEMA4G MIR608 ENSG00000272572 PAX2
GH10J100910 Enhancer 0.3 Ensembl 600.7 -0.7 -715 0.2 ZNF121 ENSG00000222072 SLF2 SEMA4G MIR608 PAX2
GH10J101828 Promoter/Enhancer 2.2 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 19.4 +921.6 921565 4.4 SP1 CREB1 HNRNPL PRDM10 ZNF629 LEF1 KDM1A ZNF692 BACH1 TARDBP PPRC1 LDB1 LZTS2 GBF1 MRPL43 HPS6 NOLC1 SUFU ENSG00000272572 SLF2
GH10J100369 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 11.5 -536.9 -536894 7 CEBPG SP1 HNRNPL CREB1 GATAD2A ATF7 TEAD4 REST ZNF629 TFE3 lnc-PKD2L1-7 OLMALINC EBAG9P1 SEC31B LZTS2 PHBP9 NDUFB8 SCD ENSG00000231188 MRPL43
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SLF2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SLF2

Genomic Locations for SLF2 Gene

Genomic Locations for SLF2 Gene
chr10:100,909,416-100,965,134
(GRCh38/hg38)
Size:
55,719 bases
Orientation:
Plus strand
chr10:102,672,326-102,724,893
(GRCh37/hg19)
Size:
52,568 bases
Orientation:
Plus strand

Genomic View for SLF2 Gene

Genes around SLF2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLF2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLF2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLF2 Gene

Proteins for SLF2 Gene

  • Protein details for SLF2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IX21-SLF2_HUMAN
    Recommended name:
    SMC5-SMC6 complex localization factor protein 2
    Protein Accession:
    Q8IX21
    Secondary Accessions:
    • A8K950
    • B1AL17
    • Q5W0L8
    • Q6GMU6
    • Q9NPE8

    Protein attributes for SLF2 Gene

    Size:
    1173 amino acids
    Molecular mass:
    131873 Da
    Quaternary structure:
    • Interacts with SLF1 (via N-terminus); this interaction links RAD18 to the SMC5-SMC6 complex (PubMed:25931565). Interacts with RAD18; this interaction is increased in a SLF1-dependent manner (PubMed:25931565). Interacts with SMC5 and SMC6 (PubMed:25931565).
    SequenceCaution:
    • Sequence=BAA91657.1; Type=Erroneous initiation; Evidence={ECO:0000305};
    Miscellaneous:
    • Localized in the locus associated with inherited infantile onset spinocerebellar ataxia (IOSCA). No mutation were found associated with IOSCA compared to control subjects. The expression level in the brain was not different between the 2 populations.

    Alternative splice isoforms for SLF2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SLF2 Gene

Post-translational modifications for SLF2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SLF2 Gene

Domains & Families for SLF2 Gene

Gene Families for SLF2 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for SLF2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SLF2 Gene

GenScript: Design optimal peptide antigens:
  • Protein FAM178A (F178A_HUMAN)
  • FAM178A protein (Q05BG6_HUMAN)
  • FAM178A protein (Q6GMU6_HUMAN)
  • FAM178A protein (Q8WW40_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8IX21

UniProtKB/Swiss-Prot:

SLF2_HUMAN :
  • Belongs to the FAM178 family.
Family:
  • Belongs to the FAM178 family.
genes like me logo Genes that share domains with SLF2: view

Function for SLF2 Gene

Molecular function for SLF2 Gene

UniProtKB/Swiss-Prot Function:
Plays a role in the DNA damage response (DDR) pathway by regulating postreplication repair of UV-damaged DNA and genomic stability maintenance (PubMed:25931565). The SLF1-SLF2 complex acts to link RAD18 with the SMC5-SMC6 complex at replication-coupled interstrand cross-links (ICL) and DNA double-strand breaks (DSBs) sites on chromatin during DNA repair in response to stalled replication forks (PubMed:25931565). Promotes the recruitment of the SMC5-SMC6 complex to DNA lesions (PubMed:25931565).

Phenotypes From GWAS Catalog for SLF2 Gene

Gene Ontology (GO) - Molecular Function for SLF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25931565
GO:0031625 ubiquitin protein ligase binding IPI 25931565
GO:0044877 protein-containing complex binding IPI 25931565
genes like me logo Genes that share ontologies with SLF2: view
genes like me logo Genes that share phenotypes with SLF2: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLF2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SLF2 Gene

Localization for SLF2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLF2 Gene

Nucleus. Note=Mainly localizes in the nucleus (PubMed:24561620). Colocalizes with PCNA on replication sites (PubMed:24561620). Associates with chromatin (PubMed:25931565). Accumulates with RAD18 and the SMC5-SMC6 complex at replication-coupled DNA interstrand repair and DNA double-strand breaks (DSBs) sites on chromatin in a ubiquitin-dependent manner (PubMed:25931565). {ECO:0000269 PubMed:24561620, ECO:0000269 PubMed:25931565}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SLF2 gene
Compartment Confidence
nucleus 5
cytosol 2
cytoskeleton 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SLF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IDA 24561620
GO:0005634 nucleus IEA,IDA 24561620
GO:0005654 nucleoplasm IDA --
GO:0035861 site of double-strand break IDA 25931565
GO:0043231 intracellular membrane-bounded organelle IDA --
genes like me logo Genes that share ontologies with SLF2: view

Pathways & Interactions for SLF2 Gene

PathCards logo

SuperPathways for SLF2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SLF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006281 DNA repair IEA --
GO:0006974 cellular response to DNA damage stimulus IEA,IDA 25931565
GO:0031334 positive regulation of protein complex assembly IMP 25931565
GO:0034184 positive regulation of maintenance of mitotic sister chromatid cohesion IMP 25931565
GO:1990166 protein localization to site of double-strand break IDA 25931565
genes like me logo Genes that share ontologies with SLF2: view

No data available for Pathways by source and SIGNOR curated interactions for SLF2 Gene

Drugs & Compounds for SLF2 Gene

No Compound Related Data Available

Transcripts for SLF2 Gene

mRNA/cDNA for SLF2 Gene

4 REFSEQ mRNAs :
17 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLF2

Alternative Splicing Database (ASD) splice patterns (SP) for SLF2 Gene

No ASD Table

Relevant External Links for SLF2 Gene

GeneLoc Exon Structure for
SLF2

Expression for SLF2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SLF2

mRNA Expression by UniProt/SwissProt for SLF2 Gene:

Q8IX21-SLF2_HUMAN
Tissue specificity: Widely expressed (PubMed:12459258). Expressed at higher level in skeletal muscle and at slightly lower level in brain, liver and heart, than in lung, kidney, spleen and thymus (PubMed:12459258).

Evidence on tissue expression from TISSUES for SLF2 Gene

  • Blood(4.7)
  • Kidney(4.2)
  • Nervous system(3.4)
  • Adrenal gland(3.3)
  • Eye(2.6)
genes like me logo Genes that share expression patterns with SLF2: view

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for SLF2 Gene

Orthologs for SLF2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SLF2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia FAM178A 30 31
  • 99.6 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia FAM178A 30 31
  • 92.18 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia FAM178A 30
  • 90.56 (n)
C26H10ORF6 31
  • 88 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Fam178a 30 31
  • 88 (n)
OneToOne
Slf2 17
Rat
(Rattus norvegicus)
Mammalia Fam178a 30
  • 87.29 (n)
Oppossum
(Monodelphis domestica)
Mammalia FAM178A 31
  • 52 (a)
OneToOne
Chicken
(Gallus gallus)
Aves C10ORF6 30
  • 66.11 (n)
FAM178A 31
  • 33 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia FAM178A 31
  • 31 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.32297 30
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia Str.7374 30
Zebrafish
(Danio rerio)
Actinopterygii fam178a 31
  • 22 (a)
OneToOne
Species where no ortholog for SLF2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for SLF2 Gene

ENSEMBL:
Gene Tree for SLF2 (if available)
TreeFam:
Gene Tree for SLF2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SLF2: view image

Paralogs for SLF2 Gene

Paralogs for SLF2 Gene

genes like me logo Genes that share paralogs with SLF2: view

Variants for SLF2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SLF2 Gene

SNP ID Clinical significance and condition Chr 10 pos Variation AA Info Type
713981 Benign: not provided 100,916,819(+) A/G MISSENSE_VARIANT
713982 Benign: not provided 100,916,834(+) A/G MISSENSE_VARIANT
rs10883563 - p.Ser541Tyr

Additional dbSNP identifiers (rs#s) for SLF2 Gene

Structural Variations from Database of Genomic Variants (DGV) for SLF2 Gene

Variant ID Type Subtype PubMed ID
nsv467443 CNV loss 19166990
nsv515627 CNV gain+loss 19592680
nsv552051 CNV loss 21841781
nsv831965 CNV loss 17160897

Variation tolerance for SLF2 Gene

Residual Variation Intolerance Score: 13.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.63; 93.12% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLF2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SLF2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLF2 Gene

Disorders for SLF2 Gene

MalaCards: The human disease database

(4) MalaCards diseases for SLF2 Gene - From: DISEASES

Disorder Aliases PubMed IDs
form agnosia
alveoli adenoma
  • adenoma of alveoli
bronchial benign neoplasm
  • bronchus neoplasm
papillorenal syndrome
  • paprs
- elite association - COSMIC cancer census association via MalaCards
Search SLF2 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with SLF2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SLF2 Gene

Publications for SLF2 Gene

  1. cDNA cloning, expression profile and genomic structure of a novel human transcript on chromosome 10q24, and its analyses as a candidate gene for infantile onset spinocerebellar ataxia. (PMID: 12459258) Nikali K … Peltonen L (Gene 2002) 2 3 4 23
  2. DNA repair. Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links. (PMID: 25931565) Räschle M … Mann M (Science (New York, N.Y.) 2015) 2 3 4
  3. Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components. (PMID: 24561620) Alabert C … Groth A (Nature cell biology 2014) 3 4
  4. The DNA sequence and comparative analysis of human chromosome 10. (PMID: 15164054) Deloukas P … Rogers J (Nature 2004) 3 4
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4

Products for SLF2 Gene

Sources for SLF2 Gene