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Aliases for SLF2 Gene

Aliases for SLF2 Gene

  • SMC5-SMC6 Complex Localization Factor 2 2 3 5
  • 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

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 Interleukin-7 Receptor Alpha Deficiency. An important paralog of this gene is FAM178B.

UniProtKB/Swiss-Prot 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 , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLF2 Gene

Genomics for SLF2 Gene

Regulatory Elements for SLF2 Gene

Enhancers for SLF2 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around SLF2 on UCSC Golden Path with GeneCards custom track

Promoters for SLF2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around SLF2 on UCSC Golden Path with GeneCards custom track

Genomic Location for SLF2 Gene

Chromosome:
10
Start:
100,912,569 bp from pter
End:
100,965,136 bp from pter
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).
    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.
    SequenceCaution:
    • Sequence=BAA91657.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for SLF2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SLF2 Gene

Proteomics data for SLF2 Gene at MOPED

Post-translational modifications for SLF2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SLF2 Gene

No data available for DME Specific Peptides for SLF2 Gene

Domains & Families for SLF2 Gene

Protein Domains for SLF2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SLF2 Gene

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

No data available for Gene Families for SLF2 Gene

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).
genes like me logo Genes that share phenotypes with SLF2: view

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , 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}.

Gene Ontology (GO) - Cellular Components for SLF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IDA 24561620
genes like me logo Genes that share ontologies with SLF2: view

No data available for Subcellular locations from COMPARTMENTS for SLF2 Gene

Pathways & Interactions for SLF2 Gene

SuperPathways for SLF2 Gene

No Data Available

Interacting Proteins for SLF2 Gene

STRING Interaction Network Preview (showing 2 interactants - click image to see details)
http://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000359292%0d%0a9606.ENSP00000385269%0d%0a9606.ENSP00000344818%0d%0a
Selected Interacting proteins: Q8IX21-SLF2_HUMAN ENSP00000359292 for SLF2 Gene via MINT STRING I2D

Gene Ontology (GO) - Biological Process for SLF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
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

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

No ASD Table

Relevant External Links for SLF2 Gene

GeneLoc Exon Structure for
SLF2
ECgene alternative splicing isoforms for
SLF2

Expression for SLF2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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).
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 and Protein tissue co-expression partners 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
cow
(Bos Taurus)
Mammalia FAM178A 35
  • 90.56 (n)
  • 88.21 (a)
C26H10ORF6 36
  • 88 (a)
OneToOne
dog
(Canis familiaris)
Mammalia FAM178A 35
  • 92.18 (n)
  • 90.75 (a)
FAM178A 36
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Fam178a 35
  • 88 (n)
  • 85.7 (a)
Fam178a 16
Fam178a 36
  • 84 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia FAM178A 35
  • 99.6 (n)
  • 99.06 (a)
FAM178A 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Fam178a 35
  • 87.29 (n)
  • 85.09 (a)
oppossum
(Monodelphis domestica)
Mammalia FAM178A 36
  • 52 (a)
OneToOne
chicken
(Gallus gallus)
Aves C10ORF6 35
  • 66.11 (n)
  • 57.34 (a)
FAM178A 36
  • 33 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia FAM178A 36
  • 31 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.7374 35
African clawed frog
(Xenopus laevis)
Amphibia Xl.32297 35
zebrafish
(Danio rerio)
Actinopterygii fam178a 36
  • 22 (a)
OneToOne
Species with no ortholog for SLF2:
  • A. gosspyii yeast (Ashbya 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 squirt (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)

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 from dbSNP and Humsavar for SLF2 Gene

SNP ID Clin Chr 10 pos Sequence Context AA Info Type
rs10883563 - 100,924,623(+) AATTT(A/C)TGGGG reference, missense
rs1535347 -- 100,928,070(-) ctctc(G/T)cgtgt intron-variant
rs1535348 -- 100,928,069(-) tctct(C/T)gtgtg intron-variant
rs12308 -- 100,964,799(-) TTAAT(G/T)GGCTA utr-variant-3-prime
rs3051160 -- 100,927,312(+) TTGAC(-/TG)TGTTT intron-variant

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)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot , Structural Variations from Database of Genomic Variants (DGV) and Relevant External Links for SLF2 Gene

Disorders for SLF2 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
interleukin-7 receptor alpha deficiency
  • il-7r
- elite association - COSMIC cancer census association via MalaCards
Search SLF2 in MalaCards View complete list of genes associated with diseases

Relevant External Links for SLF2

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SLF2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SLF2
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 67
  2. DNA repair. Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links. (PMID: 25931565) RAoschle M. … Mann M. (Science 2015) 2 3
  3. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3
  4. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein M.Y. … Mann M. (Cell 2015) 3
  5. Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components. (PMID: 24561620) Alabert C. … Groth A. (Nat. Cell Biol. 2014) 3

Products for SLF2 Gene

Sources for SLF2 Gene

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