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    SLF2 SMC5-SMC6 complex localization factor 2 [ Homo sapiens (human) ]

    Gene ID: 55719, updated on 17-Jun-2024

    Summary

    Official Symbol
    SLF2provided by HGNC
    Official Full Name
    SMC5-SMC6 complex localization factor 2provided by HGNC
    Primary source
    HGNC:HGNC:17814
    See related
    Ensembl:ENSG00000119906 MIM:610348; AllianceGenome:HGNC:17814
    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
    ATELS1; C10orf6; FAM178A
    Summary
    Enables ubiquitin protein ligase binding activity. Involved in several processes, including positive regulation of cellular component organization; positive regulation of double-strand break repair; and protein localization to site of double-strand break. Located in chromatin; nucleoplasm; and site of double-strand break. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in testis (RPKM 12.5), ovary (RPKM 7.5) and 24 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See SLF2 in Genome Data Viewer
    Location:
    10q24.31
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (100912963..100965134)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (101792183..101848510)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (102672720..102724891)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:102321666-102322304 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:102322305-102322942 Neighboring gene hypoxia inducible factor 1 subunit alpha inhibitor Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:102401951-102402580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102421749-102422248 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102440375-102440986 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102443611-102444112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102447267-102447771 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102473509-102474318 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:102496683-102497428 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:102497429-102498172 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3899 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102505530-102506071 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102509961-102510895 Neighboring gene paired box 2 Neighboring gene VISTA enhancer hs229 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102550131-102551044 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:102551431-102551607 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102562802-102563302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102567263-102567763 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102576822-102577322 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:102606788-102607987 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2709 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102633779-102634445 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:102649745-102650944 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2710 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3901 Neighboring gene Sharpr-MPRA regulatory region 3697 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2711 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3902 Neighboring gene semaphorin 4G Neighboring gene microRNA 608 Neighboring gene mitochondrial ribosomal protein L43

    Genomic regions, transcripts, and products

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC90157

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein-containing complex binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables ubiquitin protein ligase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in PML body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of Smc5-Smc6 complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in chromosome, telomeric region NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    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 

    General protein information

    Preferred Names
    SMC5-SMC6 complex localization factor protein 2
    Names
    family with sequence similarity 178, member A
    protein FAM178A
    smc5/6 localization factor 1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001136123.2NP_001129595.1  SMC5-SMC6 complex localization factor protein 2 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an exon and differs in the 3' UTR, compared to variant 1. The encoded isoform (2) is longer and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AF460992, BC030565
      Consensus CDS
      CCDS44470.1
      UniProtKB/Swiss-Prot
      Q8IX21
      Related
      ENSP00000359292.3, ENST00000370269.3
      Conserved Domains (1) summary
      pfam14816
      Location:6611028
      FAM178; Family of unknown function, FAM178
    2. NM_001243770.2NP_001230699.1  SMC5-SMC6 complex localization factor protein 2 isoform 3

      See identical proteins and their annotated locations for NP_001230699.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) is unspliced, lacks a large portion of the coding region and differs in the 3' UTR, compared to variant 1. The encoded isoform (3) is significantly shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AA829402, AF460991, BC073832
      Consensus CDS
      CCDS65918.1
      UniProtKB/Swiss-Prot
      Q8IX21
      Related
      ENSP00000476379.1, ENST00000609386.1
    3. NM_018121.4NP_060591.3  SMC5-SMC6 complex localization factor protein 2 isoform 1

      See identical proteins and their annotated locations for NP_060591.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes isoform (1).
      Source sequence(s)
      AF460991, AI282394, BC030565
      Consensus CDS
      CCDS7500.1
      UniProtKB/Swiss-Prot
      A8K950, B1AL17, Q5W0L8, Q6GMU6, Q8IX21, Q9NPE8
      Related
      ENSP00000238961.3, ENST00000238961.9
      Conserved Domains (1) summary
      pfam14816
      Location:6611028
      FAM178; Family of unknown function, FAM178

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    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
      100912963..100965134
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047425461.1XP_047281417.1  SMC5-SMC6 complex localization factor protein 2 isoform X2

    2. XM_047425462.1XP_047281418.1  SMC5-SMC6 complex localization factor protein 2 isoform X3

    3. XM_011539944.4XP_011538246.1  SMC5-SMC6 complex localization factor protein 2 isoform X2

      Conserved Domains (1) summary
      pfam14816
      Location:597964
      FAM178; Family of unknown function, FAM178
    4. XM_005269965.3XP_005270022.1  SMC5-SMC6 complex localization factor protein 2 isoform X1

      Conserved Domains (1) summary
      pfam14816
      Location:6601027
      FAM178; Family of unknown function, FAM178
    5. XM_047425463.1XP_047281419.1  SMC5-SMC6 complex localization factor protein 2 isoform X4

      UniProtKB/TrEMBL
      B1AL16

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      101792183..101848510
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054366272.1XP_054222247.1  SMC5-SMC6 complex localization factor protein 2 isoform X2

    2. XM_054366274.1XP_054222249.1  SMC5-SMC6 complex localization factor protein 2 isoform X3

    3. XM_054366273.1XP_054222248.1  SMC5-SMC6 complex localization factor protein 2 isoform X2

    4. XM_054366271.1XP_054222246.1  SMC5-SMC6 complex localization factor protein 2 isoform X1

    5. XM_054366275.1XP_054222250.1  SMC5-SMC6 complex localization factor protein 2 isoform X4

      UniProtKB/TrEMBL
      B1AL16

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_144592.1: Suppressed sequence

      Description
      NM_144592.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript, and the CDS was partial.