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

Gene ID: 55719, updated on 5-Aug-2022

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
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
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Genomic context

See SLF2 in Genome Data Viewer
Location:
10q24.31
Exon count:
21
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (100912963..100965134)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (101796334..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 paired box 2 Neighboring gene VISTA enhancer hs229 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:102649745-102650944 Neighboring gene Sharpr-MPRA regulatory region 3697 Neighboring gene semaphorin 4G Neighboring gene microRNA 608

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

Homology

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
part_of Smc5-Smc6 complex IC
Inferred by Curator
more info
PubMed 
located_in chromatin IDA
Inferred from Direct Assay
more info
PubMed 
located_in chromosome, telomeric region IC
Inferred by Curator
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
PubMed 
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
PubMed 
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)

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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_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
    Q8IX21, Q9NPE8
    Related
    ENSP00000238961.3, ENST00000238961.9
    Conserved Domains (1) summary
    pfam14816
    Location:6611028
    FAM178; Family of unknown function, FAM178

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    101796334..101848510
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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.