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

Gene ID: 55719, updated on 24-Nov-2020

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
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
Expression
Broad expression in testis (RPKM 12.5), ovary (RPKM 7.5) and 24 other tissues See more
Orthologs

Genomic context

See SLF2 in Genome Data Viewer
Location:
10q24.31
Exon count:
21
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) 10 NC_000010.11 (100909416..100965134)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (102672326..102724891)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene paired box 2 Neighboring gene VISTA enhancer hs229 Neighboring gene Sharpr-MPRA regulatory region 13917 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

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
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein-containing complex binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin protein ligase binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
chromatin IDA
Inferred from Direct Assay
more info
PubMed 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
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)

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

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20201120

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p13 Primary Assembly

    Range
    100909416..100965134
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Conserved Domains (1) summary
    pfam14816
    Location:597964
    FAM178; Family of unknown function, FAM178
  2. 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

RNA

  1. XR_001747138.1 RNA Sequence

    Related
    ENST00000649226.1

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.
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