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FANCL FA complementation group L [ Homo sapiens (human) ]

Gene ID: 55120, updated on 5-Aug-2018

Summary

Official Symbol
FANCLprovided by HGNC
Official Full Name
FA complementation group Lprovided by HGNC
Primary source
HGNC:HGNC:20748
See related
Ensembl:ENSG00000115392 MIM:608111; Vega:OTTHUMG00000129349
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
POG; PHF9; FAAP43
Summary
This gene encodes a ubiquitin ligase that is a member of the Fanconi anemia complementation group (FANC). Members of this group are related by their assembly into a common nuclear protein complex rather than by sequence similarity. This gene encodes the protein for complementation group L that mediates monoubiquitination of FANCD2 as well as FANCI. Fanconi anemia is a genetically heterogeneous recessive disorder characterized by cytogenetic instability, hypersensitivity to DNA crosslinking agents, increased chromosomal breakage, and defective DNA repair. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2018]
Expression
Ubiquitous expression in adrenal (RPKM 16.9), testis (RPKM 12.0) and 25 other tissues See more
Orthologs

Genomic context

See FANCL in Genome Data Viewer
Location:
2p16.1
Exon count:
15
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (58159243..58241681, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (58386378..58468515, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene VRK serine/threonine kinase 2 Neighboring gene formin-2-like Neighboring gene VRK2 intron CAGE-defined low expression enhancer Neighboring gene eukaryotic translation initiation factor 3 subunit F pseudogene 3 Neighboring gene long intergenic non-protein coding RNA 1795

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index.
NHGRI GWA Catalog
Biological insights from 108 schizophrenia-associated genetic loci.
NHGRI GWA Catalog
Genetic determinants of common epilepsies: a meta-analysis of genome-wide association studies.
NHGRI GWA Catalog
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
NHGRI GWA Catalog

Pathways from BioSystems

  • BARD1 signaling events, organism-specific biosystem (from Pathway Interaction Database)
    BARD1 signaling events, organism-specific biosystem
    BARD1 signaling events
  • DNA Repair, organism-specific biosystem (from REACTOME)
    DNA Repair, organism-specific biosystemDNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. Living organisms are constantly exposed to harmful metabolic by-products, enviro...
  • FA core complex, organism-specific biosystem (from KEGG)
    FA core complex, organism-specific biosystemStructural complex; Genetic information processing; Repair system
  • FA core complex, conserved biosystem (from KEGG)
    FA core complex, conserved biosystemStructural complex; Genetic information processing; Repair system
  • Fanconi Anemia Pathway, organism-specific biosystem (from REACTOME)
    Fanconi Anemia Pathway, organism-specific biosystemFanconi anemia (FA) is a genetic disease of genome instability characterized by congenital skeletal defects, aplastic anemia, susceptibility to leukemias, and cellular sensitivity to DNA damaging age...
  • Fanconi anemia pathway, organism-specific biosystem (from KEGG)
    Fanconi anemia pathway, organism-specific biosystemThe Fanconi anemia pathway is required for the efficient repair of damaged DNA, especially interstrand cross-links (ICLs). DNA ICL is directly recognized by FANCM and associated proteins, that recrui...
  • Fanconi anemia pathway, conserved biosystem (from KEGG)
    Fanconi anemia pathway, conserved biosystemThe Fanconi anemia pathway is required for the efficient repair of damaged DNA, especially interstrand cross-links (ICLs). DNA ICL is directly recognized by FANCM and associated proteins, that recrui...
  • Ubiquitin mediated proteolysis, organism-specific biosystem (from KEGG)
    Ubiquitin mediated proteolysis, organism-specific biosystemProtein ubiquitination plays an important role in eukaryotic cellular processes. It mainly functions as a signal for 26S proteasome dependent protein degradation. The addition of ubiquitin to protein...
  • Ubiquitin mediated proteolysis, conserved biosystem (from KEGG)
    Ubiquitin mediated proteolysis, conserved biosystemProtein ubiquitination plays an important role in eukaryotic cellular processes. It mainly functions as a signal for 26S proteasome dependent protein degradation. The addition of ubiquitin to protein...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ10335

Gene Ontology Provided by GOA

Function Evidence Code Pubs
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin protein ligase activity IDA
Inferred from Direct Assay
more info
PubMed 
ubiquitin protein ligase binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin-protein transferase activity IDA
Inferred from Direct Assay
more info
PubMed 
ubiquitin-protein transferase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
DNA repair IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to DNA damage stimulus IMP
Inferred from Mutant Phenotype
more info
PubMed 
gamete generation IEA
Inferred from Electronic Annotation
more info
 
interstrand cross-link repair TAS
Traceable Author Statement
more info
 
protein monoubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
regulation of cell proliferation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Fanconi anaemia nuclear complex IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
nuclear body IDA
Inferred from Direct Assay
more info
 
nuclear envelope IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
E3 ubiquitin-protein ligase FANCL
Names
Fanconi anemia complementation group L
PHD finger protein 9
RING-type E3 ubiquitin transferase FANCL
fanconi anemia group L protein
fanconi anemia-associated polypeptide of 43 kDa
NP_001108108.1
NP_060532.2
XP_005264452.1
XP_005264454.1
XP_011531241.1
XP_011531242.1
XP_011531243.1
XP_011531244.1
XP_011531246.1
XP_011531247.1
XP_016859903.1
XP_016859904.1
XP_016859905.1

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.

Genomic

  1. NG_007418.1 RefSeqGene

    Range
    5000..87137
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_501

mRNA and Protein(s)

  1. NM_001114636.1NP_001108108.1  E3 ubiquitin-protein ligase FANCL isoform 1

    See identical proteins and their annotated locations for NP_001108108.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AK001197, AK225147, BC041627, DB032206
    Consensus CDS
    CCDS46294.1
    UniProtKB/Swiss-Prot
    Q9NW38
    Related
    ENSP00000385021.3, OTTHUMP00000201190, ENST00000402135.7, OTTHUMT00000325254
    Conserved Domains (2) summary
    pfam09765
    Location:15300
    WD-3; WD-repeat region
    pfam11793
    Location:308376
    FANCL_C; FANCL C-terminal domain
  2. NM_018062.3NP_060532.2  E3 ubiquitin-protein ligase FANCL isoform 2

    See identical proteins and their annotated locations for NP_060532.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has an alternate splice site in the CDS, as compared to variant 1. The resulting isoform (2) lacks an internal segment and has identical N- and C-termini, as compared to isoform 1.
    Source sequence(s)
    AK001197, AK225147, BC009042, DB032206
    Consensus CDS
    CCDS1860.1
    UniProtKB/Swiss-Prot
    Q9NW38
    Related
    ENSP00000233741.4, OTTHUMP00000159703, ENST00000233741.8, OTTHUMT00000251497
    Conserved Domains (2) summary
    pfam09765
    Location:15295
    WD-3; WD-repeat region
    pfam11793
    Location:303371
    FANCL_C; FANCL C-terminal domain

RNA

  1. NR_156742.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks four consecutive internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC007250

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    58159243..58241681 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005264397.4XP_005264454.1  E3 ubiquitin-protein ligase FANCL isoform X11

    UniProtKB/TrEMBL
    B5MCZ6
    Related
    ENSP00000384046.1, OTTHUMP00000201194, ENST00000403676.5, OTTHUMT00000325258
    Conserved Domains (2) summary
    pfam09765
    Location:8178
    WD-3; WD-repeat region
    pfam11793
    Location:186254
    FANCL_C; FANCL C-terminal domain
  2. XM_017004416.1XP_016859905.1  E3 ubiquitin-protein ligase FANCL isoform X10

  3. XM_017004414.2XP_016859903.1  E3 ubiquitin-protein ligase FANCL isoform X4

  4. XM_011532940.3XP_011531242.1  E3 ubiquitin-protein ligase FANCL isoform X2

    Conserved Domains (2) summary
    pfam09765
    Location:15310
    WD-3; WD-repeat region
    pfam11793
    Location:318379
    FANCL_C; FANCL C-terminal domain
  5. XM_011532942.3XP_011531244.1  E3 ubiquitin-protein ligase FANCL isoform X5

    Conserved Domains (2) summary
    pfam09765
    Location:15300
    WD-3; WD-repeat region
    pfam11793
    Location:308369
    FANCL_C; FANCL C-terminal domain
  6. XM_011532941.2XP_011531243.1  E3 ubiquitin-protein ligase FANCL isoform X3

    Conserved Domains (2) summary
    pfam09765
    Location:15315
    WD-3; WD-repeat region
    pfam11793
    Location:323391
    FANCL_C; FANCL C-terminal domain
  7. XM_011532939.3XP_011531241.1  E3 ubiquitin-protein ligase FANCL isoform X1

    Conserved Domains (2) summary
    pfam09765
    Location:15315
    WD-3; WD-repeat region
    pfam11793
    Location:323384
    FANCL_C; FANCL C-terminal domain
  8. XM_011532945.2XP_011531247.1  E3 ubiquitin-protein ligase FANCL isoform X9

    Conserved Domains (2) summary
    pfam09765
    Location:8183
    WD-3; WD-repeat region
    pfam11793
    Location:191252
    FANCL_C; FANCL C-terminal domain
  9. XM_011532944.2XP_011531246.1  E3 ubiquitin-protein ligase FANCL isoform X8

    Conserved Domains (2) summary
    pfam09765
    Location:8198
    WD-3; WD-repeat region
    pfam11793
    Location:206267
    FANCL_C; FANCL C-terminal domain
  10. XM_005264395.4XP_005264452.1  E3 ubiquitin-protein ligase FANCL isoform X6

    Conserved Domains (2) summary
    pfam09765
    Location:15295
    WD-3; WD-repeat region
    pfam11793
    Location:303364
    FANCL_C; FANCL C-terminal domain
  11. XM_017004415.2XP_016859904.1  E3 ubiquitin-protein ligase FANCL isoform X7

RNA

  1. XR_002959309.1 RNA Sequence

  2. XR_001738803.2 RNA Sequence

  3. XR_001738802.2 RNA Sequence

  4. XR_939692.2 RNA Sequence

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