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FANCL Gene

protein-coding   GIFtS: 62

GC02M058298
Fanconi anemia, complementation group L
(Previous name: PHD finger protein 9 )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: PHF9)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section

Aliases
EC 6.3.2.- 3
FAAP43 2, 3
FLJ10335 1, 2
PHF9 2, 3, 5
POG 2
Descriptions
Fanconi anemia group L protein 3
Fanconi anemia, complementation group L 2
Fanconi anemia-associated polypeptide of 43 kDa 3
PHD finger protein 9 1, 2
External Ids
HGNC: 207481
Entrez Gene: 551202
UniProtKB: Q9NW383
Ensembl: ENSG000001153927
Search outside databases for aliases for FANCL gene

Previous GC identifers: GC00U912964 GC02M058360

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

EntrezGene summary for FANCL:
The Fanconi anemia complementation group (FANC) currently includes FANCA, FANCB, FANCC, FANCD1
(also called BRCA2), FANCD2, FANCE, FANCF, FANCG, FANCI, FANCJ (also called BRIP1), FANCL, FANCM
and FANCN (also called PALB2). The previously defined group FANCH is the same as FANCA. Fanconi
anemia is a genetically heterogeneous recessive disorder characterized by cytogenetic instability,
hypersensitivity to DNA crosslinking agents, increased chromosomal breakage, and defective DNA
repair. The members of the Fanconi anemia complementation group do not share sequence similarity;
they are related by their assembly into a common nuclear protein complex. This gene encodes the
protein for complementation group L. Alternative splicing results in two transcript variants
encoding different isoforms. [provided by RefSeq]

UniProtKB/Swiss-Prot: FANCL_HUMAN, Q9NW38
Function: Ubiquitin ligase protein that mediates ubiquitination of FANCD2, a key step in the DNA
damage pathway. May be required for proper primordial germ cell proliferation in the embryonic
stage, whereas it is probably not needed for spermatogonial proliferation after birth

Gene Wiki entry for FANCL

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the FANCL gene  

Entrez Gene cytogenetic band: 2p16.1   Ensembl cytogenetic band:  2p16.1   HGNC cytogenetic band: 2p16.1

FANCL Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M058298:     (about GC identifiers)

Start:
58,239,882 bp from pter
End:
58,322,018 bp from pter
Size:
82,137 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000002.10  NT_022184.14  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
About This Section

UniProtKB/Swiss-Prot: FANCL_HUMAN, Q9NW38 (See protein sequence)
Recommended Name: E3 ubiquitin-protein ligase FANCL  
Size: 375 amino acids; 42905 Da
Subunit: Interacts with GGN (By similarity). Belongs to the multisubunit FA complex composed of
FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL/PHF9 and FANCM. The complex is not found in FA
patients
Subcellular location: Cytoplasm. Nucleus
Caution: Although PubMed:12724401 reports that it contains a PHD-type zinc finger, it contains a
RING-type zinc finger. Moreover, PHD-type zinc fingers do not have any ubiquitin ligase activity
Secondary accessions: Q6GU60

REFSEQ proteins (2 alternative transcripts): 
NP_001108108.1  NP_060532.2  


ENSEMBL proteins: 
ENSP00000233741 ENSP00000386097 ENSP00000385021 ENSP00000384046 


Human Recombinant Proteins 
Browse Drug Discovery Central at Invitrogen for human recombinant proteins
Browse Purified and Recombinant Proteins at Millipore
Browse Human Recombinant Proteins at Sigma-Aldrich  
Browse R&D Systems for human recombinant proteins
Browse recombinant and purified proteins available from Enzo Life Sciences
Recombinant Proteins from Abcam (FANCL)
Human Recombinant Proteins from Abnova (FANCL)
                Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

2 Gene Ontology (GO) cellular component terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0005634 nucleus IEA--
GO:0005737 cytoplasm IEA--
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Antibodies for FANCL: 
Browse Antibodies Central at Invitrogen
Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
Sigma-Aldrich Antibodies for FANCL
Browse R&D Systems for Antibodies
Antibodies from Abcam (FANCL), each with their AbpromiseSM
Monoclonal and Polyclonal Antibodies from Abnova (FANCL)
Novus Biologicals Antibodies for FANCL

Assays for FANCL: 
Browse Invitrogen for biochemical assays
Browse Kits and Assays available from Millipore
Browse R&D Systems for biochemical assays
Browse biochemical assays available from Enzo Life Sciences

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

3 InterPro domains/families:
 IPR017907 Znf_RING_CS
 IPR001841 Znf_RING
 IPR019162 Fanconi_anemia_FancL_WD-rpt


   GeneDecks  FANCL for the domains selected above  
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Graphical View of Domain Structure for InterPro Entry Q9NW38

ProtoNet protein and cluster: Q9NW38

1 Blocks protein family: IPB001841 Zn-finger

UniProtKB/Swiss-Prot: FANCL_HUMAN, Q9NW38
Similarity: Contains 1 RING-type zinc finger

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
About This Section

Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (FANCL)
Browse for Gene Knock-down Tools from Millipore
Browse Abnova for Chimera RNAi Products
               OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_001114636

              Applied Biosystems Silencer® siRNAs for FANCL

              Sigma-Aldrich siRNA and siRNA Panels for FANCL  
                     Sigma-Aldrich shRNA Panels and shRNA for FANCL  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Clones:Invitrogen Clones for FANCL
Browse Clones for the Expression of Recombinant Proteins Available from Millipore
               OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): NM_001114636
                                 Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_001114636
                                 untagged cDNA clones in CMV expression vector (see all 2): NM_001114636 

Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
              OriGene genome-wide validated SYBR primer pairs: NM_001114636

UniProtKB/Swiss-Prot: FANCL_HUMAN, Q9NW38
Function: Ubiquitin ligase protein that mediates ubiquitination of FANCD2, a key step in the DNA
damage pathway. May be required for proper primordial germ cell proliferation in the embryonic
stage, whereas it is probably not needed for spermatogonial proliferation after birth
Enzyme Number (IUBMB): EC 6.3.2.- 

6 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Fancl):

embryogenesisendocrine/exocrine glandgrowth/sizehomeostasis/metabolismlethality-prenatal/perinatal
reproductive system

4 Gene Ontology (GO) molecular function terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0005515 protein binding IEA--
GO:0008270 zinc ion binding IEA--
GO:0016874 ligase activity IEA--
GO:0046872 metal ion binding IEA--
About this table

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
About This Section

3 Invitrogen iPath™ Online BioAtlas - Pathways for FANCL (Maps provided by GeneGo):
 ATM/ATR regulation of G1/S checkpoint
 Role of Brca1 and Brca2 in DNA repair
 ATM/ATR regulation of G2/M checkpoint

   GeneDecks  FANCL for the pathways selected above  
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3 Millipore Pathways for FANCL
 DNA damage ATM/ATR regulation of G1/S checkpoint
 Meiosis
 DNA damage Role of Brca1 and Brca2 in DNA repair

   GeneDecks  FANCL for the pathways selected above  
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1 Kegg Pathway  (Kegg details for FANCL):
 hsa04120 Ubiquitin mediated proteolysis

   GeneDecks  FANCL for the pathways selected above  
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UniProtKB/Swiss-Prot: FANCL_HUMAN, Q9NW38
Pathway: Protein modification; protein ubiquitination

 Gene Network CentralTM Interacting Genes and Proteins Network for  FANCL 


5/50 Interacting proteins for FANCL (Q9NW382 ENSP000002337413) via UniProtKB, MINT, and/or STRING (see all 50 )

InteractantInteraction Details
GeneCardExternal ID(s)
C17orf70Q0VG062, ENSP000003332833MINT-4789189 MINT-4789279 MINT-4789226 MINT-4789371 MINT-4789325 STRING (score=.963)
FANCBQ8NB912, ENSP000003268193MINT-4789189 MINT-4789279 MINT-4789226 MINT-4789371 STRING (score=.901)
FANCAO153602, ENSP000003739523MINT-4789189 MINT-4789226 MINT-4789325 STRING (score=.999)
FANCGO152872, ENSP000003679103MINT-4789189 MINT-4789226 MINT-4789325 STRING (score=.998)
FANCMQ8IYD82, ENSP000002674303MINT-4789189 MINT-4789279 MINT-4789226 STRING (score=.954)
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3 Gene Ontology (GO) biological process terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0006281 DNA repair IEA--
GO:0006974 response to DNA damage stimulus IEA--
GO:0019941 modification-dependent protein catabolic process IEA--
About this table
(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse drugs & compounds from Enzo Life Sciences
Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for FANCL

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section

Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (FANCL)
Browse for Gene Knock-down Tools from Millipore
Browse Abnova for Chimera RNAi Products
               OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_001114636

              Sigma-Aldrich siRNA and siRNA Panels for FANCL  
                     Sigma-Aldrich shRNA Panels and shRNA for FANCL  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Applied Biosystems Silencer® siRNAs: 

NM_001114636  NM_018062  

REFSEQ mRNAs for FANCL gene (2 alternative transcripts): 

NM_001114636.1   NM_018062.3   

Applied Biosystems TaqMan ® Gene Expression Assays: 

NM_001114636  NM_018062  

               OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): NM_001114636
                                 Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_001114636
                                 untagged cDNA clones in CMV expression vector (see all 2): NM_001114636 

Additional cDNA sequence: 

AK001197.1 AK225147.1 AK297736.1 AK309671.1 BC009042.1 BC037570.1 BC041627.1 BC054517.1 
CR594145.1 CR597729.1 

18 DOTS entries:

DT.75182666  DT.448234  DT.92387226  DT.120965414  DT.92440954  DT.100783920  DT.70103087  DT.86852791 
DT.92440947  DT.95279769  DT.100689663  DT.100783923  DT.120965399  DT.100026572  DT.100035558  DT.448235 
DT.92440943  DT.92440944 

24/129 AceView cDNA sequences (see all 129 ):

AA258135 CD105578 BC037570 CR594145 AU126989 AL043470 CA841300 AA258395 
AU132311 BP373332 AK001197 AA280291 BM786985 AW572256 BU156193 BU676880 
BX444601 BU621773 NM_018062 AI342480 BC054517 CB156727 CF529786 BI916786 

highest scoring ESTs for FANCL:

AL036481 AA232116 AK001197 AL043470 AU123628 AU126989 AU132311 AU133843 BC009042 BC037570 

Unigene Cluster for FANCL:

Fanconi anemia, complementation group L
Hs.631890  [show with all ESTs]
Unigene Representative Sequence: BC037570


GeneLoc Exon Structure

4 Ensembl transcripts including schematic representations:
ENST00000233741  ENST00000403295  ENST00000402135  ENST00000403676  
(Experimental results according to 1GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
About This Section

FANCL expression in normal and diseased human tissues

 Applied Biosystems TaqMan ® Gene Expression Assays for FANCL

1 / 2 / 3

4 probe-sets matching FANCL gene


Affymetrix
probe-set
Array  GeneAnnot data GeneNote data GeneTide data
# genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
33125_at2, 3 U95-A 1 1.00 1.00 0.93 1.15 AL043470 0.80 1.00 0.91 1

83634_at2, 3 U95-E 1 1.00 1.00 0.97 0.85 AL036481 1.00 1.00 1.00 1

218397_at2, 3 U133-A 1 1.00 1.00 -- -- NM_018062 0.60 1.00 0.82 1

218397_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
GeneDecks  FANCL for binary patterns associated with the probe-sets selected above  
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About this table    
Data from (Publications) and GNF BioGPS
    About these images
About these images

CGAP SAGE TAG: --

SOURCE GeneReport for Unigene cluster: Hs.631890

Expression variation in blood from EXPOLDB for FANCL

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section


Orthologs for FANCL gene from 5/10 species (see all 10 )
Organism Gene Locus Description Human
Similarity
NCBI accessions
dog
(Canis familiaris)
FANCL1   -- Fanconi anemia, complementation group L 91.38(n)
89.94(a)
612161  XM_849891.1  XP_854984.1 
chimpanzee
(Pan troglodytes)
FANCL1   -- Fanconi anemia, complementation group L 99.29(n)
99.2(a)
459251  XM_001157414.1  XP_001157414.1 
cow
(Bos taurus)
FANCL1   -- Fanconi anemia, complementation group L 90.44(n)
87.94(a)
614512  NM_001076332.1  NP_001069800.1 
rat
(Rattus norvegicus)
Fancl1   -- Fanconi anemia, complementation group L 82.53(n)
79.68(a)
305600  XM_223701.4  XP_223701.4 
mouse
(Mus musculus)
Fancl1, 5 115
Fanconi anemia, complementation group L1, 5 83.42(n)1
79.41(a)1
670301  NM_025923.21  NP_080199.11 
 AA1831875  AF5136195  (see all 18)
About this table        Species with no ortholog for FANCL

ENSEMBL Gene Tree for FANCL
(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section

  --
(According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section


10/385 NCBI SNPs in FANCL are shown (see all 385 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 134)
ABGenomic DataTranscription DataAllele Frequencies
SNP IDValidChr 2 posSequenceRecsAA
Chg
TypeMoreRecsAllele
freq
PopTotal
sample
More
------------
rs21926901,2
A,C,F,H58323846(-) AAAGTG/TTGGTG 1 -- ng319Minor allele frequency- T:0.13EU EA WA NA 2244
rs67352961,2
C,F,H58322264(+) TATTGA/TAAGAC 1 -- ng316Minor allele frequency- T:0.13MN EA EU WA 1670
rs43952401,2
F,H58323004(+) ACCTAG/CCAACA 1 -- ng314Minor allele frequency- C:0.18EU EA WA 418
rs360592571,2
C,F58284809(-) TGCTTC/TTGGTA 2 S/F mis15Minor allele frequency- T:0.00NA EU EA WA 470
rs8482911,2
C,F,H,O58242200(-) AATTCC/TCAGTG 2 S/S syn1 ese313Minor allele frequency- T:0.30EU EA WA NA 1158
rs14044601,2
A,C,F,H,O58284672(-) ATCTAA/GAAATA 1 -- int18Minor allele frequency- G:0.21MN EU EA WA NA 744
rs20983441,2
A,C,F,H,O58267255(-) AAGCCA/GGAAAA 1 -- int116Minor allele frequency- N:0.00EU EA WA NA 1470
rs7682981,2
A,C,F,H,O58264476(-) CCAACA/GTAGTC 1 -- int121Minor allele frequency- G:0.49NA NS EU EA WA 1588
rs14044591,2
A,C,F,O58284914(-) CCCCTC/GTCCAG 1 -- int1 trp32Minor allele frequency- G:0.22MN EA 1470
rs37712161,2
A,C,F,H58265344(+) TCTTAT/CAGGAA 1 -- int19Minor allele frequency- C:0.50EA EU WA 2322
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HapMap Linkage Disequilibrium images for FANCL (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, Novoseek, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
About This Section

OMIM: 608111

UniProtKB/Swiss-Prot: FANCL_HUMAN, Q9NW38

  • Defects in FANCL are a cause of Fanconi anemia (FA) [MIM:227650]. FA is a genetically
    heterogeneous, autosomal recessive disorder characterized by progressive pancytopenia, a diverse
    assortment of congenital malformations, and a predisposition to the development of malignancies.
    At the cellular level it is associated with hypersensitivity to DNA-damaging agents, chromosomal
    instability (increased chromosome breakage), and defective DNA repair
  • 2 Novoseek disease relationships for FANCL gene

    Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    fanconis anemia 94.11 2 16916645 (1), 16116424 (1)
    hnscc 57.19 2 17409780 (1), 16466850 (1)
    About this table

    GeneTests: FANCL
    Fanconi Anemia

    Human Gene Mutation Database: FANCL
    Human Genome Epidemiology Navigator: FANCL (2 documents)

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

    (in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
    About This Section

    10/34 PubMed articles for FANCL gene (see all 34 ):
    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section

     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)
    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
    About This Section

    Entrez Gene: 55120 HGNC: 20748 AceView: FANCL Ensembl:ENSG00000115392 euGenes: HUgn55120
    ECgene: FANCL H-InvDB: FANCL
    (According to HUGE)
    About This Section

      --
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

    NameDescription
    ATLAS Chromosomes in Cancer entry for FANCL Genetics and Cytogenetics in Oncology and Haematology
    Fanconi Anemia Mutation Databasehttp://www.rockefeller.edu/fanconi/mutate/jumpl.html
    GeneReviewshttp://www.genetests.org/query?gene=FANCL
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for FANCL:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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     Predesigned and custom siRNAs for FANCL Antibodies for FANCL
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
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     "Your Favorite Gene" Pathwaysfeedback


      
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     Antibodies for FANCL

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