Fancl (FA complementation group L) - Rat Genome Database

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Gene: Fancl (FA complementation group L) Rattus norvegicus
Analyze
Symbol: Fancl
Name: FA complementation group L
RGD ID: 1311427
Description: Predicted to enable ubiquitin protein ligase activity and ubiquitin protein ligase binding activity. Predicted to be involved in DNA repair and protein monoubiquitination. Predicted to act upstream of or within gamete generation and regulation of cell population proliferation. Predicted to be located in chromatin; nuclear body; and nuclear envelope. Predicted to be part of Fanconi anaemia nuclear complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in Fanconi anemia complementation group L. Orthologous to human FANCL (FA complementation group L); PARTICIPATES IN ubiquitin/proteasome degradation pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; amitrole.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: E3 ubiquitin-protein ligase FANCL; Fanconi anemia, complementation group L; LOC305600
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr814104,449,403 - 104,515,297 (+)NCBIGRCr8
mRatBN7.214100,249,733 - 100,317,958 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl14100,248,875 - 100,314,255 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx14104,569,751 - 104,647,120 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.014105,813,840 - 105,891,206 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.014102,285,669 - 102,363,036 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.014110,675,306 - 110,740,880 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl14110,676,090 - 110,740,317 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.014110,368,478 - 110,433,487 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.414107,211,448 - 107,276,828 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.114107,230,315 - 107,299,602 (+)NCBI
Celera1499,184,205 - 99,249,128 (+)NCBICelera
Cytogenetic Map14q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Downregulation of Fanconi anemia genes in sporadic head and neck squamous cell carcinoma. Wreesmann VB, etal., ORL J Otorhinolaryngol Relat Spec. 2007;69(4):218-25. Epub 2007 Apr 4.
Additional References at PubMed
PMID:12417526   PMID:12574169   PMID:16916645   PMID:17938197   PMID:19111657   PMID:19589784   PMID:20347428   PMID:21229326   PMID:22343915   PMID:24389026  


Genomics

Comparative Map Data
Fancl
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr814104,449,403 - 104,515,297 (+)NCBIGRCr8
mRatBN7.214100,249,733 - 100,317,958 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl14100,248,875 - 100,314,255 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx14104,569,751 - 104,647,120 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.014105,813,840 - 105,891,206 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.014102,285,669 - 102,363,036 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.014110,675,306 - 110,740,880 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl14110,676,090 - 110,740,317 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.014110,368,478 - 110,433,487 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.414107,211,448 - 107,276,828 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.114107,230,315 - 107,299,602 (+)NCBI
Celera1499,184,205 - 99,249,128 (+)NCBICelera
Cytogenetic Map14q22NCBI
FANCL
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38258,159,243 - 58,241,380 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl258,159,243 - 58,241,410 (-)EnsemblGRCh38hg38GRCh38
GRCh37258,386,382 - 58,468,460 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36258,239,882 - 58,322,018 (-)NCBINCBI36Build 36hg18NCBI36
Build 34258,298,030 - 58,380,165NCBI
Celera258,229,548 - 58,311,691 (-)NCBICelera
Cytogenetic Map2p16.1NCBI
HuRef258,127,658 - 58,209,806 (-)NCBIHuRef
CHM1_1258,316,641 - 58,398,744 (-)NCBICHM1_1
T2T-CHM13v2.0258,164,077 - 58,246,209 (-)NCBIT2T-CHM13v2.0
Fancl
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391126,337,084 - 26,421,883 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1126,336,135 - 26,421,876 (+)EnsemblGRCm39 Ensembl
GRCm381126,387,084 - 26,471,883 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1126,386,135 - 26,471,876 (+)EnsemblGRCm38mm10GRCm38
MGSCv371126,287,084 - 26,371,876 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361126,287,084 - 26,371,876 (+)NCBIMGSCv36mm8
Celera1128,994,935 - 29,000,755 (-)NCBICelera
Cytogenetic Map11A3.3NCBI
cM Map1115.85NCBI
Fancl
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542425,251,689 - 25,307,180 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542425,251,701 - 25,307,236 (+)NCBIChiLan1.0ChiLan1.0
FANCL
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21268,116,184 - 68,198,583 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A68,120,135 - 68,202,535 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A58,270,620 - 58,353,001 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A59,417,463 - 59,499,863 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A59,418,265 - 59,499,496 (-)Ensemblpanpan1.1panPan2
FANCL
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11058,521,480 - 58,637,352 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1058,521,552 - 58,637,482 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1058,474,427 - 58,590,338 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01059,525,256 - 59,641,260 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1059,525,317 - 59,636,793 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11059,221,915 - 59,337,621 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01059,506,524 - 59,622,215 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01059,798,922 - 59,915,100 (-)NCBIUU_Cfam_GSD_1.0
Fancl
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629224,451,294 - 24,543,595 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364914,029,388 - 4,119,976 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364914,057,312 - 4,119,966 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FANCL
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl383,337,253 - 83,436,942 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1383,136,355 - 83,436,948 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2387,936,631 - 88,021,151 (+)NCBISscrofa10.2Sscrofa10.2susScr3
FANCL
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11448,725,447 - 48,803,892 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1448,725,541 - 48,805,356 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604562,939,983 - 63,017,950 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Fancl
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248333,603,383 - 3,663,572 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248333,603,712 - 3,692,540 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Fancl
459 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:291
Count of miRNA genes:196
Interacting mature miRNAs:230
Transcripts:ENSRNOT00000029513
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1458184885103184885Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1455624247100624247Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1456631369101631369Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1470053989104886043Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1455624247100624247Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1470053989104886043Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000029513   ⟹   ENSRNOP00000036801
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl14100,248,875 - 100,314,255 (+)Ensembl
Rnor_6.0 Ensembl14110,676,090 - 110,740,317 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000102802   ⟹   ENSRNOP00000082519
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl14100,248,875 - 100,314,255 (+)Ensembl
RefSeq Acc Id: NM_001191684   ⟹   NP_001178613
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814104,450,987 - 104,515,297 (+)NCBI
mRatBN7.214100,249,945 - 100,314,255 (+)NCBI
Rnor_6.014110,676,090 - 110,740,317 (+)NCBI
Rnor_5.014110,368,478 - 110,433,487 (+)NCBI
Celera1499,184,205 - 99,249,128 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006251597   ⟹   XP_006251659
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814104,449,803 - 104,515,293 (+)NCBI
mRatBN7.214100,249,733 - 100,317,958 (+)NCBI
Rnor_6.014110,675,306 - 110,740,880 (+)NCBI
Rnor_5.014110,368,478 - 110,433,487 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039092113   ⟹   XP_038948041
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814104,449,803 - 104,515,293 (+)NCBI
mRatBN7.214100,249,930 - 100,317,958 (+)NCBI
RefSeq Acc Id: XM_039092114   ⟹   XP_038948042
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814104,449,403 - 104,483,988 (+)NCBI
mRatBN7.214100,249,733 - 100,282,946 (+)NCBI
RefSeq Acc Id: XM_063273281   ⟹   XP_063129351
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814104,449,802 - 104,478,410 (+)NCBI
RefSeq Acc Id: NP_001178613   ⟸   NM_001191684
- UniProtKB: D3ZAU3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006251659   ⟸   XM_006251597
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZUP0 (UniProtKB/TrEMBL),   D3ZAU3 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000036801   ⟸   ENSRNOT00000029513
RefSeq Acc Id: XP_038948042   ⟸   XM_039092114
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038948041   ⟸   XM_039092113
- Peptide Label: isoform X3
Ensembl Acc Id: ENSRNOP00000082519   ⟸   ENSRNOT00000102802
RefSeq Acc Id: XP_063129351   ⟸   XM_063273281
- Peptide Label: isoform X4
Protein Domains
RING-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZAU3-F1-model_v2 AlphaFold D3ZAU3 1-375 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13699527
Promoter ID:EPDNEW_R10051
Type:single initiation site
Name:Fancl_1
Description:Fanconi anemia, complementation group L
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.014110,676,079 - 110,676,139EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311427 AgrOrtholog
BioCyc Gene G2FUF-14723 BioCyc
Ensembl Genes ENSRNOG00000027249 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000029513.6 UniProtKB/TrEMBL
  ENSRNOT00000102802.1 UniProtKB/TrEMBL
Gene3D-CATH 3.10.110.10 UniProtKB/TrEMBL
  3.10.110.20 UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/TrEMBL
InterPro Fancl UniProtKB/TrEMBL
  FANCL_C UniProtKB/TrEMBL
  FANCL_d2 UniProtKB/TrEMBL
  FANCL_d3 UniProtKB/TrEMBL
  FancL_N UniProtKB/TrEMBL
  Fanconi_anemia_FancL_WD-rpt UniProtKB/TrEMBL
  UBQ-conjugating_enzyme/RWD UniProtKB/TrEMBL
  Znf_RING UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
NCBI Gene 305600 ENTREZGENE
PANTHER E3 UBIQUITIN-PROTEIN LIGASE FANCL UniProtKB/TrEMBL
  PTHR13206 UniProtKB/TrEMBL
Pfam FANCL_C UniProtKB/TrEMBL
  FANCL_d2 UniProtKB/TrEMBL
  FANCL_d3 UniProtKB/TrEMBL
  WD-3 UniProtKB/TrEMBL
PhenoGen Fancl PhenoGen
PROSITE ZF_RING_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000027249 RatGTEx
SMART FANCL_C UniProtKB/TrEMBL
Superfamily-SCOP RING/U-box UniProtKB/TrEMBL
UniProt A0A8I5ZUP0 ENTREZGENE, UniProtKB/TrEMBL
  D3ZAU3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-05-25 Fancl  FA complementation group L  Fancl  Fanconi anemia, complementation group L  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Fancl  Fanconi anemia, complementation group L   Fancl_predicted  Fanconi anemia, complementation group L (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Fancl_predicted  Fanconi anemia, complementation group L (predicted)      Symbol and Name status set to approved 70820 APPROVED