Nhlrc1 (NHL repeat containing 1) - Rat Genome Database

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Gene: Nhlrc1 (NHL repeat containing 1) Mus musculus
Analyze
Symbol: Nhlrc1
Name: NHL repeat containing 1
RGD ID: 1550145
MGI Page MGI
Description: Enables ubiquitin protein ligase activity. Involved in glycogen biosynthetic process. Acts upstream of or within several processes, including glycogen metabolic process; proteasome-mediated ubiquitin-dependent protein catabolic process; and regulation of protein modification process. Located in nucleus and perinuclear region of cytoplasm. Used to study Lafora disease. Orthologous to human NHLRC1 (NHL repeat containing E3 ubiquitin protein ligase 1).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: AI505271; B230309E09Rik; E3 ubiquitin-protein ligase NHLRC1; EPM2; EPM2B; M; malin; NHL repeat-containing protein 1; RING-type E3 ubiquitin transferase NHLRC1
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391347,166,033 - 47,168,326 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1347,166,033 - 47,168,326 (-)EnsemblGRCm39 Ensembl
GRCm381347,012,557 - 47,014,850 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1347,012,557 - 47,014,850 (-)EnsemblGRCm38mm10GRCm38
MGSCv371347,107,926 - 47,110,219 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361347,023,530 - 47,025,792 (-)NCBIMGSCv36mm8
Celera1348,097,798 - 48,100,082 (-)NCBICelera
Cytogenetic Map13A5NCBI
cM Map1324.5NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. MGDs mouse GO annotations MGD data from the GO Consortium
2. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. Mouse MP Annotation Import Pipeline RGD automated import pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12477932   PMID:12958597   PMID:15930137   PMID:16141072   PMID:16141073   PMID:16602821   PMID:17908927  
PMID:17952067   PMID:19036738   PMID:19529779   PMID:20538597   PMID:21077101   PMID:21267068   PMID:21873635   PMID:21882344   PMID:22186021   PMID:22186026   PMID:22361617   PMID:22487859  
PMID:22578008   PMID:22669944   PMID:23663739   PMID:24419970   PMID:24452334   PMID:24838580   PMID:24914213   PMID:25059425   PMID:25309313   PMID:25416783   PMID:25627694   PMID:26976331  
PMID:27041370   PMID:27107699   PMID:27975203   PMID:28063983   PMID:28181916   PMID:28536304   PMID:28619201   PMID:29408991   PMID:30152044   PMID:31042462   PMID:31108086   PMID:32785985  
PMID:32817315   PMID:33092303   PMID:33171226   PMID:34962634   PMID:36511140   PMID:36526090   PMID:36674605  


Genomics

Comparative Map Data
Nhlrc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391347,166,033 - 47,168,326 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1347,166,033 - 47,168,326 (-)EnsemblGRCm39 Ensembl
GRCm381347,012,557 - 47,014,850 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1347,012,557 - 47,014,850 (-)EnsemblGRCm38mm10GRCm38
MGSCv371347,107,926 - 47,110,219 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361347,023,530 - 47,025,792 (-)NCBIMGSCv36mm8
Celera1348,097,798 - 48,100,082 (-)NCBICelera
Cytogenetic Map13A5NCBI
cM Map1324.5NCBI
NHLRC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38618,120,440 - 18,122,677 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl618,120,440 - 18,122,677 (-)EnsemblGRCh38hg38GRCh38
GRCh37618,120,671 - 18,122,908 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36618,228,697 - 18,230,830 (-)NCBINCBI36Build 36hg18NCBI36
Build 34618,228,696 - 18,230,830NCBI
Celera619,358,725 - 19,360,858 (-)NCBICelera
Cytogenetic Map6p22.3NCBI
HuRef618,065,097 - 18,067,230 (-)NCBIHuRef
CHM1_1618,123,324 - 18,125,457 (-)NCBICHM1_1
T2T-CHM13v2.0617,992,610 - 17,994,847 (-)NCBIT2T-CHM13v2.0
Nhlrc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81717,880,570 - 17,883,411 (+)NCBIGRCr8
mRatBN7.21717,674,303 - 17,677,144 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1717,674,319 - 17,677,148 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1717,559,476 - 17,560,666 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01719,163,332 - 19,164,522 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01717,486,596 - 17,487,786 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01718,059,382 - 18,060,572 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1718,059,382 - 18,060,572 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01719,876,653 - 19,877,843 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41723,726,054 - 23,727,244 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11723,728,893 - 23,730,084 (+)NCBI
Celera1717,384,491 - 17,385,681 (+)NCBICelera
Cytogenetic Map17p14NCBI
Nhlrc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554838,078,796 - 8,079,612 (+)NCBIChiLan1.0ChiLan1.0
NHLRC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2532,779,957 - 32,782,581 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1628,765,169 - 28,767,840 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0617,969,146 - 17,970,962 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1618,321,603 - 18,322,965 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl618,321,728 - 18,322,915 (-)Ensemblpanpan1.1panPan2
NHLRC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13516,920,687 - 16,921,829 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3516,920,687 - 16,921,829 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3516,870,564 - 16,871,751 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03517,027,204 - 17,028,403 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3517,027,204 - 17,028,403 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13516,840,653 - 16,841,840 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03516,897,947 - 16,899,146 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03518,228,843 - 18,230,041 (-)NCBIUU_Cfam_GSD_1.0
Nhlrc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049467,837,346 - 7,838,742 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365523,892,372 - 3,893,559 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365523,891,350 - 3,893,566 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NHLRC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl713,816,246 - 13,817,644 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1713,816,243 - 13,817,644 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2714,558,596 - 14,559,640 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NHLRC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11754,017,947 - 54,020,015 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1754,018,703 - 54,019,887 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604418,345,896 - 18,348,172 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nhlrc1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247568,558,470 - 8,560,610 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nhlrc1
57 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:301
Count of miRNA genes:255
Interacting mature miRNAs:267
Transcripts:ENSMUST00000052747
Prediction methods:Miranda, Rnahybrid
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
26884393Humsd7_mhumerus midshaft diameter 7, 16 week (mouse)13395000076048119Mouse
1558898Hpi1_mhapatic PMN infiltration 1 (mouse)Not determined13441402553101640Mouse
1301880Hypt_mhypertension (mouse)Not determined131815679252156924Mouse
13463469Gssq1_mglomerulosclerosis severity QTL 1 (mouse)131906090853061050Mouse
12880423V25Dq7_mvitamin D inactive form serum level QTL 7 (mouse)131958398353583983Mouse
1301015Sysbp2_msystolic blood pressure 2 (mouse)Not determined132047761259821605Mouse
4142147Mvwf4_mmodifier of von Willebrand factor 4 (mouse)Not determined20477612112898424Mouse
1357591Tesq1_mtestis weight QTL 1 (mouse)Not determined132061551255720517Mouse
4142009Pregq3_mpregnancy QTL 3 (mouse)Not determined132061551272385189Mouse
10045618Heal17_mwound healing/regeneration 17 (mouse)Not determined132074693954747056Mouse
4142489Ath25_matherosclerosis 25 (mouse)Not determined2583652959836529Mouse
10401111Pgia40_mproteoglycan induced arthritis 40 (mouse)Not determined132791846961918560Mouse
1300710Pcd4ts2_mp-glycoprotein positive CD4 T cell subset 2 (mouse)Not determined132821044262210544Mouse
1357802Vtbt15_mvertebral trabecular bone trait 15 (mouse)Not determined132821737962217515Mouse
10045621Heal21_mwound healing/regeneration 21 (mouse)Not determined132821737962217515Mouse
10755533Chol18_mcholesterol 18 (mouse)133096946764969467Mouse
10755517Chol15_mcholesterol 15 (mouse)133096946764969467Mouse
12738439Twq4_mtestis weight QTL 4 (mouse)133112911065129110Mouse
14696729Kidlq2_mkidney weight, left QTL 2 (mouse)133134473665344736Mouse
1301299Sluc23_msusceptibility to lung cancer 23 (mouse)Not determined133492194368922081Mouse
10412235Scgq5_mspontaneous crescentic glomerulonephritis QTL 5 (mouse)Not determined133606090896239162Mouse
1357587Pfat3_mpredicted fat percentage 3 (mouse)Not determined133610153070101640Mouse
1301734Acsns2_mAngiostrongylus costaricensis nematode susceptibility 2 (mouse)Not determined133610153070101640Mouse
1300561Heal7_mwound healing/regeneration 7 (mouse)Not determined133614482070144904Mouse
1300862Cfbw5_mcystic fibrosis body weight 5 (mouse)Not determined133872035872720517Mouse
1300985Bmd13_mbone mineral density 13 (mouse)Not determined133962924973629397Mouse
1302157Bwem2_mbody weight day 30 males 2 (mouse)Not determined133962924973629397Mouse
1301801Cpfd5_mcerebellum pattern fissures (mouse)Not determined133962924973629397Mouse
15039353Nmrs35_mNAFLD-associated magnetic resonance shift 35 (mouse)134058825374588253Mouse
1300668Pas10_mpulmonary adenoma susceptibility 10 (mouse)Not determined134148904275489158Mouse
12738427Lfibq24_mliver fibrosis QTL 24 (mouse)134425810752758667Mouse
4142331Bxs6_mBXSB/MpJ autoimmune nephritis 6 (mouse)Not determined4521044283744746Mouse
10412109Bxs7_mBXSB/MpJ autoimmune nephritis 7 (mouse)Not determined134521044283744746Mouse

Markers in Region
AI505271  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381347,012,713 - 47,012,830UniSTSGRCm38
MGSCv371347,108,082 - 47,108,199UniSTSGRCm37
Celera1348,097,954 - 48,098,071UniSTS
Cytogenetic Map13A5UniSTS
Whitehead/MRC_RH13487.79UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000052747   ⟹   ENSMUSP00000054990
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1347,166,033 - 47,168,326 (-)Ensembl
GRCm38.p6 Ensembl1347,012,557 - 47,014,850 (-)Ensembl
RefSeq Acc Id: NM_175340   ⟹   NP_780549
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391347,166,033 - 47,168,326 (-)NCBI
GRCm381347,012,557 - 47,014,850 (-)ENTREZGENE
MGSCv371347,107,926 - 47,110,219 (-)RGD
Celera1348,097,798 - 48,100,082 (-)RGD
cM Map13 ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_780549 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI18952 (Get FASTA)   NCBI Sequence Viewer  
  AAI18953 (Get FASTA)   NCBI Sequence Viewer  
  BAC32478 (Get FASTA)   NCBI Sequence Viewer  
  DAA01953 (Get FASTA)   NCBI Sequence Viewer  
  EDL41034 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000054990
  ENSMUSP00000054990.3
GenBank Protein Q8BR37 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_780549   ⟸   NM_175340
- UniProtKB: Q8BR37 (UniProtKB/Swiss-Prot),   Q0VF71 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000054990   ⟸   ENSMUST00000052747
Protein Domains
RING-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8BR37-F1-model_v2 AlphaFold Q8BR37 1-401 view protein structure

Promoters
RGD ID:8680242
Promoter ID:EPDNEW_M18152
Type:multiple initiation site
Name:Nhlrc1_1
Description:Mus musculus NHL repeat containing 1 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381347,014,857 - 47,014,917EPDNEW
RGD ID:6824185
Promoter ID:MM_KWN:13994
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   Kidney,   Lung,   Spleen
Transcripts:NM_175340
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361347,109,729 - 47,110,229 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2145264 AgrOrtholog
Ensembl Genes ENSMUSG00000044231 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000052747 ENTREZGENE
  ENSMUST00000052747.4 UniProtKB/Swiss-Prot
Gene3D-CATH 2.120.10.30 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.40.10.500 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro 6-blade_b-propeller_TolB-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NHL_repeat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_RING UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_RING_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:105193 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:2145264 ENTREZGENE
NCBI Gene 105193 ENTREZGENE
PANTHER E3 UBIQUITIN-PROTEIN LIGASE NHLRC1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  E3 UBIQUITIN-PROTEIN LIGASE NHLRC1-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nhlrc1 PhenoGen
PROSITE NHL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_RING_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_RING_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART RING UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP NHL repeat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RING/U-box UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt NHLC1_MOUSE UniProtKB/Swiss-Prot
  Q0VF71 ENTREZGENE, UniProtKB/TrEMBL
  Q8BR37 ENTREZGENE