Nhlrc1 (NHL repeat containing E3 ubiquitin protein ligase 1) - Rat Genome Database

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Gene: Nhlrc1 (NHL repeat containing E3 ubiquitin protein ligase 1) Rattus norvegicus
Analyze
Symbol: Nhlrc1
Name: NHL repeat containing E3 ubiquitin protein ligase 1
RGD ID: 735081
Description: Predicted to enable translation repressor activity and ubiquitin protein ligase activity. Predicted to be involved in negative regulation of translation; proteasome-mediated ubiquitin-dependent protein catabolic process; and protein polyubiquitination. Predicted to act upstream of or within several processes, including glycogen biosynthetic process; regulation of protein localization to plasma membrane; and regulation of protein modification process. Predicted to be located in perinuclear region of cytoplasm. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in Lafora disease. Orthologous to human NHLRC1 (NHL repeat containing E3 ubiquitin protein ligase 1); PARTICIPATES IN ubiquitin/proteasome degradation pathway; INTERACTS WITH 2,4-dinitrotoluene; acetamide; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: E3 ubiquitin-protein ligase NHLRC1; Epm2b; malin; NHL repeat containing 1; NHL repeat-containing protein 1; RING-type E3 ubiquitin transferase NHLRC1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21717,674,375 - 17,675,565 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1717,674,319 - 17,677,148 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1717,559,476 - 17,560,666 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01719,163,332 - 19,164,522 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01717,486,596 - 17,487,786 (+)NCBIRnor_WKY
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
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
References

References - curated
# Reference Title Reference Citation
1. Mutations in NHLRC1 cause progressive myoclonus epilepsy. Chan EM, etal., Nat Genet 2003 Oct;35(2):125-7. Epub 2003 Sep 7.
2. 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.
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. GOA pipeline RGD automated data 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:15930137   PMID:17908927   PMID:18070875   PMID:19529779   PMID:23663739   PMID:24914213   PMID:25416783   PMID:26976331   PMID:28536304  


Genomics

Comparative Map Data
Nhlrc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21717,674,375 - 17,675,565 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1717,674,319 - 17,677,148 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1717,559,476 - 17,560,666 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01719,163,332 - 19,164,522 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01717,486,596 - 17,487,786 (+)NCBIRnor_WKY
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
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38618,120,440 - 18,122,677 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 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
(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
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
PanPan1.1618,321,603 - 18,322,965 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl618,321,728 - 18,322,915 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0617,969,146 - 17,970,962 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
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 (-)EnsemblSpeTri2.0
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

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:29
Count of miRNA genes:28
Interacting mature miRNAs:29
Transcripts:ENSRNOT00000031656
Prediction methods: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
9590316Scort21Serum corticosterone level QTL 214.750.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17122871563Rat
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17131701463Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17131990913Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17137830672Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17160781592Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat
1641902Colcr7Colorectal carcinoma resistance QTL 73.350.0044intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)17211514921881669Rat
1300123Bp194Blood pressure QTL 1942.82arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)17211514934551001Rat
631499Stl1Serum triglyceride level QTL 13.6blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)17327139827389946Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)17429913021293263Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented dorsal coat/hair area to total dorsal coat/hair area ratio (CMO:0001811)17429913021293263Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17429913035837242Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17429913060781592Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17429913069599340Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17429913069599340Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17429913069599340Rat
2293648Bmd31Bone mineral density QTL 314.50.0001femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)17435448727028127Rat
2293664Bmd28Bone mineral density QTL 285.10.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)17435448727028127Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17452803849528038Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17452803849528038Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17886846253868462Rat
1582199Insul5Insulin level QTL 53.40.0119blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)17920136523653323Rat
1582208Kidm32Kidney mass QTL 323.90.0018kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17920136523653323Rat
1582224Epfw4Epididymal fat weight QTL 43.50.0058epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)17920136523653323Rat
1582225Bw67Body weight QTL 676.20.0001body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582226Bw64Body weight QTL 644.20.0017body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582241Bw70Body weight QTL 704.60.0003body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582245Bw73Body weight QTL 734.60.0004body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582258Bw76Body weight QTL 764.60.0005body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
2300002Iddm36Insulin dependent diabetes mellitus QTL 361.98blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)17999128640540197Rat
1549900Iddm20Insulin dependent diabetes mellitus QTL 203.7pancreas integrity trait (VT:0010560)percentage of study population developing diabetes mellitus during a period of time (CMO:0001114)171398677321975515Rat
1331720Rf43Renal function QTL 432.881kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)171533061323017269Rat
1331765Hrtrt15Heart rate QTL 154.094heart pumping trait (VT:2000009)heart rate (CMO:0000002)171533061355836425Rat
1354640Scl32Serum cholesterol level QTL 325.4blood HDL cholesterol amount (VT:0000184)blood high density lipoprotein cholesterol level (CMO:0000052)171578159260781592Rat
1354659Scl68Serum cholesterol level QTL 683.9blood VLDL cholesterol amount (VT:0005144)blood very low density lipoprotein cholesterol level (CMO:0000648)171578159260781592Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 2 52
Low 3 41 57 41 19 41 8 9 22 35 41 11 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000031656   ⟹   ENSRNOP00000030625
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1717,674,319 - 17,677,148 (+)Ensembl
Rnor_6.0 Ensembl1718,059,382 - 18,060,572 (+)Ensembl
RefSeq Acc Id: NM_199236   ⟹   NP_954706
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21717,674,375 - 17,675,565 (+)NCBI
Rnor_6.01718,059,382 - 18,060,572 (+)NCBI
Rnor_5.01719,876,653 - 19,877,843 (-)NCBI
RGSC_v3.41723,726,054 - 23,727,244 (+)RGD
Celera1717,384,491 - 17,385,681 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_954706 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein DAA01959 (Get FASTA)   NCBI Sequence Viewer  
  EDL98158 (Get FASTA)   NCBI Sequence Viewer  
  Q6IMG5 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_954706   ⟸   NM_199236
- UniProtKB: Q6IMG5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000030625   ⟸   ENSRNOT00000031656

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6IMG5-F1-model_v2 AlphaFold Q6IMG5 1-396 view protein structure

Transcriptome

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

Promoters
RGD ID:13700367
Promoter ID:EPDNEW_R10890
Type:single initiation site
Name:Nhlrc1_1
Description:NHL repeat containing E3 ubiquitin protein ligase 1
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_6.01718,059,338 - 18,059,398EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:735081 AgrOrtholog
BioCyc Gene G2FUF-9907 BioCyc
Ensembl Genes ENSRNOG00000026286 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000030625 ENTREZGENE
  ENSRNOP00000030625.2 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000031656 ENTREZGENE
  ENSRNOT00000031656.3 UniProtKB/Swiss-Prot
Gene3D-CATH 2.120.10.30 UniProtKB/Swiss-Prot
  3.30.40.10 UniProtKB/Swiss-Prot
InterPro 6-blade_b-propeller_TolB-like UniProtKB/Swiss-Prot
  NHL_repeat UniProtKB/Swiss-Prot
  Znf_RING UniProtKB/Swiss-Prot
  Znf_RING/FYVE/PHD UniProtKB/Swiss-Prot
  Znf_RING_CS UniProtKB/Swiss-Prot
KEGG Report rno:364682 UniProtKB/Swiss-Prot
NCBI Gene 364682 ENTREZGENE
PANTHER E3 UBIQUITIN-PROTEIN LIGASE NHLRC1 UniProtKB/Swiss-Prot
  E3 UBIQUITIN-PROTEIN LIGASE NHLRC1-RELATED UniProtKB/Swiss-Prot
Pfam zf-RING_5 UniProtKB/Swiss-Prot
PhenoGen Nhlrc1 PhenoGen
PROSITE NHL UniProtKB/Swiss-Prot
  ZF_RING_1 UniProtKB/Swiss-Prot
  ZF_RING_2 UniProtKB/Swiss-Prot
SMART RING UniProtKB/Swiss-Prot
Superfamily-SCOP NHL repeat UniProtKB/Swiss-Prot
  RING/U-box UniProtKB/Swiss-Prot
UniProt NHLC1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-12-31 Nhlrc1  NHL repeat containing E3 ubiquitin protein ligase 1  Nhlrc1  NHL repeat containing 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Nhlrc1  NHL repeat containing 1    malin  Name updated 1299863 APPROVED
2004-09-10 Nhlrc1  malin  Epm2b    Symbol and Name updated 1299863 APPROVED