Nudcd3 (NudC domain containing 3) - Rat Genome Database

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Gene: Nudcd3 (NudC domain containing 3) Rattus norvegicus
Analyze
Symbol: Nudcd3
Name: NudC domain containing 3
RGD ID: 1642416
Description: Predicted to be involved in cilium assembly and protein localization to pericentriolar material. Predicted to be part of cytoplasmic dynein complex. Orthologous to human NUDCD3 (NudC domain containing 3); INTERACTS WITH 3-chloropropane-1,2-diol; bisphenol A; furan.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC100911029; MGC125083; nudC domain-containing protein 3; nudC domain-containing protein 3-like
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
GRCr81485,190,276 - 85,273,655 (-)NCBIGRCr8
mRatBN7.21480,976,330 - 81,059,183 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1480,976,328 - 81,058,962 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1485,390,032 - 85,460,097 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01486,630,122 - 86,700,184 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01483,079,445 - 83,149,509 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01486,326,413 - 86,333,397 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1486,326,421 - 86,333,424 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01487,215,882 - 87,294,823 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1479,872,148 - 79,942,035 (-)NCBICelera
Cytogenetic Map14q21NCBI
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

Biological Process

Cellular Component

Molecular Function

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15632090   PMID:23551859   PMID:25205765  


Genomics

Comparative Map Data
Nudcd3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81485,190,276 - 85,273,655 (-)NCBIGRCr8
mRatBN7.21480,976,330 - 81,059,183 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1480,976,328 - 81,058,962 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1485,390,032 - 85,460,097 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01486,630,122 - 86,700,184 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01483,079,445 - 83,149,509 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01486,326,413 - 86,333,397 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1486,326,421 - 86,333,424 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01487,215,882 - 87,294,823 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1479,872,148 - 79,942,035 (-)NCBICelera
Cytogenetic Map14q21NCBI
NUDCD3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38744,379,119 - 44,490,658 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl744,379,119 - 44,490,658 (-)EnsemblGRCh38hg38GRCh38
GRCh37744,418,718 - 44,530,257 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36744,388,490 - 44,496,910 (-)NCBINCBI36Build 36hg18NCBI36
Build 34744,196,429 - 44,303,486NCBI
Celera744,520,966 - 44,629,392 (-)NCBICelera
Cytogenetic Map7p13NCBI
HuRef744,306,068 - 44,414,495 (-)NCBIHuRef
CHM1_1744,426,260 - 44,534,742 (-)NCBICHM1_1
T2T-CHM13v2.0744,538,885 - 44,650,393 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2744,461,485 - 44,569,909 (-)NCBI
Nudcd3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39116,055,705 - 6,150,190 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl116,055,691 - 6,150,415 (-)EnsemblGRCm39 Ensembl
GRCm38116,105,691 - 6,201,619 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl116,105,691 - 6,200,415 (-)EnsemblGRCm38mm10GRCm38
MGSCv37116,005,694 - 6,100,454 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36116,005,709 - 6,100,165 (-)NCBIMGSCv36mm8
Celera116,594,209 - 6,683,040 (-)NCBICelera
Cytogenetic Map11A1NCBI
cM Map113.91NCBI
Nudcd3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554567,558,768 - 7,647,149 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554567,558,768 - 7,645,051 (+)NCBIChiLan1.0ChiLan1.0
NUDCD3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2649,296,410 - 49,403,078 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1797,621,148 - 97,727,817 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0745,094,217 - 45,205,327 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1745,166,752 - 45,274,475 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl745,166,752 - 45,274,475 (-)Ensemblpanpan1.1panPan2
NUDCD3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha162,248,778 - 2,307,451 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01614,554,175 - 14,612,956 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1614,554,438 - 14,612,934 (+)EnsemblROS_Cfam_1.0 Ensembl
UNSW_CanFamBas_1.01614,186,158 - 14,244,859 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01614,166,372 - 14,224,973 (+)NCBIUU_Cfam_GSD_1.0
Nudcd3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118100,105,917 - 100,212,885 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647819,317,465 - 19,424,713 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647819,317,648 - 19,424,525 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NUDCD3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1850,759,221 - 50,830,332 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11850,759,069 - 50,830,336 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21855,661,671 - 55,732,837 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NUDCD3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12114,177,167 - 14,283,419 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2114,177,173 - 14,284,469 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660628,257,199 - 8,363,759 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nudcd3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247407,612,511 - 7,717,064 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247407,613,307 - 7,716,942 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nudcd3
263 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:27
Count of miRNA genes:27
Interacting mature miRNAs:27
Transcripts:ENSRNOT00000073733
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
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143766971982669719Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143766971982669719Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143766971982669719Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143766971982669719Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143905723783368335Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144226252995023211Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)145002321195023211Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1455147478100147478Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1455624247100624247Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1455624247100624247Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1456631369101631369Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1458184885103184885Rat
70153Bp59Blood pressure QTL 593.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)146875779683368335Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1470053989104886043Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1470053989104886043Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)147341532392554092Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)147341532392554092Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532395876975Rat
631213Bw60Body weight QTL604.51retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)147995092195876975Rat

Markers in Region
D14Rat129  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera1479,874,091 - 79,874,301UniSTS
SHRSP x BN Map1444.4UniSTS
SHRSP x BN Map1444.4RGD
RH137742  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01487,238,533 - 87,238,721UniSTSRnor5.0
Celera1479,888,709 - 79,888,897UniSTS
RH 3.4 Map14574.6UniSTS
AU049178  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21481,027,550 - 81,027,827 (+)MAPPERmRatBN7.2
Rnor_6.01479,105,018 - 79,105,296NCBIRnor6.0
Rnor_5.01487,261,173 - 87,261,451UniSTSRnor5.0
Celera1479,911,129 - 79,911,407UniSTS


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 3 43 48 32 19 32 8 11 74 35 41 11 8
Low 9 9 9
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000083191   ⟹   ENSRNOP00000072079
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1480,988,665 - 81,058,899 (-)Ensembl
Rnor_6.0 Ensembl1486,326,421 - 86,333,424 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000098063   ⟹   ENSRNOP00000078032
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1480,976,328 - 81,058,919 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107496   ⟹   ENSRNOP00000092579
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1480,980,373 - 81,058,962 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000112627   ⟹   ENSRNOP00000087625
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1480,976,332 - 81,058,919 (-)Ensembl
RefSeq Acc Id: NM_001103362   ⟹   NP_001096832
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81485,200,810 - 85,272,883 (-)NCBI
mRatBN7.21480,986,864 - 81,058,943 (-)NCBI
Rnor_6.01486,326,413 - 86,333,397 (-)NCBI
Rnor_5.01487,215,882 - 87,294,823 (-)NCBI
Celera1479,872,148 - 79,942,035 (-)RGD
Sequence:
RefSeq Acc Id: NM_001419338   ⟹   NP_001406267
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81485,190,276 - 85,272,883 (-)NCBI
mRatBN7.21480,976,330 - 81,058,943 (-)NCBI
RefSeq Acc Id: XR_005492870
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81485,197,782 - 85,273,655 (-)NCBI
mRatBN7.21480,983,837 - 81,059,183 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001096832   ⟸   NM_001103362
- Peptide Label: isoform 2
- UniProtKB: Q32PY7 (UniProtKB/TrEMBL),   A0A0G2K226 (UniProtKB/TrEMBL),   A0A8I6AIG0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072079   ⟸   ENSRNOT00000083191
RefSeq Acc Id: ENSRNOP00000087625   ⟸   ENSRNOT00000112627
RefSeq Acc Id: ENSRNOP00000078032   ⟸   ENSRNOT00000098063
RefSeq Acc Id: ENSRNOP00000092579   ⟸   ENSRNOT00000107496
RefSeq Acc Id: NP_001406267   ⟸   NM_001419338
- Peptide Label: isoform 1
- UniProtKB: A0A8I5Y9V8 (UniProtKB/TrEMBL),   A6IKS1 (UniProtKB/TrEMBL)
Protein Domains
CS

Transcriptome

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

Promoters
RGD ID:13699469
Promoter ID:EPDNEW_R9993
Type:initiation region
Name:Nudcd3_1
Description:NudC domain containing 3
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_6.01486,333,417 - 86,333,477EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1642416 AgrOrtholog
BioCyc Gene G2FUF-15103 BioCyc
Ensembl Genes ENSRNOG00000056148 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000083191 ENTREZGENE
  ENSRNOT00000083191.2 UniProtKB/TrEMBL
  ENSRNOT00000098063 ENTREZGENE
  ENSRNOT00000098063.1 UniProtKB/TrEMBL
  ENSRNOT00000107496.1 UniProtKB/TrEMBL
  ENSRNOT00000112627.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.790 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7443892 IMAGE-MGC_LOAD
InterPro CS-like_domain UniProtKB/TrEMBL
  HSP20-like_chaperone UniProtKB/TrEMBL
  NudC_fam UniProtKB/TrEMBL
  NudC_N_dom UniProtKB/TrEMBL
  p23_NUDCD3 UniProtKB/TrEMBL
KEGG Report rno:100125378 UniProtKB/TrEMBL
MGC_CLONE MGC:125083 IMAGE-MGC_LOAD
NCBI Gene 100125378 ENTREZGENE
PANTHER PTHR12356 UniProtKB/TrEMBL
  PTHR12356:SF19 UniProtKB/TrEMBL
Pfam Nudc_N UniProtKB/TrEMBL
  PF04969 UniProtKB/TrEMBL
PhenoGen Nudcd3 PhenoGen
PROSITE PS51203 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000056148 RatGTEx
Superfamily-SCOP HSP20_chap UniProtKB/TrEMBL
UniProt A0A0G2K226 ENTREZGENE
  A0A8I5Y9V8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6A4I4_RAT UniProtKB/TrEMBL
  A0A8I6AIG0 ENTREZGENE, UniProtKB/TrEMBL
  A6IKS1 ENTREZGENE, UniProtKB/TrEMBL
  Q32PY7 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary A0A0G2K226 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Nudcd3  NudC domain containing 3  LOC100911029  nudC domain-containing protein 3-like  Data merged from RGD:6495238 737654 PROVISIONAL
2012-07-05 LOC100911029  nudC domain-containing protein 3-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2007-09-15 Nudcd3  NudC domain containing 3      Symbol and Name status set to provisional 70820 PROVISIONAL