Nubp1 (NUBP iron-sulfur cluster assembly factor 1) - Rat Genome Database

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Gene: Nubp1 (NUBP iron-sulfur cluster assembly factor 1) Rattus norvegicus
Analyze
Symbol: Nubp1
Name: NUBP iron-sulfur cluster assembly factor 1 (Ensembl:nucleotide binding protein 1)
RGD ID: 1310514
Description: Predicted to enable iron-sulfur cluster binding activity. Predicted to be involved in intracellular iron ion homeostasis; iron-sulfur cluster assembly; and regulation of cell growth. Predicted to act upstream of or within centrosome localization; negative regulation of centrosome duplication; and protein localization to cell cortex. Predicted to be located in plasma membrane. Predicted to be active in cytosol. Orthologous to human NUBP1 (NUBP iron-sulfur cluster assembly factor 1, cytosolic); PARTICIPATES IN cytosolic iron-sulfur cluster protein assembly pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4,6-trinitrotoluene; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: cytosolic Fe-S cluster assembly factor NUBP1; LOC287042; MGC108970; NBP 1; nucleotide binding protein 1; nucleotide binding protein 1 (MinD homolog, E. coli); nucleotide-binding protein 1
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
GRCr8105,766,157 - 5,777,648 (-)NCBIGRCr8
mRatBN7.2105,259,328 - 5,270,848 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx109,955,670 - 9,967,161 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0109,476,783 - 9,488,274 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0105,115,152 - 5,126,642 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0105,333,378 - 5,343,949 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl105,333,378 - 5,344,121 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0104,155,446 - 4,166,017 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4105,206,634 - 5,217,205 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1105,206,633 - 5,217,205 (-)NCBI
Celera104,276,872 - 4,287,443 (-)NCBICelera
Cytogenetic Map10q11NCBI
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
centriole  (IEA)
cilium  (IEA)
cytosol  (IBA,ISO,ISS)
nucleus  (IEA)
plasma membrane  (ISO)

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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Iron-sulfur cluster biogenesis in mammalian cells: New insights into the molecular mechanisms of cluster delivery. Maio N and Rouault TA, Biochim Biophys Acta. 2015 Jun;1853(6):1493-512. doi: 10.1016/j.bbamcr.2014.09.009. Epub 2014 Sep 19.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. Biogenesis of cytosolic and nuclear iron-sulfur proteins and their role in genome stability. Paul VD and Lill R, Biochim Biophys Acta. 2015 Jun;1853(6):1528-39. doi: 10.1016/j.bbamcr.2014.12.018. Epub 2015 Jan 10.
6. GOA pipeline RGD automated data pipeline
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:16638812   PMID:18573874   PMID:23028652   PMID:23376485  


Genomics

Comparative Map Data
Nubp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8105,766,157 - 5,777,648 (-)NCBIGRCr8
mRatBN7.2105,259,328 - 5,270,848 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx109,955,670 - 9,967,161 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0109,476,783 - 9,488,274 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0105,115,152 - 5,126,642 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0105,333,378 - 5,343,949 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl105,333,378 - 5,344,121 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0104,155,446 - 4,166,017 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4105,206,634 - 5,217,205 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1105,206,633 - 5,217,205 (-)NCBI
Celera104,276,872 - 4,287,443 (-)NCBICelera
Cytogenetic Map10q11NCBI
NUBP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381610,743,842 - 10,769,351 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1610,743,786 - 10,769,351 (+)EnsemblGRCh38hg38GRCh38
GRCh371610,837,699 - 10,863,208 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361610,745,199 - 10,770,709 (+)NCBINCBI36Build 36hg18NCBI36
Build 341610,745,217 - 10,770,709NCBI
Celera1611,007,059 - 11,032,475 (+)NCBICelera
Cytogenetic Map16p13.13NCBI
HuRef1610,756,412 - 10,781,588 (+)NCBIHuRef
CHM1_11610,837,712 - 10,863,204 (+)NCBICHM1_1
T2T-CHM13v2.01610,779,762 - 10,805,269 (+)NCBIT2T-CHM13v2.0
Nubp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391610,229,802 - 10,242,317 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1610,229,812 - 10,242,292 (+)EnsemblGRCm39 Ensembl
GRCm381610,411,884 - 10,424,453 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1610,411,948 - 10,424,428 (+)EnsemblGRCm38mm10GRCm38
MGSCv371610,412,031 - 10,424,521 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361610,325,553 - 10,337,109 (+)NCBIMGSCv36mm8
Celera1611,045,448 - 11,057,938 (+)NCBICelera
Cytogenetic Map16A1NCBI
cM Map165.61NCBI
Nubp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554427,717,422 - 7,732,496 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554427,717,422 - 7,732,496 (-)NCBIChiLan1.0ChiLan1.0
NUBP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21811,236,566 - 11,315,874 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11615,012,495 - 15,091,492 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0169,681,800 - 9,708,673 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11610,906,347 - 10,931,799 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1610,906,719 - 10,931,800 (+)Ensemblpanpan1.1panPan2
NUBP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1631,900,540 - 31,922,087 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl631,896,596 - 31,921,989 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha633,282,660 - 33,304,486 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0632,082,705 - 32,104,573 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl632,081,940 - 32,104,479 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1631,896,734 - 31,918,569 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0631,770,561 - 31,792,362 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0632,194,799 - 32,216,643 (-)NCBIUU_Cfam_GSD_1.0
Nubp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344111,126,784 - 111,140,480 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365308,971,380 - 8,986,033 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365308,970,963 - 8,985,925 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NUBP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl332,311,779 - 32,340,034 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1332,311,774 - 32,340,120 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2333,045,133 - 33,072,061 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NUBP1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1510,224,965 - 10,248,328 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl510,225,173 - 10,249,047 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606819,923,874 - 19,947,229 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nubp1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248248,024,575 - 8,040,364 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248248,024,459 - 8,040,353 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nubp1
141 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:53
Count of miRNA genes:42
Interacting mature miRNAs:52
Transcripts:ENSRNOT00000003479
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
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10129497586Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402719233348Rat
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10476552719816042Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
1549898Neuinf3Neuroinflammation QTL 326.4nervous system integrity trait (VT:0010566)MHC Class II RT1A-positive spinal cord ventral horn area to total spinal cord ventral horn area ratio (CMO:0001980)1034063205387112Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402717245662Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat

Markers in Region
RH144077  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2105,262,977 - 5,263,093 (+)MAPPERmRatBN7.2
Rnor_6.0105,336,109 - 5,336,225NCBIRnor6.0
Rnor_5.0104,158,177 - 4,158,293UniSTSRnor5.0
RGSC_v3.4105,209,365 - 5,209,481UniSTSRGSC3.4
Celera104,279,603 - 4,279,719UniSTS
Cytogenetic Map10q11UniSTS


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: ENSRNOT00000003479   ⟹   ENSRNOP00000003479
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl105,333,378 - 5,344,121 (-)Ensembl
RefSeq Acc Id: NM_001009619   ⟹   NP_001009619
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8105,766,157 - 5,777,648 (-)NCBI
mRatBN7.2105,259,328 - 5,270,848 (-)NCBI
Rnor_6.0105,333,378 - 5,343,949 (-)NCBI
Rnor_5.0104,155,446 - 4,166,017 (-)NCBI
RGSC_v3.4105,206,634 - 5,217,205 (-)RGD
Celera104,276,872 - 4,287,443 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001009619 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH88221 (Get FASTA)   NCBI Sequence Viewer  
  EDL96223 (Get FASTA)   NCBI Sequence Viewer  
  EDL96224 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00055024577
  ENSRNOP00060017494
  ENSRNOP00065002839
GenBank Protein Q5I0L4 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001009619   ⟸   NM_001009619
- UniProtKB: Q5I0L4 (UniProtKB/Swiss-Prot),   A6K4K2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000003479   ⟸   ENSRNOT00000003479
Protein Domains
AAA+ ATPase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5I0L4-F1-model_v2 AlphaFold Q5I0L4 1-320 view protein structure

Transcriptome

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

Promoters
RGD ID:13696945
Promoter ID:EPDNEW_R7470
Type:multiple initiation site
Name:Nubp1_1
Description:nucleotide binding protein 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_6.0105,343,962 - 5,344,022EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310514 AgrOrtholog
BioCyc Gene G2FUF-26131 BioCyc
Ensembl Genes ENSRNOG00000002574 Ensembl
  ENSRNOG00055018023 UniProtKB/Swiss-Prot
  ENSRNOG00060012974 UniProtKB/Swiss-Prot
  ENSRNOG00065002864 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00055030530 UniProtKB/Swiss-Prot
  ENSRNOT00060022079 UniProtKB/Swiss-Prot
  ENSRNOT00065003985 UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.50.300 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7321552 IMAGE-MGC_LOAD
InterPro AAA+_ATPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Mrp/NBP35_ATP-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Mrp_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NUBP1/Nbp35 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  YlxH/NBP35 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:287042 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:108970 IMAGE-MGC_LOAD
NCBI Gene 287042 ENTREZGENE
PANTHER CYTOSOLIC FE-S CLUSTER ASSEMBLY FACTOR NUBP1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NUCLEOTIDE-BINDING PROTEIN NBP35 YEAST -RELATED UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
Pfam ParA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nubp1 PhenoGen
PROSITE MRP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000002574 RatGTEx
  ENSRNOG00055018023 RatGTEx
  ENSRNOG00060012974 RatGTEx
  ENSRNOG00065002864 RatGTEx
SMART AAA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP P-loop containing nucleoside triphosphate hydrolases UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
UniProt A6K4K1_RAT UniProtKB/TrEMBL
  A6K4K2 ENTREZGENE, UniProtKB/TrEMBL
  NUBP1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-03-09 Nubp1  NUBP iron-sulfur cluster assembly factor 1  Nubp1  NUBP iron-sulfur cluster assembly factor 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2021-12-23 Nubp1  NUBP iron-sulfur cluster assembly factor 1  Nubp1  nucleotide binding protein 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Nubp1  nucleotide binding protein 1  Nubp1_predicted  nucleotide binding protein 1 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Nubp1_predicted  nucleotide binding protein 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED