Fam53c (family with sequence similarity 53, member C) - Rat Genome Database

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Pathways
Gene: Fam53c (family with sequence similarity 53, member C) Rattus norvegicus
Analyze
Symbol: Fam53c
Name: family with sequence similarity 53, member C
RGD ID: 1593851
Description: Predicted to be involved in protein import into nucleus. Predicted to be active in nucleus. Orthologous to human FAM53C (family with sequence similarity 53 member C); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; cadmium dichloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC685405; similar to family 53, member C protein
RGD Orthologs
Human
Mouse
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81826,638,781 - 26,652,294 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1826,638,062 - 26,652,290 (+)EnsemblGRCr8
mRatBN7.21826,364,050 - 26,378,173 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1826,364,039 - 26,376,775 (+)EnsemblmRatBN7.2
Rnor_6.01827,558,094 - 27,572,633 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1827,558,089 - 27,570,508 (+)Ensemblrn6Rnor6.0
Rnor_5.01827,271,347 - 27,285,827 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41827,237,519 - 27,245,127 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1826,101,508 - 26,115,709 (+)NCBICelera
Cytogenetic Map18p12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleus  (IBA)

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Fam53c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81826,638,781 - 26,652,294 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1826,638,062 - 26,652,290 (+)EnsemblGRCr8
mRatBN7.21826,364,050 - 26,378,173 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1826,364,039 - 26,376,775 (+)EnsemblmRatBN7.2
Rnor_6.01827,558,094 - 27,572,633 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1827,558,089 - 27,570,508 (+)Ensemblrn6Rnor6.0
Rnor_5.01827,271,347 - 27,285,827 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41827,237,519 - 27,245,127 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1826,101,508 - 26,115,709 (+)NCBICelera
Cytogenetic Map18p12NCBI
FAM53C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385138,337,557 - 138,349,729 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5138,331,935 - 138,349,729 (+)Ensemblhg38GRCh38
GRCh375137,673,246 - 137,685,418 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map5q31.2NCBI
HuRef5132,864,145 - 132,876,338 (+)NCBIHuRef
CHM1_15137,105,947 - 137,118,143 (+)NCBICHM1_1
T2T-CHM13v2.05138,863,774 - 138,875,947 (+)NCBIT2T-CHM13v2.0
Fam53c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391834,891,885 - 34,906,813 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1834,891,959 - 34,906,813 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381834,758,831 - 34,773,760 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1834,758,906 - 34,773,760 (+)Ensemblmm10GRCm38
MGSCv371834,918,560 - 34,933,414 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361834,884,880 - 34,899,734 (+)NCBIMGSCv36mm8
Celera1835,213,020 - 35,227,872 (+)NCBICelera
Cytogenetic Map18B1NCBI
cM Map1818.72NCBI
Fam53c
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1159,585,745 - 9,597,575 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Fam53c
145 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:127
Count of miRNA genes:101
Interacting mature miRNAs:110
Transcripts:ENSRNOT00000027499
Prediction methods:Microtar, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2301410Bp317Blood pressure QTL 3170.004arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181221923726822399Rat
1331733Bp233Blood pressure QTL 2333.97196arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182507112683910656Rat
2301409Cm70Cardiac mass QTL 700.001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)18706572852065728Rat
1358358Sradr6Stress Responsive Adrenal Weight QTL 62.49adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)182201556261600538Rat
1331735Rf44Renal function QTL 442.981urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)181564228031610627Rat
61382Bp46Blood pressure QTL 4618.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181221668431644508Rat
12904716Am21Aortic mass QTL 210.005aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)18706572852065728Rat
1331741Bp232Blood pressure QTL 2323.59112arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)182349405785487725Rat
12904714Cm131Cardiac mass QTL 1310.002heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)18706572852065728Rat
12904715Cm132Cardiac mass QTL 1320.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)18706572852065728Rat
6903345Bp349Blood pressure QTL 3493.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)18391722648917226Rat
2313082Bss85Bone structure and strength QTL 850.80.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)181522610142690662Rat
6903347Bp350Blood pressure QTL 3504.4arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)18131610627Rat
2312568Glom21Glomerulus QTL 2120.005kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)18546045542690191Rat
6903349Bp351Blood pressure QTL 3513.5arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)18391722648917226Rat
631509Sald2Serum aldosterone level QTL 22.9blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)182641582171415821Rat
6903351Bp352Blood pressure QTL 3523.3arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)18391722648917226Rat
1331766Bp236Blood pressure QTL 2363.022arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)18131610627Rat
631264Scl22Serum cholesterol level QTL 226.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)181221668431644508Rat
1331775Bp235Blood pressure QTL 2353.201arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181564228031610627Rat
2325839Bp348Blood pressure QTL 3480.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)18144930869Rat
12904680Bw189Body weight QTL 1890.019body mass (VT:0001259)body weight (CMO:0000012)181221923726822399Rat
1600373Mamtr6Mammary tumor resistance QTL 6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)181955353285493247Rat
2293708Bss46Bone structure and strength QTL 468.80.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)181206648257066482Rat
12904693Am20Aortic mass QTL 200.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)181221923726822399Rat
1578667Bss21Bone structure and strength QTL 213.5femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)181206648285493247Rat
12904695Kidm73Kidney mass QTL 730.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)181221923726822399Rat
2312598Bp340Blood pressure QTL 3400.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)18381190230809809Rat
12904689Cm128Cardiac mass QTL 1280.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)181221923726822399Rat
12904690Cm129Cardiac mass QTL 1290.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)181221923726822399Rat
2300180Bmd67Bone mineral density QTL 674.80.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)18134566578Rat
12904691Cm130Cardiac mass QTL 1300.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)181221923726822399Rat
2299160Iddm35Insulin dependent diabetes mellitus QTL 352.79blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)18448264849482648Rat
1331753Bp231Blood pressure QTL 2313.643arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)18154490981Rat
1578661Bss20Bone structure and strength QTL 203.7femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)181206648285493247Rat
11565454Kidm59Kidney mass QTL 590.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)18706572852065728Rat
1331754Bp230Blood pressure QTL 2304.61609arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181564228086134022Rat
2293661Bss50Bone structure and strength QTL 504.640.0003lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)18134566578Rat
61375Bp41Blood pressure QTL 412.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)18430735449307354Rat

Markers in Region
RH48553  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21826,375,232 - 26,375,352 (+)MAPPERmRatBN7.2
Rnor_6.01827,569,693 - 27,569,812NCBIRnor6.0
Rnor_5.01827,282,887 - 27,283,006UniSTSRnor5.0
RGSC_v3.41827,244,865 - 27,244,984UniSTSRGSC3.4
Celera1826,112,769 - 26,112,888UniSTS
Cytogenetic Map18p12UniSTS
RH140997  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21826,377,838 - 26,378,030 (+)MAPPERmRatBN7.2
Rnor_6.01827,572,299 - 27,572,490NCBIRnor6.0
Rnor_5.01827,285,493 - 27,285,684UniSTSRnor5.0
RGSC_v3.41827,247,471 - 27,247,662UniSTSRGSC3.4
Celera1826,115,375 - 26,115,566UniSTS
RH 3.4 Map18369.6UniSTS
Cytogenetic Map18p12UniSTS


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 164 91 90 59 92 59 6 356 192 11 143 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000027499   ⟹   ENSRNOP00000027499
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1826,638,552 - 26,652,288 (+)Ensembl
mRatBN7.2 Ensembl1826,364,660 - 26,376,775 (+)Ensembl
Rnor_6.0 Ensembl1827,558,089 - 27,570,508 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000115195   ⟹   ENSRNOP00000085560
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1826,638,062 - 26,652,290 (+)Ensembl
mRatBN7.2 Ensembl1826,364,039 - 26,376,775 (+)Ensembl
RefSeq Acc Id: NM_001427416   ⟹   NP_001414345
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81826,638,781 - 26,652,290 (+)NCBI
RefSeq Acc Id: XM_063277591   ⟹   XP_063133661
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81826,641,943 - 26,652,294 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001414345 (Get FASTA)   NCBI Sequence Viewer  
  XP_063133661 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000027499
  ENSRNOP00000027499.2
  ENSRNOP00000085560.2
Ensembl Acc Id: ENSRNOP00000027499   ⟸   ENSRNOT00000027499
Ensembl Acc Id: ENSRNOP00000085560   ⟸   ENSRNOT00000115195
RefSeq Acc Id: NP_001414345   ⟸   NM_001427416
- UniProtKB: D3ZH55 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063133661   ⟸   XM_063277591
- Peptide Label: isoform X1
- UniProtKB: A0A8I6A450 (UniProtKB/TrEMBL),   A6J2W2 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZH55-F1-model_v2 AlphaFold D3ZH55 1-390 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1593851 AgrOrtholog
BioCyc Gene G2FUF-7943 BioCyc
Ensembl Genes ENSRNOG00000020261 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027499 ENTREZGENE
  ENSRNOT00000027499.7 UniProtKB/TrEMBL
  ENSRNOT00000115195.2 UniProtKB/TrEMBL
InterPro FAM53 UniProtKB/TrEMBL
NCBI Gene 685405 ENTREZGENE
PANTHER PROTEIN FAM53C UniProtKB/TrEMBL
  PTHR28567 UniProtKB/TrEMBL
Pfam FAM53 UniProtKB/TrEMBL
PhenoGen Fam53c PhenoGen
RatGTEx ENSRNOG00000020261 RatGTEx
UniProt A0A8I6A450 ENTREZGENE, UniProtKB/TrEMBL
  A6J2W2 ENTREZGENE, UniProtKB/TrEMBL
  D3ZH55 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-24 Fam53c  family with sequence similarity 53, member C  LOC682083  similar to family 53, member C protein  Data merged from RGD:1588085 1643240 APPROVED
2010-04-21 Fam53c  family with sequence similarity 53, member C  LOC685405  similar to family 53, member C protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC685405  similar to family 53, member C protein      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC682083  similar to family 53, member C protein      Symbol and Name status set to provisional 70820 PROVISIONAL