Fam43a (family with sequence similarity 43, member A) - Rat Genome Database
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Gene: Fam43a (family with sequence similarity 43, member A) Rattus norvegicus
Analyze
Symbol: Fam43a
Name: family with sequence similarity 43, member A
RGD ID: 1304790
Description: Orthologous to human FAM43A (family with sequence similarity 43 member A); INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: hypothetical protein LOC288031; LOC288031; MGC116410; RGD1304790; similar to CG8312-PA
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21170,128,253 - 70,131,401 (-)NCBI
Rnor_6.0 Ensembl1173,676,601 - 73,678,984 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01173,676,601 - 73,679,003 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01176,748,265 - 76,750,667 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41172,010,484 - 72,012,886 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11172,068,960 - 72,078,160 (-)NCBI
Celera11128,018 - 130,420 (+)NCBICelera
Cytogenetic Map11q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(R)-pantothenic acid  (ISO)
1-naphthyl isothiocyanate  (EXP)
15-acetyldeoxynivalenol  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-hydroxypropanoic acid  (ISO)
3-chloropropane-1,2-diol  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
4-hydroxyphenyl retinamide  (ISO)
acetamide  (EXP)
acrylamide  (EXP,ISO)
afimoxifene  (ISO)
aflatoxin B1  (EXP,ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
avobenzone  (ISO)
azathioprine  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
Benzo[k]fluoranthene  (ISO)
beta-naphthoflavone  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
butanal  (ISO)
carbon nanotube  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
entinostat  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
furan  (EXP)
genistein  (ISO)
glycidol  (EXP)
hydroquinone  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
leflunomide  (ISO)
lipopolysaccharide  (ISO)
methotrexate  (ISO)
methylisothiazolinone  (ISO)
N-nitrosodimethylamine  (EXP)
nickel sulfate  (ISO)
oxaliplatin  (EXP)
panobinostat  (ISO)
paracetamol  (ISO)
pentanal  (ISO)
phenylmercury acetate  (ISO)
progesterone  (ISO)
propanal  (ISO)
quercitrin  (ISO)
rac-lactic acid  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
zinc atom  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
1. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932  


Genomics

Comparative Map Data
Fam43a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21170,128,253 - 70,131,401 (-)NCBI
Rnor_6.0 Ensembl1173,676,601 - 73,678,984 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01173,676,601 - 73,679,003 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01176,748,265 - 76,750,667 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41172,010,484 - 72,012,886 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11172,068,960 - 72,078,160 (-)NCBI
Celera11128,018 - 130,420 (+)NCBICelera
Cytogenetic Map11q22NCBI
FAM43A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3194,685,883 - 194,689,037 (+)EnsemblGRCh38hg38GRCh38
GRCh383194,685,883 - 194,689,037 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh373194,406,612 - 194,409,766 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363195,887,911 - 195,891,055 (+)NCBINCBI36hg18NCBI36
Build 343195,887,918 - 195,891,061NCBI
Celera3192,820,433 - 192,823,578 (+)NCBI
Cytogenetic Map3q29NCBI
HuRef3191,784,777 - 191,787,922 (+)NCBIHuRef
CHM1_13194,369,331 - 194,372,476 (+)NCBICHM1_1
Fam43a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391630,418,541 - 30,421,615 (+)NCBIGRCm39mm39
GRCm39 Ensembl1630,418,541 - 30,421,615 (+)Ensembl
GRCm381630,599,723 - 30,602,797 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1630,599,723 - 30,602,797 (+)EnsemblGRCm38mm10GRCm38
MGSCv371630,599,809 - 30,602,883 (+)NCBIGRCm37mm9NCBIm37
MGSCv361630,519,470 - 30,522,502 (+)NCBImm8
Celera1631,114,283 - 31,117,357 (+)NCBICelera
Cytogenetic Map16B2NCBI
Fam43a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542014,203,879 - 14,205,165 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542014,202,955 - 14,206,087 (-)NCBIChiLan1.0ChiLan1.0
FAM43A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13202,291,669 - 202,294,824 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3202,292,603 - 202,293,877 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03191,981,521 - 191,984,684 (+)NCBIMhudiblu_PPA_v0panPan3
FAM43A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13331,070,520 - 31,073,393 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3331,070,951 - 31,073,312 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3331,101,312 - 31,103,894 (-)NCBI
ROS_Cfam_1.03331,329,672 - 31,332,254 (-)NCBI
UMICH_Zoey_3.13331,123,619 - 31,126,204 (-)NCBI
UNSW_CanFamBas_1.03331,158,810 - 31,161,371 (-)NCBI
UU_Cfam_GSD_1.03331,784,902 - 31,787,487 (-)NCBI
Fam43a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602124,110,293 - 124,113,397 (+)NCBI
SpeTri2.0NW_004936711136,411 - 139,558 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FAM43A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13131,663,485 - 131,664,759 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113131,662,474 - 131,665,653 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213141,266,879 - 141,269,989 (+)NCBISscrofa10.2Sscrofa10.2susScr3
FAM43A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11588,771,634 - 88,774,770 (+)NCBI
ChlSab1.1 Ensembl1588,772,565 - 88,773,836 (+)Ensembl
Fam43a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473063,205,027 - 63,208,444 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111901627290463843Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)111947517979734728Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112831466586994795Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)113043533986714631Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113215552082443118Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113590063480900634Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114309033886714631Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114658320986714631Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114726402386994547Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114726402386994547Rat
4889859Pur28Proteinuria QTL 2819.50.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)114790104978471527Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115785881090463843Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115994302390463843Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)116010984287141948Rat
631506Bp104Blood pressure QTL 1042.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)116265336586714475Rat
70208Niddm22Non-insulin dependent diabetes mellitus QTL 223.61blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)116265336586714483Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116449467190463843Rat
1549848Bvd6Brain ventricular dilatation QTL 63.10.0001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)116934231986312439Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116964970890463843Rat
1354656Bvd3Brain ventricular dilatation QTL 33.640.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)117272002986994795Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:62
Count of miRNA genes:55
Interacting mature miRNAs:57
Transcripts:ENSRNOT00000002355
Prediction methods:Microtar, 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.


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 6 5 11 12 20 18 11
Low 1 37 52 41 8 41 8 11 62 15 23 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000002355   ⟹   ENSRNOP00000002355
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1173,676,601 - 73,678,984 (-)Ensembl
RefSeq Acc Id: NM_001039002   ⟹   NP_001034091
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21170,128,253 - 70,131,401 (-)NCBI
Rnor_6.01173,676,601 - 73,679,003 (-)NCBI
Rnor_5.01176,748,265 - 76,750,667 (-)NCBI
RGSC_v3.41172,010,484 - 72,012,886 (-)RGD
Celera11128,018 - 130,420 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001034091 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH99231 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001034091   ⟸   NM_001039002
- UniProtKB: Q4KLG0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002355   ⟸   ENSRNOT00000002355
Protein Domains
PID

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
11 76749868 76749869 G A snv SBH/Ygl (MCW), SBN/Ygl (MCW), Crl:SD (UDEL), LE/OrlBarth (UDEL), SS/JrHsdMcwi (MCW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
11 73678204 73678205 G A snv SBH/Ygl (MCW), M520/N (MCW), SS/JrHsdMcwi (MCW), SBN/Ygl (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
11 72012087 72012088 G A snv SS/JrHsdMcwi (MDC), LCR/2Mco (UMich), SS/JrHsdMcwi (MCW), BBDP/WorN (ICL), LH/MavRrrc (ICL), LL/MavRrrc (ICL), SBH/Ygl (ICL), SBN/Ygl (ICL), SS/Jr (ICL), SS/JrHsdMcwi (ICL), WAG/Rij (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), M520/N (KNAW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304790 AgrOrtholog
Ensembl Genes ENSRNOG00000001728 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000052587 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000002355 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000072127 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002355 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000087174 UniProtKB/TrEMBL
Gene3D-CATH 2.30.29.30 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7442928 IMAGE-MGC_LOAD
InterPro FAM43A/B_PTB UniProtKB/TrEMBL
  PH_type UniProtKB/TrEMBL
  PTB/PI_dom UniProtKB/TrEMBL
KEGG Report rno:100909474 UniProtKB/TrEMBL
  rno:288031 UniProtKB/TrEMBL
MGC_CLONE MGC:116410 IMAGE-MGC_LOAD
NCBI Gene 288031 ENTREZGENE
Pfam PID_2 UniProtKB/TrEMBL
PhenoGen Fam43a PhenoGen
SMART PTB UniProtKB/TrEMBL
UniProt Q4KLG0 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary F1M8K2 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-06 Fam43a  family with sequence similarity 43, member A  RGD1304790  similar to CG8312-PA  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1304790  similar to CG8312-PA  RGD1304790_predicted  similar to CG8312-PA (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1304790_predicted  similar to CG8312-PA (predicted)  LOC288031_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC288031_predicted  similar to CG8312-PA (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL