Fam89a (family with sequence similarity 89, member A) - Rat Genome Database

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Gene: Fam89a (family with sequence similarity 89, member A) Rattus norvegicus
Analyze
Symbol: Fam89a
Name: family with sequence similarity 89, member A
RGD ID: 1309879
Description: Orthologous to human FAM89A (family with sequence similarity 89 member A); INTERACTS WITH 1-naphthyl isothiocyanate; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC361441; mammary tumor virus receptor 2 isoform-like; MGC124908; RGD1309879; similar to mammary tumor virus receptor 2 isoform 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81969,607,391 - 69,620,019 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1969,607,391 - 69,620,019 (-)EnsemblGRCr8
mRatBN7.21952,710,002 - 52,722,630 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1952,710,019 - 52,722,631 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1959,494,876 - 59,507,700 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01960,345,371 - 60,358,082 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01962,421,326 - 62,434,148 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01957,502,308 - 57,514,896 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1957,502,308 - 57,514,896 (-)Ensemblrn6Rnor6.0
Rnor_5.01968,206,945 - 68,219,533 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41954,922,521 - 54,935,109 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1952,078,534 - 52,091,064 (-)NCBICelera
RGSC_v3.11954,927,404 - 54,939,990 (-)NCBI
Cytogenetic Map19q12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(1->4)-beta-D-glucan  (ISO)
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-hydroxypropanoic acid  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (EXP)
allopurinol  (EXP)
amiodarone  (ISO)
atrazine  (ISO)
Benzo[k]fluoranthene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bromobenzene  (EXP)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
chlordecone  (ISO)
chloroacetaldehyde  (ISO)
cidofovir anhydrous  (ISO)
cisplatin  (ISO)
clodronic acid  (ISO)
clofibric acid  (EXP)
cobalt dichloride  (EXP)
copper(II) chloride  (ISO)
cyclosporin A  (ISO)
dimethylarsinic acid  (ISO)
dorsomorphin  (ISO)
endosulfan  (EXP)
fenofibrate  (ISO)
flutamide  (EXP)
ibuprofen  (ISO)
ifosfamide  (ISO)
indole-3-methanol  (EXP)
leflunomide  (ISO)
mercury dibromide  (ISO)
methylarsonic acid  (ISO)
N-nitrosodiethylamine  (EXP)
nefazodone  (EXP)
orphenadrine  (EXP)
panobinostat  (ISO)
paracetamol  (EXP,ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
rac-lactic acid  (ISO)
SB 431542  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
tamoxifen  (ISO)
temozolomide  (ISO)
testosterone  (EXP)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triphenyl phosphate  (EXP)
tunicamycin  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15326124   PMID:15489334  


Genomics

Comparative Map Data
Fam89a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81969,607,391 - 69,620,019 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1969,607,391 - 69,620,019 (-)EnsemblGRCr8
mRatBN7.21952,710,002 - 52,722,630 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1952,710,019 - 52,722,631 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1959,494,876 - 59,507,700 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01960,345,371 - 60,358,082 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01962,421,326 - 62,434,148 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01957,502,308 - 57,514,896 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1957,502,308 - 57,514,896 (-)Ensemblrn6Rnor6.0
Rnor_5.01968,206,945 - 68,219,533 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41954,922,521 - 54,935,109 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1952,078,534 - 52,091,064 (-)NCBICelera
RGSC_v3.11954,927,404 - 54,939,990 (-)NCBI
Cytogenetic Map19q12NCBI
FAM89A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381231,018,958 - 231,040,254 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1231,018,958 - 231,040,254 (-)Ensemblhg38GRCh38
GRCh371231,154,704 - 231,176,000 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361229,221,545 - 229,242,608 (-)NCBIBuild 36Build 36hg18NCBI36
Celera1204,421,289 - 204,422,460 (-)NCBICelera
Cytogenetic Map1q42.2NCBI
HuRef1201,638,650 - 201,659,947 (-)NCBIHuRef
CHM1_11232,428,406 - 232,449,694 (-)NCBICHM1_1
T2T-CHM13v2.01230,399,853 - 230,421,165 (-)NCBIT2T-CHM13v2.0
Fam89a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398125,466,996 - 125,478,605 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8125,466,996 - 125,478,571 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm388124,740,257 - 124,751,866 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8124,740,257 - 124,751,832 (-)Ensemblmm10GRCm38
MGSCv378127,264,157 - 127,275,709 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv368127,626,347 - 127,637,899 (-)NCBIMGSCv36mm8
Celera8129,049,740 - 129,061,526 (-)NCBICelera
Cytogenetic Map8E2NCBI
cM Map872.81NCBI
Fam89a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554927,646,757 - 7,665,500 (+)Ensembl
ChiLan1.0NW_0049554927,646,755 - 7,665,500 (+)NCBIChiLan1.0ChiLan1.0
FAM89A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2118,165,345 - 18,186,655 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1118,361,018 - 18,382,618 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01206,569,308 - 206,590,599 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11211,595,932 - 211,616,861 (-)NCBIPanPan1.1PanPan1.1panPan2
FAM89A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.148,378,406 - 8,398,472 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha48,369,990 - 8,390,246 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.048,403,670 - 8,423,133 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl48,403,591 - 8,424,970 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.148,406,443 - 8,426,697 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.048,529,252 - 8,548,685 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.048,758,487 - 8,778,750 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Fam89a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934443,371,801 - 43,381,601 (+)NCBIHiC_Itri_2
FAM89A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1459,367,739 - 59,388,749 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11459,367,745 - 59,388,793 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21464,032,199 - 64,049,984 (+)NCBISscrofa10.2Sscrofa10.2susScr3
FAM89A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12568,290,665 - 68,309,447 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2568,291,575 - 68,309,411 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605570,197,004 - 70,215,808 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Fam89a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462477518,611,999 - 18,629,798 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462477518,611,986 - 18,629,798 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Fam89a
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11744,263,588 - 44,276,550 (-)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:87
Count of miRNA genes:80
Interacting mature miRNAs:82
Transcripts:ENSRNOT00000025705
Prediction methods:Miranda, Rnahybrid
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
2313395Anxrr26Anxiety related response QTL 26aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)194438513474246245Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)193253961574246245Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)196124916174246245Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)193177788874246245Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)194622677874246245Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191032907674246245Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)194172254674246245Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19219431774246245Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)193236531174246245Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19219431774246245Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)193628974246245Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191083361874246245Rat


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 66 146 90 90 59 86 59 6 340 184 11 126 73 91 31 16 16

Sequence


Ensembl Acc Id: ENSRNOT00000025705   ⟹   ENSRNOP00000025705
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1969,607,391 - 69,620,019 (-)Ensembl
mRatBN7.2 Ensembl1952,710,019 - 52,722,631 (-)Ensembl
Rnor_6.0 Ensembl1957,502,308 - 57,514,896 (-)Ensembl
RefSeq Acc Id: NM_001011711   ⟹   NP_001011711
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81969,607,391 - 69,620,019 (-)NCBI
mRatBN7.21952,710,002 - 52,722,630 (-)NCBI
Rnor_6.01957,502,308 - 57,514,896 (-)NCBI
Rnor_5.01968,206,945 - 68,219,533 (-)NCBI
RGSC_v3.41954,922,521 - 54,935,109 (-)RGD
Celera1952,078,534 - 52,091,064 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001011711 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI07922 (Get FASTA)   NCBI Sequence Viewer  
  AAS75315 (Get FASTA)   NCBI Sequence Viewer  
  EDL96739 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000025705
  ENSRNOP00000025705.4
GenBank Protein Q6Q0N2 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001011711   ⟸   NM_001011711
- UniProtKB: Q6Q0N2 (UniProtKB/Swiss-Prot),   A6KJ17 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000025705   ⟸   ENSRNOT00000025705

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6Q0N2-F1-model_v2 AlphaFold Q6Q0N2 1-176 view protein structure

Transcriptome

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

Promoters
RGD ID:13701240
Promoter ID:EPDNEW_R11763
Type:multiple initiation site
Name:Fam89a_1
Description:family with sequence similarity 89, member A
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_6.01957,514,894 - 57,514,954EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309879 AgrOrtholog
BioCyc Gene G2FUF-5234 BioCyc
Ensembl Genes ENSRNOG00000019022 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000025705 ENTREZGENE
  ENSRNOT00000025705.8 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7445343 IMAGE-MGC_LOAD
KEGG Report rno:361441 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124908 IMAGE-MGC_LOAD
NCBI Gene 361441 ENTREZGENE
PANTHER LEUCINE REPEAT ADAPTER PROTEIN 25 UniProtKB/Swiss-Prot
  PROTEIN FAM89A UniProtKB/Swiss-Prot
PhenoGen Fam89a PhenoGen
RatGTEx ENSRNOG00000019022 RatGTEx
UniProt A6KJ17 ENTREZGENE, UniProtKB/TrEMBL
  FA89A_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-05-19 Fam89a  family with sequence similarity 89, member A  RGD1309879  similar to mammary tumor virus receptor 2 isoform 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1309879  similar to mammary tumor virus receptor 2 isoform 2  RGD1309879_predicted  similar to mammary tumor virus receptor 2 isoform 2 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1309879_predicted  similar to mammary tumor virus receptor 2 isoform 2 (predicted)  LOC361441_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC361441_predicted  similar to mammary tumor virus receptor 2 isoform 2 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL