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

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Gene: Fam89a (family with sequence similarity 89, member A) Mus musculus
Analyze
Symbol: Fam89a
Name: family with sequence similarity 89, member A
RGD ID: 1320460
MGI Page MGI
Description: Is expressed in cranial ganglion and otocyst. Orthologous to human FAM89A (family with sequence similarity 89 member A).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 2310031A18Rik
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398125,466,996 - 125,478,605 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8125,466,996 - 125,478,571 (-)EnsemblGRCm39 Ensembl
GRCm388124,740,257 - 124,751,866 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8124,740,257 - 124,751,832 (-)EnsemblGRCm38mm10GRCm38
MGSCv378127,264,157 - 127,275,709 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368127,626,347 - 127,637,899 (-)NCBIMGSCv36mm8
Celera8129,049,740 - 129,061,526 (-)NCBICelera
Cytogenetic Map8E2NCBI
cM Map872.81NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

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:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:15031102   PMID:16141072   PMID:16141073   PMID:21267068  


Genomics

Comparative Map Data
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 Ensembl
GRCm388124,740,257 - 124,751,866 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8124,740,257 - 124,751,832 (-)EnsemblGRCm38mm10GRCm38
MGSCv378127,264,157 - 127,275,709 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368127,626,347 - 127,637,899 (-)NCBIMGSCv36mm8
Celera8129,049,740 - 129,061,526 (-)NCBICelera
Cytogenetic Map8E2NCBI
cM Map872.81NCBI
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 (-)EnsemblGRCh38hg38GRCh38
GRCh371231,154,704 - 231,176,000 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361229,221,545 - 229,242,608 (-)NCBINCBI36Build 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
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81969,607,391 - 69,620,019 (-)NCBIGRCr8
mRatBN7.21952,710,002 - 52,722,630 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1952,710,019 - 52,722,631 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1959,494,876 - 59,507,700 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01960,345,371 - 60,358,082 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01962,421,326 - 62,434,148 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01957,502,308 - 57,514,896 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1957,502,308 - 57,514,896 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01968,206,945 - 68,219,533 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41954,922,521 - 54,935,109 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11954,927,404 - 54,939,990 (-)NCBI
Celera1952,078,534 - 52,091,064 (-)NCBICelera
Cytogenetic Map19q12NCBI
Fam89a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554927,646,757 - 7,665,500 (+)EnsemblChiLan1.0
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_Tasha
ROS_Cfam_1.048,403,670 - 8,423,133 (+)NCBIROS_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_1.0
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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462477518,611,986 - 18,629,798 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Fam89a
452 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:217
Count of miRNA genes:195
Interacting mature miRNAs:199
Transcripts:ENSMUST00000055257
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
27095912Pglq14_mpelvic girdle length QTL 14, 16 week (mouse)874126628126826739Mouse
27226796Scvln16_msacral vertebrae length 2, 16 week (mouse)889726628130027694Mouse
1357494Obsty2_mobesity 2 (mouse)Not determined896245241129745061Mouse
12880431Fgf23lq2_mFGF23 serum level QTL 2 (mouse)897626632130127694Mouse
11252141Fdr2_mfat response to dietary restriction 2 (mouse)898390634130127694Mouse
1301481Lith11_mlithogenic gene 11 (mouse)Not determined898563635130127694Mouse
1302105Im1_mImmunoregulatory 1 (mouse)Not determined899828531130127694Mouse
1301080Sluc9_msusceptibility to lung cancer 9 (mouse)Not determined899828531130127694Mouse
4141435Fbtq3_mfemoral bone trait QTL 3 (mouse)Not determined8100965309130127694Mouse
1301316Dntcs1_mdental caries susceptibility 1 (mouse)Not determined8103443553127781786Mouse
11532691Sluc38_msusceptibility to lung cancer 38 (mouse)8105033977130127694Mouse
11532692Sluc38a_msusceptibility to lung cancer 38a (mouse)8105033977130127694Mouse
14746994Manh65_mmandible shape 65 (mouse)8106489629130127694Mouse
10412273Fcd1_mfunctional capillary density 1 (mouse)Not determined8110415083130127694Mouse
10412274Leci1_mleukocyte endothelial cell interactions 1 (mouse)Not determined8110415083130127694Mouse
12904938Edlmmq7_mextensor digitorum longus muscle mass QTL 7 (mouse)8111481497130127694Mouse
12904960Gmmq6_mgastrocnemius muscle mass QTL 6 (mouse)8111481497130127694Mouse
4141546Mrdq3_mmodifier of retinal degeneration QTL 3 (mouse)Not determined114439420126055880Mouse
26884375Skwq2_mskull length QTL 2, 5 week (mouse)8120726739130027694Mouse
1357841Phdlc2_mplasma HDL cholesterol 2 (mouse)Not determined8125191161129745061Mouse


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000055257   ⟹   ENSMUSP00000058156
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl8125,466,996 - 125,478,571 (-)Ensembl
GRCm38.p6 Ensembl8124,740,257 - 124,751,832 (-)Ensembl
RefSeq Acc Id: NM_001081120   ⟹   NP_001074589
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm398125,466,996 - 125,478,605 (-)NCBI
GRCm388124,740,257 - 124,751,866 (-)NCBI
MGSCv378127,264,157 - 127,275,709 (-)RGD
Celera8129,049,740 - 129,061,526 (-)RGD
cM Map8 ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_001074589 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH23460 (Get FASTA)   NCBI Sequence Viewer  
  AAI15735 (Get FASTA)   NCBI Sequence Viewer  
  AAI15820 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000058156
  ENSMUSP00000058156.6
GenBank Protein Q14BJ1 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001074589   ⟸   NM_001081120
- UniProtKB: Q8R3X3 (UniProtKB/Swiss-Prot),   Q14BJ1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000058156   ⟸   ENSMUST00000055257

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q14BJ1-F1-model_v2 AlphaFold Q14BJ1 1-175 view protein structure

Promoters
RGD ID:8668641
Promoter ID:EPDNEW_M12352
Type:initiation region
Name:Fam89a_1
Description:Mus musculus family with sequence similarity 89, member A , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm388124,751,848 - 124,751,908EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1916877 AgrOrtholog
Ensembl Genes ENSMUSG00000043068 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000055257 ENTREZGENE
  ENSMUST00000055257.7 UniProtKB/Swiss-Prot
KEGG Report mmu:69627 UniProtKB/Swiss-Prot
MGD MGI:1916877 ENTREZGENE
NCBI Gene 69627 ENTREZGENE
PANTHER LEUCINE REPEAT ADAPTER PROTEIN 25 UniProtKB/Swiss-Prot
  PROTEIN FAM89A UniProtKB/Swiss-Prot
PhenoGen Fam89a PhenoGen
UniProt FA89A_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE
  Q8R3X3 ENTREZGENE
UniProt Secondary Q8R3X3 UniProtKB/Swiss-Prot