Fam78a (family with sequence similarity 78, member A) - Rat Genome Database

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Gene: Fam78a (family with sequence similarity 78, member A) Rattus norvegicus
Analyze
Symbol: Fam78a
Name: family with sequence similarity 78, member A
RGD ID: 1566351
Description: Orthologous to human FAM78A (family with sequence similarity 78 member A); INTERACTS WITH (+)-schisandrin B; 3-chloropropane-1,2-diol; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC499776; RGD1566351; similar to RIKEN cDNA A130092J06 gene
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
GRCr8335,753,712 - 35,771,600 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl335,753,712 - 35,770,448 (-)EnsemblGRCr8
mRatBN7.2315,355,958 - 15,376,330 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl315,355,955 - 15,373,812 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx318,425,573 - 18,442,182 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0327,010,559 - 27,027,168 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0325,261,310 - 25,277,926 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0311,086,016 - 11,105,151 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl311,087,299 - 11,102,515 (-)Ensemblrn6Rnor6.0
Rnor_5.0316,438,610 - 16,454,692 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4311,183,349 - 11,197,249 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera310,103,056 - 10,122,065 (-)NCBICelera
Cytogenetic Map3p12NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Fam78a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8335,753,712 - 35,771,600 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl335,753,712 - 35,770,448 (-)EnsemblGRCr8
mRatBN7.2315,355,958 - 15,376,330 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl315,355,955 - 15,373,812 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx318,425,573 - 18,442,182 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0327,010,559 - 27,027,168 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0325,261,310 - 25,277,926 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0311,086,016 - 11,105,151 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl311,087,299 - 11,102,515 (-)Ensemblrn6Rnor6.0
Rnor_5.0316,438,610 - 16,454,692 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4311,183,349 - 11,197,249 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera310,103,056 - 10,122,065 (-)NCBICelera
Cytogenetic Map3p12NCBI
FAM78A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389131,258,078 - 131,281,045 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9131,258,076 - 131,277,365 (-)Ensemblhg38GRCh38
GRCh379134,133,465 - 134,153,422 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369133,123,286 - 133,141,727 (-)NCBIBuild 36Build 36hg18NCBI36
Build 349131,163,019 - 131,181,460NCBI
Celera9104,672,525 - 104,690,968 (-)NCBICelera
Cytogenetic Map9q34.13NCBI
HuRef9103,624,314 - 103,642,697 (-)NCBIHuRef
CHM1_19134,283,073 - 134,301,504 (-)NCBICHM1_1
T2T-CHM13v2.09143,466,357 - 143,489,327 (-)NCBIT2T-CHM13v2.0
Fam78a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39231,932,720 - 31,977,484 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl231,940,067 - 31,974,869 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm39 Ensembl231,940,098 - 31,954,923 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38232,045,969 - 32,087,472 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl232,050,055 - 32,084,857 (-)Ensemblmm10GRCm38
MGSCv37231,922,405 - 31,939,225 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36231,888,894 - 31,905,714 (-)NCBIMGSCv36mm8
Celera231,770,221 - 31,787,261 (-)NCBICelera
Cytogenetic Map2BNCBI
cM Map222.0NCBI
Fam78a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555131,060,020 - 1,073,817 (-)Ensembl
ChiLan1.0NW_0049555131,060,145 - 1,073,817 (-)NCBIChiLan1.0ChiLan1.0
FAM78A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2118,079,269 - 8,099,238 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan198,081,612 - 8,104,304 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09102,380,073 - 102,399,992 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19131,024,410 - 131,042,975 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9131,024,410 - 131,042,975 (-)EnsemblpanPan2panpan1.1
FAM78A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1952,805,512 - 52,818,197 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl952,805,927 - 52,818,190 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha952,070,680 - 52,083,918 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0953,706,556 - 53,719,802 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl953,707,023 - 53,719,288 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1952,484,097 - 52,499,461 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0952,804,604 - 52,817,833 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0952,897,599 - 52,910,840 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Fam78a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947198,317,563 - 198,327,887 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648718,083,859 - 18,096,699 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493648718,086,085 - 18,096,656 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FAM78A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1271,242,333 - 271,257,836 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11271,242,312 - 271,257,839 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21305,271,852 - 305,284,934 (-)NCBISscrofa10.2Sscrofa10.2susScr3
FAM78A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1126,862,627 - 6,881,942 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl126,863,189 - 6,881,991 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660798,627,260 - 8,645,621 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Fam78a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247604,623,937 - 4,639,240 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247604,621,149 - 4,639,175 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Fam78a
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v153,547,813 - 3,565,872 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Fam78a
178 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:46
Count of miRNA genes:43
Interacting mature miRNAs:46
Transcripts:ENSRNOT00000035580
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)32267715050766390Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)32905627547904329Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
10450811Scl73Serum cholesterol level QTL 734.70.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3655634751556347Rat
10450808Scl72Serum cholesterol level QTL 724.40.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
10450806Scl71Serum cholesterol level QTL 715.80.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)32862533967641995Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)3612543751125437Rat
8693641Alc30Alcohol consumption QTL 3020.739drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)33083238444921701Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)33540319997383526Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3136721849Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31141509147Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3655634751556347Rat
1558657Cm43Cardiac mass QTL 436.63e-08heart mass (VT:0007028)heart wet weight (CMO:0000069)32267715050766390Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)31527234860272348Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)32905627547904329Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35675975141509147Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3655634751556347Rat


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 67 162 91 90 59 92 59 6 356 192 11 141 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000035580   ⟹   ENSRNOP00000032068
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl335,753,712 - 35,770,448 (-)Ensembl
mRatBN7.2 Ensembl315,355,955 - 15,373,812 (-)Ensembl
Rnor_6.0 Ensembl311,087,299 - 11,102,515 (-)Ensembl
RefSeq Acc Id: NM_001399463   ⟹   NP_001386392
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8335,753,712 - 35,770,448 (-)NCBI
mRatBN7.2315,355,958 - 15,372,696 (-)NCBI
RefSeq Acc Id: XM_575110   ⟹   XP_575110
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8335,755,995 - 35,771,600 (-)NCBI
mRatBN7.2315,355,958 - 15,373,791 (-)NCBI
Rnor_6.0311,086,016 - 11,105,151 (-)NCBI
Rnor_5.0316,438,610 - 16,454,692 (-)NCBI
RGSC_v3.4311,183,349 - 11,197,249 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001386392 (Get FASTA)   NCBI Sequence Viewer  
  XP_575110 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000032068
  ENSRNOP00000032068.3
RefSeq Acc Id: XP_575110   ⟸   XM_575110
- Peptide Label: isoform X1
- UniProtKB: D3ZW92 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000032068   ⟸   ENSRNOT00000035580
RefSeq Acc Id: NP_001386392   ⟸   NM_001399463
- UniProtKB: D3ZW92 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZW92-F1-model_v2 AlphaFold D3ZW92 1-283 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:1566351 AgrOrtholog
BioCyc Gene G2FUF-50163 BioCyc
Ensembl Genes ENSRNOG00000023352 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000035580 ENTREZGENE
  ENSRNOT00000035580.6 UniProtKB/TrEMBL
InterPro FAM78 UniProtKB/TrEMBL
NCBI Gene 499776 ENTREZGENE
PANTHER PTHR31655 UniProtKB/TrEMBL
  PTHR31655:SF3 UniProtKB/TrEMBL
PhenoGen Fam78a PhenoGen
RatGTEx ENSRNOG00000023352 RatGTEx
UniProt D3ZW92 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Fam78a  family with sequence similarity 78, member A  RGD1566351_predicted  similar to RIKEN cDNA A130092J06 gene (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1566351_predicted  similar to RIKEN cDNA A130092J06 gene (predicted)  LOC499776  similar to RIKEN cDNA A130092J06 gene  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC499776  similar to RIKEN cDNA A130092J06 gene      Symbol and Name status set to provisional 70820 PROVISIONAL