Fam47a (family with sequence similarity 47, member A) - Rat Genome Database

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Gene: Fam47a (family with sequence similarity 47, member A) Rattus norvegicus
Analyze
Symbol: Fam47a
Name: family with sequence similarity 47, member A
RGD ID: 2324262
Description: Predicted to be involved in transcription initiation-coupled chromatin remodeling. Predicted to be part of chromatin. Orthologous to several human genes including FAM47A (family with sequence similarity 47 member A); INTERACTS WITH CGP 52608 (ortholog); resveratrol (ortholog); valproic acid (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC100362696; rCG36469-like; uncharacterized protein LOC100362696
RGD Orthologs
Human
Bonobo
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X46,649,284 - 46,650,940 (+)NCBIGRCr8
mRatBN7.2X42,762,231 - 42,763,887 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX42,762,229 - 42,763,883 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0X45,965,258 - 45,966,930 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX45,965,301 - 45,966,934 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X46,183,917 - 46,185,531 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X64,506,270 - 64,507,565 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX43,410,152 - 43,411,824 (+)NCBICelera
Cytogenetic MapXq21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
chromatin  (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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Fam47a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X46,649,284 - 46,650,940 (+)NCBIGRCr8
mRatBN7.2X42,762,231 - 42,763,887 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX42,762,229 - 42,763,883 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0X45,965,258 - 45,966,930 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX45,965,301 - 45,966,934 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X46,183,917 - 46,185,531 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X64,506,270 - 64,507,565 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX43,410,152 - 43,411,824 (+)NCBICelera
Cytogenetic MapXq21NCBI
FAM47A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X34,129,752 - 34,132,314 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX34,129,752 - 34,132,314 (-)EnsemblGRCh38hg38GRCh38
GRCh37X34,147,869 - 34,150,431 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X34,057,794 - 34,060,349 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X33,907,533 - 33,910,085NCBI
CeleraX38,275,096 - 38,277,674 (-)NCBICelera
Cytogenetic MapXp21.1NCBI
HuRefX31,885,862 - 31,888,440 (-)NCBIHuRef
CHM1_1X34,178,212 - 34,180,790 (-)NCBICHM1_1
T2T-CHM13v2.0X33,727,875 - 33,730,437 (-)NCBIT2T-CHM13v2.0
FAM47A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X35,960,097 - 35,967,398 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X35,963,474 - 35,970,775 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X26,764,406 - 26,767,087 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X34,300,250 - 34,302,333 (-)NCBIpanpan1.1PanPan1.1panPan2

Variants

.
Variants in Fam47a
3 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:92
Count of miRNA genes:79
Interacting mature miRNAs:80
Transcripts:ENSRNOT00000005141
Prediction methods:Microtar, Miranda, Pita
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X143491017Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X292789847927898Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7440600049406000Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X449454949494549Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
71116Niddm16Non-insulin dependent diabetes mellitus QTL 167.81blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X1529780260297802Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat


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 integumental system musculoskeletal system nervous system reproductive system respiratory system appendage
High
Medium 7
Low 1 4
Below cutoff 1 1 1 1 6 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000005141   ⟹   ENSRNOP00000055260
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX42,762,229 - 42,763,883 (+)Ensembl
Rnor_6.0 EnsemblX45,965,301 - 45,966,934 (+)Ensembl
RefSeq Acc Id: NM_001408917   ⟹   NP_001395846
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X46,649,284 - 46,650,940 (+)NCBI
mRatBN7.2X42,762,231 - 42,763,887 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001395846 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL96069 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000055260
  ENSRNOP00000055260.3
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000055260   ⟸   ENSRNOT00000005141
RefSeq Acc Id: NP_001395846   ⟸   NM_001408917
- UniProtKB: D3ZB93 (UniProtKB/TrEMBL),   A6IPU4 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZB93-F1-model_v2 AlphaFold D3ZB93 1-431 view protein structure

Transcriptome

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

Promoters
RGD ID:13701828
Promoter ID:EPDNEW_R12350
Type:multiple initiation site
Name:Fam47a_1
Description:family with sequence similarity 47, 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_6.0X45,965,290 - 45,965,350EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2324262 AgrOrtholog
BioCyc Gene G2FUF-2386 BioCyc
Ensembl Genes ENSRNOG00000003836 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000005141 ENTREZGENE
  ENSRNOT00000005141.8 UniProtKB/TrEMBL
InterPro FAM47 UniProtKB/TrEMBL
KEGG Report rno:100362696 UniProtKB/TrEMBL
NCBI Gene 100362696 ENTREZGENE
PANTHER FAMILY WITH SEQUENCE SIMILARITY 47, MEMBER A UniProtKB/TrEMBL
  PTHR46449 UniProtKB/TrEMBL
Pfam FAM47 UniProtKB/TrEMBL
PhenoGen Fam47a PhenoGen
RatGTEx ENSRNOG00000003836 RatGTEx
UniProt A6IPU4 ENTREZGENE, UniProtKB/TrEMBL
  D3ZB93 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-08-30 Fam47a  family with sequence similarity 47, member A  LOC100362696  rCG36469-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-06 LOC100362696  rCG36469-like      Symbol and Name status set to provisional 70820 PROVISIONAL