Fam228a (family with sequence similarity 228, member A) - Rat Genome Database

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Gene: Fam228a (family with sequence similarity 228, member A) Rattus norvegicus
Analyze
Symbol: Fam228a
Name: family with sequence similarity 228, member A
RGD ID: 1359275
Description: Orthologous to human FAM228A (family with sequence similarity 228 member A); INTERACTS WITH bisphenol A; PCB138; trichloroethene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical LOC313936; hypothetical protein LOC313936; LOC313936; UPF0638 protein C2orf84 homolog
RGD Orthologs
Human
Mouse
Bonobo
Squirrel
Pig
Green Monkey
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8633,447,427 - 33,469,553 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl633,447,427 - 33,468,989 (-)EnsemblGRCr8
mRatBN7.2627,727,982 - 27,750,140 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl627,727,984 - 27,750,061 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx628,020,227 - 28,042,333 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0628,336,142 - 28,358,248 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0627,810,677 - 27,832,789 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd634,890,519 - 34,912,625 (-)NCBIDahl_SR_JrHsd
Lyon_Normotensive634,326,771 - 34,348,885 (-)NCBILyon_Normotensive
Lyon_Hypertensive632,122,593 - 32,144,699 (-)NCBILyon_Hypertensive
F344_StmMcwi631,339,821 - 31,361,927 (-)NCBIF344_StmMcwi
Rnor_6.0630,074,331 - 30,097,876 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl630,074,303 - 30,097,790 (+)Ensemblrn6Rnor6.0
Rnor_5.0639,791,232 - 39,812,896 (-)NCBIRnor_5.0Rnor_5.0rn5
Celera627,197,392 - 27,219,790 (-)NCBICelera
Cytogenetic Map6q14NCBI
JBrowse:




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

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
3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.

Genomics

Comparative Map Data
Fam228a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8633,447,427 - 33,469,553 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl633,447,427 - 33,468,989 (-)EnsemblGRCr8
mRatBN7.2627,727,982 - 27,750,140 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl627,727,984 - 27,750,061 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx628,020,227 - 28,042,333 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0628,336,142 - 28,358,248 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0627,810,677 - 27,832,789 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd634,890,519 - 34,912,625 (-)NCBIDahl_SR_JrHsd
Lyon_Normotensive634,326,771 - 34,348,885 (-)NCBILyon_Normotensive
Lyon_Hypertensive632,122,593 - 32,144,699 (-)NCBILyon_Hypertensive
F344_StmMcwi631,339,821 - 31,361,927 (-)NCBIF344_StmMcwi
Rnor_6.0630,074,331 - 30,097,876 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl630,074,303 - 30,097,790 (+)Ensemblrn6Rnor6.0
Rnor_5.0639,791,232 - 39,812,896 (-)NCBIRnor_5.0Rnor_5.0rn5
Celera627,197,392 - 27,219,790 (-)NCBICelera
Cytogenetic Map6q14NCBI
FAM228A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38224,175,053 - 24,191,698 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl224,175,051 - 24,200,849 (+)Ensemblhg38GRCh38
GRCh37224,397,922 - 24,414,567 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36224,251,476 - 24,268,071 (+)NCBIBuild 36Build 36hg18NCBI36
Celera224,238,260 - 24,254,860 (+)NCBICelera
Cytogenetic Map2p23.3NCBI
HuRef224,136,803 - 24,153,398 (+)NCBIHuRef
CHM1_1224,327,343 - 24,343,940 (+)NCBICHM1_1
T2T-CHM13v2.0224,209,749 - 24,226,392 (+)NCBIT2T-CHM13v2.0
Fam228a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39124,763,668 - 4,788,652 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl124,763,670 - 4,788,430 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38124,713,805 - 4,738,439 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl124,713,670 - 4,738,430 (-)Ensemblmm10GRCm38
MGSCv37124,720,611 - 4,745,189 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36124,727,701 - 4,752,070 (-)NCBIMGSCv36mm8
Celera124,645,428 - 4,670,006 (-)NCBICelera
Cytogenetic Map12A1.1NCBI
cM Map122.09NCBI
FAM228A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v212102,318,721 - 102,442,037 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A102,322,684 - 102,352,856 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A24,168,688 - 24,197,586 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A24,268,825 - 24,294,617 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A24,268,825 - 24,285,466 (+)EnsemblpanPan2panpan1.1
Fam228a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)		 No map positions available.
FAM228A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.13114,501,837 - 114,537,384 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23121,775,453 - 121,800,912 (-)NCBISscrofa10.2Sscrofa10.2susScr3
FAM228A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11483,454,788 - 83,478,353 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1483,459,761 - 83,475,696 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604528,692,379 - 28,728,004 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Fam228a
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1725,372,336 - 25,387,645 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Fam228a
172 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:165
Count of miRNA genes:123
Interacting mature miRNAs:138
Transcripts:ENSRNOT00000070908
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6197587946975879Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)62009763565097635Rat
8552910Pigfal5Plasma insulin-like growth factor 1 level QTL 54.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)62265388967653889Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)62009763565097635Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6323998948239989Rat
1331779Rf38Renal function QTL 382.876kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)63118500276185002Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6197587946975879Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6197587946975879Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6144788383Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6197587946975879Rat
2292616Ept15Estrogen-induced pituitary tumorigenesis QTL 154.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6144788383Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6197587946975879Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62661831486868070Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)620859430113082285Rat
2301964Bp323Blood pressure QTL 3234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6186868070Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6323998948239989Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6323998948239989Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)63332884178328841Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62661831486868070Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6140163351Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)63093763275937632Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)63332884178328841Rat
70199Coreg1Compensatory renal growth QTL 111.8kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)61459947363457687Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)61608937261967788Rat
1358190Ept1Estrogen-induced pituitary tumorigenesis QTL 14.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6144788383Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6323998948239989Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)62228825767288257Rat

Markers in Region
D6Wox1  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8633,468,765 - 33,468,855 (+)Marker Load Pipeline
Rnor_6.0630,075,062 - 30,075,151NCBIRnor6.0
Rnor_5.0639,812,086 - 39,812,175UniSTSRnor5.0
Celera627,219,055 - 27,219,140UniSTS
RH 3.4 Map6116.99RGD
RH 3.4 Map6116.99UniSTS
RH 2.0 Map6249.8RGD
Cytogenetic Map6q12UniSTS


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
7 10 25 117 65 65 35 65 35 5 221 111 5 96 61 66 30 2 2

Sequence


Ensembl Acc Id: ENSRNOT00000070908   ⟹   ENSRNOP00000065885
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl633,447,427 - 33,468,975 (-)Ensembl
mRatBN7.2 Ensembl627,727,984 - 27,750,061 (-)Ensembl
Rnor_6.0 Ensembl630,074,303 - 30,097,790 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000094984   ⟹   ENSRNOP00000091169
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl633,447,427 - 33,468,989 (-)Ensembl
mRatBN7.2 Ensembl627,727,984 - 27,741,158 (-)Ensembl
RefSeq Acc Id: NM_001014074   ⟹   NP_001014096
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8633,447,427 - 33,469,537 (-)NCBI
mRatBN7.2627,727,982 - 27,750,093 (-)NCBI
Dahl_SR_JrHsd634,890,519 - 34,912,625 (-)NCBI
Lyon_Normotensive634,326,771 - 34,348,885 (-)NCBI
Lyon_Hypertensive632,122,593 - 32,144,699 (-)NCBI
F344_StmMcwi631,339,821 - 31,361,927 (-)NCBI
Rnor_6.0630,074,412 - 30,097,769 (+)NCBI
Rnor_5.0639,791,232 - 39,812,896 (-)NCBI
Celera627,197,392 - 27,219,790 (-)RGD
Sequence:
RefSeq Acc Id: XM_006239858   ⟹   XP_006239920
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8633,447,427 - 33,469,553 (-)NCBI
mRatBN7.2627,727,997 - 27,750,140 (-)NCBI
Rnor_6.0630,074,331 - 30,097,876 (+)NCBI
Rnor_5.0639,791,232 - 39,812,896 (-)NCBI
Sequence:
RefSeq Acc Id: XM_063261880   ⟹   XP_063117950
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8633,447,427 - 33,469,392 (-)NCBI
RefSeq Acc Id: NP_001014096   ⟸   NM_001014074
- UniProtKB: Q5XIN5 (UniProtKB/Swiss-Prot),   A6HAI8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006239920   ⟸   XM_006239858
- Peptide Label: isoform X1
- UniProtKB: Q5XIN5 (UniProtKB/Swiss-Prot),   A6HAI8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000065885   ⟸   ENSRNOT00000070908
Ensembl Acc Id: ENSRNOP00000091169   ⟸   ENSRNOT00000094984
RefSeq Acc Id: XP_063117950   ⟸   XM_063261880
- Peptide Label: isoform X2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5XIN5-F1-model_v2 AlphaFold Q5XIN5 1-306 view protein structure

Transcriptome

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

Promoters
RGD ID:13694481
Promoter ID:EPDNEW_R5004
Type:initiation region
Name:Fam228a_1
Description:family with sequence similarity 228, 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_6.0630,074,331 - 30,074,391EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359275 AgrOrtholog
BioCyc Gene G2FUF-38268 BioCyc
Ensembl Genes ENSRNOG00000050114 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000070908 ENTREZGENE
  ENSRNOT00000070908.3 UniProtKB/Swiss-Prot
  ENSRNOT00000094984 ENTREZGENE
IMAGE_CLONE IMAGE:7134934 IMAGE-MGC_LOAD
InterPro FAM228 UniProtKB/Swiss-Prot
KEGG Report rno:313936 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94467 IMAGE-MGC_LOAD
NCBI Gene 313936 ENTREZGENE
PANTHER PROTEIN FAM228A UniProtKB/Swiss-Prot
  PTHR28584 UniProtKB/Swiss-Prot
PhenoGen Fam228a PhenoGen
RatGTEx ENSRNOG00000050114 RatGTEx
UniProt A0A8I6AD49_RAT UniProtKB/TrEMBL
  A6HAI8 ENTREZGENE, UniProtKB/TrEMBL
  F228A_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-11-30 Fam228a  family with sequence similarity 228, member A  LOC313936  hypothetical LOC313936  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-29 LOC313936  hypothetical LOC313936      Symbol and Name status set to provisional 70820 PROVISIONAL