Frem3 (FRAS1 related extracellular matrix 3) - Rat Genome Database

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Gene: Frem3 (FRAS1 related extracellular matrix 3) Rattus norvegicus
Analyze
Symbol: Frem3
Name: FRAS1 related extracellular matrix 3
RGD ID: 1562701
Description: Predicted to be involved in anatomical structure morphogenesis. Predicted to be located in basement membrane. Orthologous to human FREM3 (FRAS1 related extracellular matrix 3); INTERACTS WITH 2,2',5,5'-tetrachlorobiphenyl; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Fras1 related extracellular matrix protein 3; FRAS1-related extracellular matrix protein 3; LOC307767; RGD1562701; similar to Fras1 related extracellular matrix protein 1
RGD Orthologs
Human
Mouse
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
GRCr81944,212,842 - 44,271,137 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1944,212,769 - 44,271,336 (-)EnsemblGRCr8
mRatBN7.21927,308,469 - 27,366,771 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1927,308,469 - 27,366,771 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1934,166,801 - 34,225,130 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01934,820,857 - 34,879,175 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01937,040,538 - 37,098,883 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01930,973,329 - 31,032,331 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1930,973,329 - 31,031,817 (-)Ensemblrn6Rnor6.0
Rnor_5.01941,877,775 - 41,936,252 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41929,159,168 - 29,217,781 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1926,824,893 - 26,883,435 (-)NCBICelera
Cytogenetic Map19q11NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:17251066   PMID:17462874   PMID:17596926   PMID:22664934  


Genomics

Comparative Map Data
Frem3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81944,212,842 - 44,271,137 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1944,212,769 - 44,271,336 (-)EnsemblGRCr8
mRatBN7.21927,308,469 - 27,366,771 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1927,308,469 - 27,366,771 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1934,166,801 - 34,225,130 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01934,820,857 - 34,879,175 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01937,040,538 - 37,098,883 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01930,973,329 - 31,032,331 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1930,973,329 - 31,031,817 (-)Ensemblrn6Rnor6.0
Rnor_5.01941,877,775 - 41,936,252 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41929,159,168 - 29,217,781 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1926,824,893 - 26,883,435 (-)NCBICelera
Cytogenetic Map19q11NCBI
FREM3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh384143,577,302 - 143,700,675 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl4143,577,302 - 143,700,675 (-)Ensemblhg38GRCh38
GRCh374144,498,455 - 144,621,828 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 364144,717,905 - 144,841,278 (-)NCBIBuild 36Build 36hg18NCBI36
Celera4141,828,573 - 141,951,867 (-)NCBICelera
Cytogenetic Map4q31.21NCBI
HuRef4140,228,646 - 140,351,456 (-)NCBIHuRef
CHM1_14144,475,765 - 144,598,998 (-)NCBICHM1_1
T2T-CHM13v2.04146,894,539 - 147,017,927 (-)NCBIT2T-CHM13v2.0
Frem3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39881,337,668 - 81,422,186 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl881,337,709 - 81,421,985 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38880,611,039 - 80,695,557 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl880,611,080 - 80,695,356 (+)Ensemblmm10GRCm38
MGSCv37883,134,938 - 83,219,456 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36883,506,785 - 83,591,303 (+)NCBIMGSCv36mm8
Celera884,884,297 - 84,969,451 (+)NCBICelera
Cytogenetic Map8C2NCBI
cM Map838.35NCBI
FREM3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v23141,449,208 - 141,584,507 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan14141,836,986 - 141,949,008 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v04135,935,713 - 136,046,140 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.14147,237,823 - 147,367,264 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4147,237,823 - 147,367,264 (-)EnsemblpanPan2panpan1.1
FREM3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha1543,275,987 - 43,283,269 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01543,543,971 - 43,622,133 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.11542,820,412 - 42,827,645 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01542,904,179 - 42,911,457 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01543,175,576 - 43,182,809 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Frem3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530147,347,897 - 47,413,004 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365354,785,226 - 4,850,346 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365354,785,232 - 4,850,406 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FREM3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1884,122,183 - 84,178,551 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2889,278,812 - 89,333,418 (+)NCBISscrofa10.2Sscrofa10.2susScr3
FREM3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1790,430,562 - 90,543,880 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl790,430,565 - 90,541,048 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366603770,036,721 - 70,146,594 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Frem3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248532,999,418 - 3,062,534 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Frem3
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11719,379,179 - 19,446,286 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Frem3
367 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:129
Count of miRNA genes:105
Interacting mature miRNAs:112
Transcripts:ENSRNOT00000059896
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
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)191922068964220689Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19799775052997750Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)193628974246245Rat
61328Eae8Experimental allergic encephalomyelitis QTL 84nervous system integrity trait (VT:0010566)percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)194172060949971820Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)193253961574246245Rat
1558656Prcs1Prostate cancer susceptibility QTL 15prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)193128753251431640Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19799775052997750Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)193177788874246245Rat
1554318Bmd5Bone mineral density QTL 512.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)192318858668188586Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)194172254674246245Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19219431774246245Rat
1354633Bw28Body weight QTL 286.04body mass (VT:0001259)body weight (CMO:0000012)194072709254856850Rat
61407Scl12Serum cholesterol level QTL 120.001blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)193009938347207961Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19799775052997750Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191032907674246245Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)19574806450748064Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)193236531174246245Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)192409397369093973Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191083361874246245Rat
2303628Vencon9Ventilatory control QTL 90.005respiration trait (VT:0001943)minute ventilation (CMO:0000132)192318858668188586Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19799775052997750Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)192010930665109306Rat
1354607Gmadr1Adrenal mass QTL 15.83adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)194072709254856850Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19219431774246245Rat
1354600Salc2Saline consumption QTL 29.910.001drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)194072709254856850Rat

Markers in Region
D19Rat110  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81944,260,968 - 44,261,185 (+)Marker Load Pipeline
mRatBN7.21927,356,602 - 27,356,819 (+)MAPPERmRatBN7.2
Rnor_6.01931,021,649 - 31,021,865NCBIRnor6.0
Rnor_5.01941,926,084 - 41,926,300UniSTSRnor5.0
RGSC_v3.41929,207,613 - 29,207,829UniSTSRGSC3.4
RGSC_v3.41929,207,612 - 29,207,828RGDRGSC3.4
Celera1926,873,267 - 26,873,483UniSTS
RGSC_v3.11929,212,435 - 29,212,922RGD
SHRSP x BN Map1920.3398RGD
SHRSP x BN Map1920.3398UniSTS
Cytogenetic Map19q11UniSTS
RH142598  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21927,308,654 - 27,308,773 (+)MAPPERmRatBN7.2
Rnor_6.01930,973,515 - 30,973,633NCBIRnor6.0
Rnor_5.01941,877,961 - 41,878,079UniSTSRnor5.0
RGSC_v3.41929,159,354 - 29,159,472UniSTSRGSC3.4
Celera1926,825,079 - 26,825,197UniSTS
Cytogenetic Map19q11UniSTS


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
10 1 5 136 28 38 12 38 12 6 104 57 7 130 25 68 26 16 16

Sequence


Ensembl Acc Id: ENSRNOT00000059896   ⟹   ENSRNOP00000056641
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1944,212,842 - 44,271,336 (-)Ensembl
mRatBN7.2 Ensembl1927,308,469 - 27,366,771 (-)Ensembl
Rnor_6.0 Ensembl1930,973,329 - 31,031,817 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000160388   ⟹   ENSRNOP00000110220
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1944,212,842 - 44,271,336 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000161079   ⟹   ENSRNOP00000111589
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1944,213,208 - 44,271,336 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000163033   ⟹   ENSRNOP00000101654
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1944,212,769 - 44,271,336 (-)Ensembl
RefSeq Acc Id: NM_001191699   ⟹   NP_001178628
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81944,212,842 - 44,271,137 (-)NCBI
mRatBN7.21927,308,469 - 27,366,771 (-)NCBI
Rnor_6.01930,973,329 - 31,031,817 (-)NCBI
Rnor_5.01941,877,775 - 41,936,252 (-)NCBI
Celera1926,824,893 - 26,883,435 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001178628 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL92302 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000056641
  ENSRNOP00000056641.3
  ENSRNOP00000101654.1
  ENSRNOP00000110220.1
  ENSRNOP00000111589.1
RefSeq Acc Id: NP_001178628   ⟸   NM_001191699
- Peptide Label: precursor
- UniProtKB: D3ZYN7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000056641   ⟸   ENSRNOT00000059896
Ensembl Acc Id: ENSRNOP00000110220   ⟸   ENSRNOT00000160388
Ensembl Acc Id: ENSRNOP00000111589   ⟸   ENSRNOT00000161079
Ensembl Acc Id: ENSRNOP00000101654   ⟸   ENSRNOT00000163033
Protein Domains
Calx-beta

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZYN7-F1-model_v2 AlphaFold D3ZYN7 1-2124 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:1562701 AgrOrtholog
BioCyc Gene G2FUF-5971 BioCyc
Ensembl Genes ENSRNOG00000039152 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000059896 ENTREZGENE
  ENSRNOT00000059896.5 UniProtKB/TrEMBL
  ENSRNOT00000160388.1 UniProtKB/TrEMBL
  ENSRNOT00000161079.1 UniProtKB/TrEMBL
  ENSRNOT00000163033.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.2030 UniProtKB/TrEMBL
InterPro CalX-like_sf UniProtKB/TrEMBL
  Calx_beta UniProtKB/TrEMBL
  CSPG_rpt UniProtKB/TrEMBL
  FRAS1-rel_N UniProtKB/TrEMBL
  FRAS1_ECM UniProtKB/TrEMBL
KEGG Report rno:307767 UniProtKB/TrEMBL
NCBI Gene 307767 ENTREZGENE
PANTHER MATRIX PROTEIN, PUTATIVE-RELATED UniProtKB/TrEMBL
  PTHR45739:SF5 UniProtKB/TrEMBL
Pfam Cadherin_3 UniProtKB/TrEMBL
  Calx-beta UniProtKB/TrEMBL
  Frem_N UniProtKB/TrEMBL
PhenoGen Frem3 PhenoGen
PROSITE CSPG UniProtKB/TrEMBL
RatGTEx ENSRNOG00000039152 RatGTEx
SMART Calx_beta UniProtKB/TrEMBL
Superfamily-SCOP SSF141072 UniProtKB/TrEMBL
UniProt A0ABK0L9R9_RAT UniProtKB/TrEMBL
  A0ABK0LKW6_RAT UniProtKB/TrEMBL
  A0ABK0M0J4_RAT UniProtKB/TrEMBL
  D3ZYN7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-25 Frem3  FRAS1 related extracellular matrix 3  Frem3  Fras1 related extracellular matrix protein 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-29 Frem3  Fras1 related extracellular matrix protein 3  RGD1562701_predicted  similar to Fras1 related extracellular matrix protein 1 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1562701_predicted  similar to Fras1 related extracellular matrix protein 1 (predicted)  LOC307767  similar to Fras1 related extracellular matrix protein 1  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC307767  similar to Fras1 related extracellular matrix protein 1      Symbol and Name status set to provisional 70820 PROVISIONAL