Fsd1 (fibronectin type III and SPRY domain containing 1) - Rat Genome Database

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Gene: Fsd1 (fibronectin type III and SPRY domain containing 1) Rattus norvegicus
Analyze
Symbol: Fsd1
Name: fibronectin type III and SPRY domain containing 1
RGD ID: 1583850
Description: Predicted to enable identical protein binding activity and microtubule binding activity. Predicted to be involved in cytoplasmic microtubule organization; regulation of cytokinesis; and regulation of mitotic spindle organization. Predicted to be located in centrosome. Predicted to be active in microtubule. Orthologous to human FSD1 (fibronectin type III and SPRY domain containing 1); INTERACTS WITH bisphenol A; cadmium dichloride; thioacetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: fibronectin type 3 and SPRY domain-containing protein; fibronectin type 3 and SPRY domain-containing protein-like1; fibronectin type III and SPRY domain-containing protein 1; Fsd1l1; LOC301506; similar to fibronectin type 3 and SPRY domain-containing protein
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
GRCr89905,418 - 908,938 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl9905,430 - 915,364 (+)EnsemblGRCr8
mRatBN7.29818,241 - 821,761 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl9818,263 - 828,185 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx91,265,272 - 1,268,793 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.096,612,522 - 6,616,042 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.095,570,304 - 5,573,825 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0911,076,670 - 11,080,190 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl911,067,369 - 11,080,155 (-)Ensemblrn6Rnor6.0
Rnor_5.0910,061,938 - 10,065,458 (-)NCBIRnor_5.0Rnor_5.0rn5
Celera97,684,706 - 7,688,226 (-)NCBICelera
Cytogenetic Map9q11NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
centrosome  (IEA,ISO)
cleavage furrow  (IEA)
cytosol  (IEA,ISO)
microtubule  (IBA,IEA,ISO)
nucleus  (IEA)

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. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12154070   PMID:12445389   PMID:12477932  


Genomics

Comparative Map Data
Fsd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr89905,418 - 908,938 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl9905,430 - 915,364 (+)EnsemblGRCr8
mRatBN7.29818,241 - 821,761 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl9818,263 - 828,185 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx91,265,272 - 1,268,793 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.096,612,522 - 6,616,042 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.095,570,304 - 5,573,825 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0911,076,670 - 11,080,190 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl911,067,369 - 11,080,155 (-)Ensemblrn6Rnor6.0
Rnor_5.0910,061,938 - 10,065,458 (-)NCBIRnor_5.0Rnor_5.0rn5
Celera97,684,706 - 7,688,226 (-)NCBICelera
Cytogenetic Map9q11NCBI
FSD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38194,304,598 - 4,323,836 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl194,304,595 - 4,323,843 (+)Ensemblhg38GRCh38
GRCh37194,304,595 - 4,323,833 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36194,255,691 - 4,274,838 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34194,255,690 - 4,274,838NCBI
Celera19627,256 - 628,117 (-)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef194,068,531 - 4,086,554 (+)NCBIHuRef
CHM1_1194,304,209 - 4,323,460 (+)NCBICHM1_1
T2T-CHM13v2.0194,287,878 - 4,307,238 (+)NCBIT2T-CHM13v2.0
Fsd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391756,293,475 - 56,303,881 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1756,293,509 - 56,303,881 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381755,986,462 - 55,996,883 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1755,986,509 - 55,996,881 (+)Ensemblmm10GRCm38
MGSCv371756,125,934 - 56,136,304 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361755,579,804 - 55,590,174 (+)NCBIMGSCv36mm8
Celera1759,405,038 - 59,415,407 (+)NCBICelera
Cytogenetic Map17DNCBI
cM Map1729.1NCBI
Fsd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554954,549,220 - 4,561,073 (-)Ensembl
ChiLan1.0NW_0049554954,549,067 - 4,561,223 (-)NCBIChiLan1.0ChiLan1.0
FSD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2208,701,598 - 8,722,162 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1197,931,823 - 7,951,570 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0193,327,681 - 3,347,176 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1194,274,389 - 4,294,179 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl194,274,389 - 4,294,179 (+)EnsemblpanPan2panpan1.1
FSD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12055,333,937 - 55,344,861 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2055,333,785 - 55,344,843 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2055,062,100 - 55,080,355 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02055,993,017 - 56,011,507 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2055,993,071 - 56,004,636 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12055,053,501 - 55,071,720 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02055,534,443 - 55,552,704 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02055,733,089 - 55,751,345 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Fsd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118215,365,410 - 215,373,017 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365882,461,411 - 2,469,507 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365882,461,582 - 2,469,373 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FSD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl274,471,744 - 74,485,786 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1274,471,744 - 74,485,788 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2274,964,692 - 74,978,738 (-)NCBISscrofa10.2Sscrofa10.2susScr3
FSD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.164,042,375 - 4,059,579 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl64,042,500 - 4,059,600 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660814,150,841 - 4,166,902 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Fsd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248285,344,068 - 5,359,906 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248285,347,861 - 5,359,825 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Fsd1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1487,379,128 - 87,389,164 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Fsd1
5 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:212
Count of miRNA genes:143
Interacting mature miRNAs:178
Transcripts:ENSRNOT00000072830
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
631533Iresp3Immunoglobin response QTL316.2blood immunoglobulin E amount (VT:0002492)serum immunoglobulin E level (CMO:0002101)916094576Rat
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9121707400Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)949664545496645Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)949664545496645Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)9131250552Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)949664545496645Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9141763315Rat

Markers in Region
RH91102  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.29827,981 - 828,122 (-)MAPPERmRatBN7.2
Rnor_6.0911,070,385 - 11,070,525NCBIRnor6.0
Rnor_5.0910,055,653 - 10,055,793UniSTSRnor5.0
Celera97,678,365 - 7,678,505UniSTS
Cytogenetic Map9q32UniSTS


Expression

RNA-SEQ Expression

circulatory system
ectoderm
hemolymphoid system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
sensory system
visual system
9 29 3 36 21 9 27 15 31 16 16

Sequence


Ensembl Acc Id: ENSRNOT00000072830   ⟹   ENSRNOP00000065407
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl9905,450 - 915,361 (+)Ensembl
mRatBN7.2 Ensembl9818,263 - 828,185 (+)Ensembl
Rnor_6.0 Ensembl911,067,369 - 11,080,155 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000132617   ⟹   ENSRNOP00000109195
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl9905,430 - 915,364 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000145553   ⟹   ENSRNOP00000108169
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl9905,450 - 915,361 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000172943   ⟹   ENSRNOP00000102154
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl9905,450 - 915,361 (+)Ensembl
RefSeq Acc Id: NM_001106918   ⟹   NP_001100388
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr89905,418 - 908,938 (+)NCBI
mRatBN7.29818,241 - 821,761 (+)NCBI
Rnor_6.0911,076,670 - 11,080,190 (-)NCBI
Rnor_5.0910,061,938 - 10,065,458 (-)NCBI
Celera97,684,706 - 7,688,226 (-)RGD
Sequence:
RefSeq Acc Id: NP_001100388   ⟸   NM_001106918
- Sequence:
Ensembl Acc Id: ENSRNOP00000065407   ⟸   ENSRNOT00000072830
Ensembl Acc Id: ENSRNOP00000108169   ⟸   ENSRNOT00000145553
Ensembl Acc Id: ENSRNOP00000102154   ⟸   ENSRNOT00000172943
Ensembl Acc Id: ENSRNOP00000109195   ⟸   ENSRNOT00000132617
Protein Domains
B-box C-terminal   B30.2/SPRY   COS   Fibronectin type-III

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B1H2A2-F1-model_v2 AlphaFold B1H2A2 1-496 view protein structure

Transcriptome

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

Promoters
RGD ID:13696479
Promoter ID:EPDNEW_R7000
Type:multiple initiation site
Name:Fsd1_1
Description:Fibronectin type III and SPRY domain-containing protein 1
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_6.0911,080,169 - 11,080,229EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1583850 AgrOrtholog
BioCyc Gene G2FUF-28570 BioCyc
Ensembl Genes ENSRNOG00000050318 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000072830.4 UniProtKB/TrEMBL
  ENSRNOT00000132617.1 UniProtKB/TrEMBL
  ENSRNOT00000145553.1 UniProtKB/TrEMBL
  ENSRNOT00000172943.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.5.170 UniProtKB/TrEMBL
  2.60.120.920 UniProtKB/TrEMBL
  2.60.40.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:8362685 IMAGE-MGC_LOAD
InterPro B30.2/SPRY UniProtKB/TrEMBL
  B30.2/SPRY_sf UniProtKB/TrEMBL
  Bbox_C UniProtKB/TrEMBL
  ConA-like_dom_sf UniProtKB/TrEMBL
  COS_domain UniProtKB/TrEMBL
  E3_ligase_FN3/SPRY UniProtKB/TrEMBL
  FN3_dom UniProtKB/TrEMBL
  FN3_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  SPRY/PRY_FSD1 UniProtKB/TrEMBL
  SPRY_dom UniProtKB/TrEMBL
KEGG Report rno:301506 UniProtKB/TrEMBL
MGC_CLONE MGC:188678 IMAGE-MGC_LOAD
NCBI Gene 301506 ENTREZGENE
PANTHER E3 UBIQUITIN-PROTEIN LIGASE TRIM36-RELATED UniProtKB/TrEMBL
  FIBRONECTIN TYPE III AND SPRY DOMAIN-CONTAINING PROTEIN 1 UniProtKB/TrEMBL
Pfam fn3 UniProtKB/TrEMBL
  SPRY UniProtKB/TrEMBL
PhenoGen Fsd1 PhenoGen
PROSITE B302_SPRY UniProtKB/TrEMBL
  COS UniProtKB/TrEMBL
  FN3 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000050318 RatGTEx
SMART BBC UniProtKB/TrEMBL
  FN3 UniProtKB/TrEMBL
  SPRY UniProtKB/TrEMBL
Superfamily-SCOP SSF49265 UniProtKB/TrEMBL
  SSF49899 UniProtKB/TrEMBL
UniProt A0A9K3Y875 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0LBU7_RAT UniProtKB/TrEMBL
  A0ABK0LKJ5_RAT UniProtKB/TrEMBL
  A0ABK0M350_RAT UniProtKB/TrEMBL
  A6KR21_RAT UniProtKB/TrEMBL
  B1H2A2 ENTREZGENE, UniProtKB/TrEMBL
  M0R7H8 ENTREZGENE
UniProt Secondary M0R7H8 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-10-02 Fsd1  fibronectin type III and SPRY domain containing 1  Fsd1l1  fibronectin type 3 and SPRY domain-containing protein-like1  Data merged from RGD:15005932 737654 PROVISIONAL
2020-10-01 Fsd1l1  fibronectin type 3 and SPRY domain-containing protein-like1  Fsd1  fibronectin type 3 and SPRY domain-containing protein  Name and Symbol changed 629549 APPROVED
2019-11-08 Fsd1  fibronectin type 3 and SPRY domain-containing protein      Symbol and Name status set to provisional 45752 PROVISIONAL
2008-09-25 Fsd1  fibronectin type III and SPRY domain containing 1  Fsd1  fibronectin type 3 and SPRY domain-containing protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-04 Fsd1  fibronectin type 3 and SPRY domain-containing protein  LOC301506  similar to fibronectin type 3 and SPRY domain-containing protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC301506  similar to fibronectin type 3 and SPRY domain-containing protein      Symbol and Name status set to provisional 70820 PROVISIONAL