Fdcsp (follicular dendritic cell secreted protein) - Rat Genome Database

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Gene: Fdcsp (follicular dendritic cell secreted protein) Rattus norvegicus
Analyze
Symbol: Fdcsp
Name: follicular dendritic cell secreted protein
RGD ID: 1359468
Description: Orthologous to human FDCSP (follicular dendritic cell secreted protein); INTERACTS WITH acrylamide; sodium fluoride; aflatoxin B1 (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: follicular dendritic cell secreted; follicular dendritic cell secreted peptide; LOC494224
RGD Orthologs
Human
Mouse
Bonobo
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81420,447,761 - 20,453,227 (-)NCBIGRCr8
mRatBN7.21420,169,691 - 20,173,983 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1420,169,691 - 20,173,983 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1420,100,114 - 20,104,407 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01421,419,000 - 21,423,293 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01420,149,774 - 20,154,066 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01421,818,999 - 21,823,687 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1421,819,395 - 21,823,687 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01421,729,348 - 21,733,772 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41421,690,466 - 21,694,758 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11421,690,465 - 21,694,758 (-)NCBI
Celera1419,572,307 - 19,576,599 (-)NCBICelera
Cytogenetic Map14p21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16259954  


Genomics

Comparative Map Data
Fdcsp
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81420,447,761 - 20,453,227 (-)NCBIGRCr8
mRatBN7.21420,169,691 - 20,173,983 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1420,169,691 - 20,173,983 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1420,100,114 - 20,104,407 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01421,419,000 - 21,423,293 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01420,149,774 - 20,154,066 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01421,818,999 - 21,823,687 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1421,819,395 - 21,823,687 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01421,729,348 - 21,733,772 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41421,690,466 - 21,694,758 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11421,690,465 - 21,694,758 (-)NCBI
Celera1419,572,307 - 19,576,599 (-)NCBICelera
Cytogenetic Map14p21NCBI
FDCSP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38470,226,124 - 70,235,252 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl470,226,124 - 70,235,252 (+)EnsemblGRCh38hg38GRCh38
GRCh37471,091,841 - 71,100,969 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36471,126,404 - 71,135,558 (+)NCBINCBI36Build 36hg18NCBI36
Build 34471,272,574 - 71,281,729NCBI
Celera468,449,575 - 68,458,729 (+)NCBICelera
Cytogenetic Map4q13.3NCBI
HuRef466,894,015 - 66,903,196 (+)NCBIHuRef
CHM1_1471,128,208 - 71,137,390 (+)NCBICHM1_1
T2T-CHM13v2.0473,565,445 - 73,574,935 (+)NCBIT2T-CHM13v2.0
BC037156
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39588,056,638 - 88,062,030 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl588,056,638 - 88,062,030 (+)EnsemblGRCm39 Ensembl
GRCm38587,908,779 - 87,914,171 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl587,908,779 - 87,914,171 (+)EnsemblGRCm38mm10GRCm38
MGSCv37588,337,804 - 88,343,196 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36588,983,365 - 88,988,729 (+)NCBIMGSCv36mm8
MGSCv36587,513,203 - 87,518,567 (+)NCBIMGSCv36mm8
Cytogenetic Map5E1NCBI
cM Map545.0NCBI
FDCSP
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2359,847,452 - 59,857,051 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1460,044,013 - 60,053,618 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0453,988,378 - 53,998,028 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1460,331,941 - 60,341,589 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl460,331,243 - 60,341,647 (-)Ensemblpanpan1.1panPan2
FDCSP
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1718,711,145 - 18,721,926 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl718,716,973 - 18,721,350 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660844,202,678 - 4,211,798 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Fdcsp
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248901,641,993 - 1,645,026 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Fdcsp
31 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:130
Count of miRNA genes:106
Interacting mature miRNAs:114
Transcripts:ENSRNOT00000046005
Prediction methods:Microtar, Miranda, Rnahybrid
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
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
619619Rf4Renal disease susceptibility QTL 44.10.002urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14381307421217635Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14381307424531477Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14381307430767156Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062228035204Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141103081230320092Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141487516830883947Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141762256142337007Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat


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 endocrine system hemolymphoid system nervous system renal system reproductive system respiratory system
High
Medium
Low 1 6
Below cutoff 4 5 6 1 11 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000046005   ⟹   ENSRNOP00000050171
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1420,169,691 - 20,173,983 (-)Ensembl
Rnor_6.0 Ensembl1421,819,395 - 21,823,687 (-)Ensembl
RefSeq Acc Id: NM_001009505   ⟹   NP_001009505
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81420,448,935 - 20,453,227 (-)NCBI
mRatBN7.21420,169,691 - 20,173,983 (-)NCBI
Rnor_6.01421,819,395 - 21,823,687 (-)NCBI
Rnor_5.01421,729,348 - 21,733,772 (-)NCBI
RGSC_v3.41421,690,466 - 21,694,758 (-)RGD
Celera1419,572,307 - 19,576,599 (-)RGD
Sequence:
RefSeq Acc Id: XM_063273447   ⟹   XP_063129517
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81420,447,761 - 20,453,227 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001009505 (Get FASTA)   NCBI Sequence Viewer  
  XP_063129517 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAD77806 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000050171
  ENSRNOP00000050171.1
Reference Protein Sequences
RefSeq Acc Id: NP_001009505   ⟸   NM_001009505
- Peptide Label: precursor
- UniProtKB: Q5R1M6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000050171   ⟸   ENSRNOT00000046005
RefSeq Acc Id: XP_063129517   ⟸   XM_063273447
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5R1M6-F1-model_v2 AlphaFold Q5R1M6 1-81 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:1359468 AgrOrtholog
BioCyc Gene G2FUF-16140 BioCyc
Ensembl Genes ENSRNOG00000030258 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000046005 ENTREZGENE
  ENSRNOT00000046005.2 UniProtKB/TrEMBL
InterPro FDC-SP UniProtKB/TrEMBL
KEGG Report rno:494224 UniProtKB/TrEMBL
NCBI Gene 494224 ENTREZGENE
Pfam FDC-SP UniProtKB/TrEMBL
PhenoGen Fdcsp PhenoGen
PROSITE PROKAR_LIPOPROTEIN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000030258 RatGTEx
UniProt Q5R1M6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-08 Fdcsp  follicular dendritic cell secreted protein  LOC494224  follicular dendritic cell secreted  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-29 LOC494224  follicular dendritic cell secreted      Symbol and Name status set to provisional 70820 PROVISIONAL