Scarf2 (scavenger receptor class F, member 2) - Rat Genome Database

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Gene: Scarf2 (scavenger receptor class F, member 2) Rattus norvegicus
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Symbol: Scarf2
Name: scavenger receptor class F, member 2
RGD ID: 1306013
Description: Predicted to enable scavenger receptor activity. Predicted to be involved in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules. Human ortholog(s) of this gene implicated in Van den Ende-Gupta syndrome. Orthologous to human SCARF2 (scavenger receptor class F member 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC287949; scavenger receptor class F member 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81196,680,237 - 96,691,686 (-)NCBIGRCr8
mRatBN7.21183,175,956 - 83,187,415 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1183,175,963 - 83,187,348 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1191,904,665 - 91,916,242 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01184,565,809 - 84,577,384 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01183,619,425 - 83,631,004 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01187,722,350 - 87,733,734 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1187,722,350 - 87,733,734 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01190,774,764 - 90,786,150 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41185,164,352 - 85,175,734 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11185,204,942 - 85,216,190 (-)NCBI
Celera1181,947,834 - 81,959,191 (-)NCBICelera
Cytogenetic Map11q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12154095   PMID:21423176  


Genomics

Comparative Map Data
Scarf2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81196,680,237 - 96,691,686 (-)NCBIGRCr8
mRatBN7.21183,175,956 - 83,187,415 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1183,175,963 - 83,187,348 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1191,904,665 - 91,916,242 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01184,565,809 - 84,577,384 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01183,619,425 - 83,631,004 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01187,722,350 - 87,733,734 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1187,722,350 - 87,733,734 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01190,774,764 - 90,786,150 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41185,164,352 - 85,175,734 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11185,204,942 - 85,216,190 (-)NCBI
Celera1181,947,834 - 81,959,191 (-)NCBICelera
Cytogenetic Map11q23NCBI
SCARF2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382220,424,584 - 20,437,825 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2220,424,584 - 20,437,826 (-)EnsemblGRCh38hg38GRCh38
GRCh372220,778,874 - 20,792,112 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362219,108,875 - 19,122,146 (-)NCBINCBI36Build 36hg18NCBI36
Build 342219,103,428 - 19,116,700NCBI
Celera224,265,595 - 4,278,869 (-)NCBICelera
Cytogenetic Map22q11.21NCBI
HuRef224,042,935 - 4,056,177 (-)NCBIHuRef
CHM1_12220,779,147 - 20,792,422 (-)NCBICHM1_1
T2T-CHM13v2.02220,828,870 - 20,842,097 (-)NCBIT2T-CHM13v2.0
Scarf2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391617,615,146 - 17,626,158 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1617,615,146 - 17,626,157 (+)EnsemblGRCm39 Ensembl
GRCm381617,797,282 - 17,808,294 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1617,797,282 - 17,808,293 (+)EnsemblGRCm38mm10GRCm38
MGSCv371617,797,375 - 17,808,380 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361617,710,845 - 17,721,850 (+)NCBIMGSCv36mm8
Celera1618,370,364 - 18,381,368 (+)NCBICelera
Cytogenetic Map16A3NCBI
cM Map1611.03NCBI
Scarf2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544218,996,070 - 19,001,624 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495544218,995,253 - 19,006,499 (-)NCBIChiLan1.0ChiLan1.0
SCARF2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22330,045,538 - 30,058,828 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12232,588,487 - 32,605,806 (-)NCBINHGRI_mPanPan1
PanPan1.12219,110,083 - 19,125,371 (-)NCBIpanpan1.1PanPan1.1panPan2
SCARF2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12630,231,967 - 30,243,693 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2630,233,669 - 30,239,151 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2630,192,318 - 30,203,226 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02631,641,745 - 31,652,659 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2631,640,949 - 31,652,659 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12629,687,887 - 29,698,800 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02629,312,241 - 29,323,140 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02630,401,424 - 30,412,344 (-)NCBIUU_Cfam_GSD_1.0
Scarf2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118139,838,756 - 139,850,253 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366192,903,824 - 2,914,518 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366192,900,536 - 2,915,306 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCARF2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1450,812,984 - 50,824,521 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11450,813,161 - 50,824,434 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21454,454,973 - 54,471,772 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SCARF2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1195,265,730 - 5,282,092 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl195,268,630 - 5,282,092 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660851,654,069 - 1,668,053 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Scarf2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624945393,412 - 404,958 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624945392,615 - 404,961 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Scarf2
111 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:407
Count of miRNA genes:203
Interacting mature miRNAs:228
Transcripts:ENSRNOT00000000313
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116034659086241447Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116642214886241447Rat
2302043Pia27Pristane induced arthritis QTL 2718.60.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)118256654583440803Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)116642214886241447Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat

Markers in Region
RH138822  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21183,191,424 - 83,191,545 (-)MAPPERmRatBN7.2
Rnor_6.01187,718,154 - 87,718,274NCBIRnor6.0
Rnor_5.01190,770,599 - 90,770,719UniSTSRnor5.0
RGSC_v3.41185,179,793 - 85,179,913UniSTSRGSC3.4
Celera1181,963,267 - 81,963,387UniSTS
RH 3.4 Map11710.1UniSTS
Cytogenetic Map11q23UniSTS
RH131807  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21183,191,027 - 83,191,210 (-)MAPPERmRatBN7.2
Rnor_6.01187,718,489 - 87,718,671NCBIRnor6.0
Rnor_5.01190,770,934 - 90,771,116UniSTSRnor5.0
RGSC_v3.41185,179,396 - 85,179,578UniSTSRGSC3.4
Celera1181,962,870 - 81,963,052UniSTS
RH 3.4 Map11707.6UniSTS
Cytogenetic Map11q23UniSTS
RH135933  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21183,175,979 - 83,176,183 (-)MAPPERmRatBN7.2
Rnor_6.01187,733,514 - 87,733,717NCBIRnor6.0
Rnor_5.01190,785,923 - 90,786,126UniSTSRnor5.0
RGSC_v3.41185,164,369 - 85,164,572UniSTSRGSC3.4
Celera1181,947,851 - 81,948,054UniSTS
Cytogenetic Map11q23UniSTS


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
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000000313   ⟹   ENSRNOP00000000313
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1183,175,963 - 83,187,348 (-)Ensembl
Rnor_6.0 Ensembl1187,722,350 - 87,733,734 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000095028   ⟹   ENSRNOP00000091964
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1183,175,963 - 83,187,249 (-)Ensembl
RefSeq Acc Id: NM_001105864   ⟹   NP_001099334
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81196,680,243 - 96,691,626 (-)NCBI
mRatBN7.21183,175,963 - 83,187,348 (-)NCBI
Rnor_6.01187,722,350 - 87,733,734 (+)NCBI
Rnor_5.01190,774,764 - 90,786,150 (+)NCBI
RGSC_v3.41185,164,352 - 85,175,734 (-)RGD
Celera1181,947,834 - 81,959,191 (-)RGD
Sequence:
RefSeq Acc Id: XM_039088078   ⟹   XP_038944006
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81196,680,237 - 96,691,685 (-)NCBI
mRatBN7.21183,175,956 - 83,187,415 (-)NCBI
RefSeq Acc Id: XM_039088079   ⟹   XP_038944007
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81196,680,237 - 96,691,686 (-)NCBI
mRatBN7.21183,175,956 - 83,187,415 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001099334 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944006 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944007 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL77905 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000000313.6
  ENSRNOP00000091964.1
RefSeq Acc Id: NP_001099334   ⟸   NM_001105864
- Peptide Label: precursor
- UniProtKB: A6JSK2 (UniProtKB/TrEMBL),   A0A8I6AH58 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000000313   ⟸   ENSRNOT00000000313
RefSeq Acc Id: XP_038944007   ⟸   XM_039088079
- Peptide Label: isoform X2
- UniProtKB: A0A8I6AH58 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038944006   ⟸   XM_039088078
- Peptide Label: isoform X1
- UniProtKB: D3ZBQ5 (UniProtKB/TrEMBL),   A0A8I6AH58 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000091964   ⟸   ENSRNOT00000095028
Protein Domains
EGF-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZBQ5-F1-model_v2 AlphaFold D3ZBQ5 1-833 view protein structure

Transcriptome

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

Promoters
RGD ID:13698325
Promoter ID:EPDNEW_R8850
Type:multiple initiation site
Name:Scarf2_1
Description:scavenger receptor class F, member 2
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_6.01187,722,386 - 87,722,446EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306013 AgrOrtholog
BioCyc Gene G2FUF-20614 BioCyc
Ensembl Genes ENSRNOG00000000288 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000313.8 UniProtKB/TrEMBL
  ENSRNOT00000095028.1 UniProtKB/TrEMBL
Gene3D-CATH Tie2 ligand-binding domain superfamily UniProtKB/TrEMBL
InterPro EGF_3 UniProtKB/TrEMBL
  Growth_fac_rcpt UniProtKB/TrEMBL
  Laminin_EGF UniProtKB/TrEMBL
  SREC1/2 UniProtKB/TrEMBL
KEGG Report rno:287949 UniProtKB/TrEMBL
NCBI Gene 287949 ENTREZGENE
PANTHER PTHR24043 UniProtKB/TrEMBL
  PTHR24043:SF5 UniProtKB/TrEMBL
Pfam Laminin_EGF UniProtKB/TrEMBL
PhenoGen Scarf2 PhenoGen
PRINTS EGFLAMININ UniProtKB/TrEMBL
PROSITE EGF_1 UniProtKB/TrEMBL
  EGF_3 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000000288 RatGTEx
SMART EGF UniProtKB/TrEMBL
  EGF_Lam UniProtKB/TrEMBL
Superfamily-SCOP Grow_fac_recept UniProtKB/TrEMBL
UniProt A0A8I6AH58 ENTREZGENE, UniProtKB/TrEMBL
  A6JSK2 ENTREZGENE, UniProtKB/TrEMBL
  D3ZBQ5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Scarf2  scavenger receptor class F, member 2   Scarf2_predicted  scavenger receptor class F, member 2 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Scarf2_predicted  scavenger receptor class F, member 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED