Human Gene SCARF2 (uc002zsk.2)
  Description: Homo sapiens scavenger receptor class F, member 2 (SCARF2), transcript variant 2, mRNA.
RefSeq Summary (NM_182895): The protein encoded by this gene is similar to SCARF1/SREC-I, a scavenger receptor protein that mediates the binding and degradation of acetylated low density lipoprotein (Ac-LDL). This protein has only little activity of internalizing modified low density lipoproteins (LDL), but it can interact with SCARF1 through its extracellular domain. The association of this protein with SCARF1 is suppressed by the presence of scavenger ligands. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr22:20,778,874-20,792,146 Size: 13,273 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg19 chr22:20,779,665-20,792,041 Size: 12,377 Coding Exon Count: 11 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:20,778,874-20,792,146)mRNA (may differ from genome)Protein (865 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
HGNCLynxMalacardsMGIOMIMPubMed
UniProtKBBioGrid CRISPR DB

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SCARF2
CDC HuGE Published Literature: SCARF2

-  MalaCards Disease Associations
  MalaCards Gene Search: SCARF2
Diseases sorted by gene-association score: van den ende-gupta syndrome* (1591), marden walker like syndrome* (400), van den ende-gupta sndrome* (100), sclerocornea (14), eyelid disease (10), blepharophimosis (9), caffey disease (8)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 30.63 RPKM in Artery - Aorta
Total median expression: 413.30 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -39.80105-0.379 Picture PostScript Text
3' UTR -376.60791-0.476 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  Pfam Domains:
PF12661 - Human growth factor-like EGF

SCOP Domains:
57184 - Growth factor receptor domain

ModBase Predicted Comparative 3D Structure on Q96GP6-2
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AF088043 - Homo sapiens full length insert cDNA clone ZD58C02.
BC000584 - Homo sapiens scavenger receptor class F, member 2, mRNA (cDNA clone IMAGE:3163559), partial cds.
BC009326 - Homo sapiens scavenger receptor class F, member 2, mRNA (cDNA clone IMAGE:4125591), partial cds.
AK075058 - Homo sapiens cDNA FLJ90577 fis, clone OVARC1002058.
AB052951 - Homo sapiens SRECRP mRNA for SRECRP-1, complete cds.
AB024433 - Homo sapiens mRNA for NSR1, chromosome 22q11.2, complete cds.
AF522196 - Homo sapiens scavenger receptor type F mRNA, complete cds.
JD471498 - Sequence 452522 from Patent EP1572962.
JD278809 - Sequence 259833 from Patent EP1572962.
JD454829 - Sequence 435853 from Patent EP1572962.
JD475652 - Sequence 456676 from Patent EP1572962.
JD408353 - Sequence 389377 from Patent EP1572962.
JD395823 - Sequence 376847 from Patent EP1572962.
JD270947 - Sequence 251971 from Patent EP1572962.
JD185802 - Sequence 166826 from Patent EP1572962.
JD454213 - Sequence 435237 from Patent EP1572962.
JD207938 - Sequence 188962 from Patent EP1572962.
JD538433 - Sequence 519457 from Patent EP1572962.
JD406646 - Sequence 387670 from Patent EP1572962.
BC172421 - Synthetic construct Homo sapiens clone IMAGE:100069115, MGC:199126 scavenger receptor class F, member 2 (SCARF2) mRNA, encodes complete protein.
JD106366 - Sequence 87390 from Patent EP1572962.
JD163406 - Sequence 144430 from Patent EP1572962.
JD218398 - Sequence 199422 from Patent EP1572962.
JD395024 - Sequence 376048 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_182895, NP_878315, Q96GP6-2, SREC2, SREPCR
UCSC ID: uc002zsk.2
RefSeq Accession: NM_182895
Protein: Q96GP6-2, splice isoform of Q96GP6 CCDS: CCDS13779.1, CCDS46666.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_182895.2
exon count: 11CDS single in 3' UTR: no RNA size: 3508
ORF size: 2598CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4706.00frame shift in genome: no % Coverage: 99.60
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.