Human Gene SSC4D (ENST00000275560.4) from GENCODE V44
  Description: Homo sapiens scavenger receptor cysteine rich family member with 4 domains (SSC4D), mRNA. (from RefSeq NM_080744)
RefSeq Summary (NM_080744): The scavenger receptor cysteine-rich (SRCR) superfamily is an ancient and highly conserved group of cell surface and/or secreted proteins, some of which are involved in the development of the immune system and the regulation of both innate and adaptive immune responses. Group B SRCR domains usually contain 8 regularly spaced cysteines that give rise to a well-defined intradomain disulfide-bond pattern.[supplied by OMIM, Apr 2004].
Gencode Transcript: ENST00000275560.4
Gencode Gene: ENSG00000146700.9
Transcript (Including UTRs)
   Position: hg38 chr7:76,389,337-76,409,697 Size: 20,361 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg38 chr7:76,390,059-76,404,439 Size: 14,381 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Methods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:76,389,337-76,409,697)mRNA (may differ from genome)Protein (575 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGencodeGeneCardsHPRD
LynxMalacardsMGIneXtProtOMIMPubMed
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SRB4D_HUMAN
DESCRIPTION: RecName: Full=Scavenger receptor cysteine-rich domain-containing group B protein; AltName: Full=S4-SRCRB; Flags: Precursor;
SUBCELLULAR LOCATION: Secreted (Potential).
INDUCTION: Not induced by a combination of IL1A/interleukin-1 alpha, IL6/interleukin-6 and dexamethasone.
SIMILARITY: Contains 4 SRCR domains.
SEQUENCE CAUTION: Sequence=AAH15651.1; Type=Miscellaneous discrepancy; Note=Intron retention; Sequence=BAD18764.1; Type=Frameshift; Positions=25;

-  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


-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 3.79 RPKM in Pituitary
Total median expression: 32.46 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -116.40350-0.333 Picture PostScript Text
3' UTR -281.00722-0.389 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
  InterPro Domains: Graphical view of domain structure
IPR001190 - Srcr_rcpt
IPR017448 - Srcr_rcpt-rel

Pfam Domains:
PF00530 - Scavenger receptor cysteine-rich domain

ModBase Predicted Comparative 3D Structure on Q8WTU2
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-  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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005044 scavenger receptor activity

Biological Process:
GO:0006898 receptor-mediated endocytosis

Cellular Component:
GO:0005576 extracellular region
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  AJ312755 - Homo sapiens mRNA for scavenger receptor cysteine-rich protein SRCRB-S4D, (SRCRB-S4D gene).
BC015651 - Homo sapiens scavenger receptor cysteine rich domain containing, group B (4 domains), mRNA (cDNA clone IMAGE:4762075), complete cds.
AK172783 - Homo sapiens cDNA FLJ23944 fis, clone HEP04328.
JD217203 - Sequence 198227 from Patent EP1572962.
JD134745 - Sequence 115769 from Patent EP1572962.
JD444986 - Sequence 426010 from Patent EP1572962.
JD323613 - Sequence 304637 from Patent EP1572962.
JD206852 - Sequence 187876 from Patent EP1572962.
BC113840 - Homo sapiens scavenger receptor cysteine rich domain containing, group B (4 domains), mRNA (cDNA clone IMAGE:40001325), complete cds.
JD252899 - Sequence 233923 from Patent EP1572962.
JD379165 - Sequence 360189 from Patent EP1572962.
JD167714 - Sequence 148738 from Patent EP1572962.
JD143129 - Sequence 124153 from Patent EP1572962.
JD389381 - Sequence 370405 from Patent EP1572962.
JD130546 - Sequence 111570 from Patent EP1572962.
JD204918 - Sequence 185942 from Patent EP1572962.
JD291001 - Sequence 272025 from Patent EP1572962.
JD419246 - Sequence 400270 from Patent EP1572962.
JD256191 - Sequence 237215 from Patent EP1572962.
JD227312 - Sequence 208336 from Patent EP1572962.
JD109290 - Sequence 90314 from Patent EP1572962.
JD385321 - Sequence 366345 from Patent EP1572962.
JF432453 - Synthetic construct Homo sapiens clone IMAGE:100073664 scavenger receptor cysteine rich domain containing, group B (4 domains) (SRCRB4D) gene, encodes complete protein.
KJ903794 - Synthetic construct Homo sapiens clone ccsbBroadEn_13188 SRCRB4D gene, encodes complete protein.
BC167843 - Synthetic construct Homo sapiens clone IMAGE:100068233, MGC:195850 scavenger receptor cysteine rich domain containing, group B (4 domains) (SRCRB4D) mRNA, encodes complete protein.
JD332799 - Sequence 313823 from Patent EP1572962.
JD061738 - Sequence 42762 from Patent EP1572962.
JD037571 - Sequence 18595 from Patent EP1572962.
JD100038 - Sequence 81062 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000275560.1, ENST00000275560.2, ENST00000275560.3, NM_080744, Q2HIZ5, Q6ZMG3, Q8WTU2, Q96BF5, SRB4D_HUMAN, SRCRB4D, uc003ufb.1, uc003ufb.2, uc003ufb.3, uc003ufb.4, uc003ufb.5
UCSC ID: ENST00000275560.4
RefSeq Accession: NM_080744
Protein: Q8WTU2 (aka SRB4D_HUMAN)
CCDS: CCDS5585.1

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