Human Gene SRPX (ENST00000378533.4) from GENCODE V44
  Description: Homo sapiens sushi repeat containing protein X-linked (SRPX), transcript variant 1, mRNA. (from RefSeq NM_006307)
Gencode Transcript: ENST00000378533.4
Gencode Gene: ENSG00000101955.15
Transcript (Including UTRs)
   Position: hg38 chrX:38,149,339-38,220,871 Size: 71,533 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg38 chrX:38,149,711-38,220,792 Size: 71,082 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:38,149,339-38,220,871)mRNA (may differ from genome)Protein (464 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SRPX_HUMAN
DESCRIPTION: RecName: Full=Sushi repeat-containing protein SRPX; Flags: Precursor;
FUNCTION: May be involved in phagocytosis during disk shedding, cell adhesion to cells other than the pigment epithelium or signal transduction.
SUBCELLULAR LOCATION: Cell surface (Probable). Note=Possibly surface of photoreceptor cell.
TISSUE SPECIFICITY: Retina and heart; less in placenta, pancreas, lung, liver, skeletal muscle, kidney and brain.
SIMILARITY: Contains 1 HYR domain.
SIMILARITY: Contains 3 Sushi (CCP/SCR) domains.

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: SRPX
Diseases sorted by gene-association score: retinitis pigmentosa 3 (6), retinitis pigmentosa (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 141.69 RPKM in Adipose - Visceral (Omentum)
Total median expression: 1391.60 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 -27.8079-0.352 Picture PostScript Text
3' UTR -68.90372-0.185 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
IPR016060 - Complement_control_module
IPR025232 - DUF4174
IPR003410 - Hyalin
IPR000436 - Sushi_SCR_CCP

Pfam Domains:
PF13778 - Domain of unknown function (DUF4174)
PF02494 - HYR domain
PF00084 - Sushi repeat (SCR repeat)

ModBase Predicted Comparative 3D Structure on P78539
FrontTopSide
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
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0001845 phagolysosome assembly
GO:0006914 autophagy
GO:0007155 cell adhesion
GO:0034976 response to endoplasmic reticulum stress
GO:0060244 negative regulation of cell proliferation involved in contact inhibition
GO:2001241 positive regulation of extrinsic apoptotic signaling pathway in absence of ligand

Cellular Component:
GO:0005776 autophagosome
GO:0005783 endoplasmic reticulum
GO:0009986 cell surface
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  LF211414 - JP 2014500723-A/18917: Polycomb-Associated Non-Coding RNAs.
MA446991 - JP 2018138019-A/18917: Polycomb-Associated Non-Coding RNAs.
KJ892528 - Synthetic construct Homo sapiens clone ccsbBroadEn_01922 SRPX gene, encodes complete protein.
LF214065 - JP 2014500723-A/21568: Polycomb-Associated Non-Coding RNAs.
MA449642 - JP 2018138019-A/21568: Polycomb-Associated Non-Coding RNAs.
BC020684 - Homo sapiens sushi-repeat-containing protein, X-linked, mRNA (cDNA clone MGC:22406 IMAGE:4731946), complete cds.
AK125542 - Homo sapiens cDNA FLJ43554 fis, clone PROST2018090, highly similar to SUSHI REPEAT-CONTAINING PROTEIN SRPX PRECURSOR.
EU668359 - Homo sapiens epididymis secretory sperm binding protein Li 83p (HEL-S-83p) mRNA, complete cds.
U61374 - Human novel protein with short consensus repeats of six cysteines mRNA, complete cds.
U78093 - Human sushi-repeat-containing protein precursor (SRPX) mRNA, complete cds.
LF379216 - JP 2014500723-A/186719: Polycomb-Associated Non-Coding RNAs.
MA614793 - JP 2018138019-A/186719: Polycomb-Associated Non-Coding RNAs.
JD289478 - Sequence 270502 from Patent EP1572962.
JD439271 - Sequence 420295 from Patent EP1572962.
JD087901 - Sequence 68925 from Patent EP1572962.
AK293127 - Homo sapiens cDNA FLJ56529 complete cds, highly similar to Sushi repeat-containing protein SRPX precursor.
AK289430 - Homo sapiens cDNA FLJ76202 complete cds, highly similar to Homo sapiens sushi-repeat-containing protein, X-linked (SRPX), mRNA.
AK298802 - Homo sapiens cDNA FLJ57806 complete cds, highly similar to Sushi repeat-containing protein SRPX precursor.
JD473370 - Sequence 454394 from Patent EP1572962.
JD048649 - Sequence 29673 from Patent EP1572962.
AB527644 - Synthetic construct DNA, clone: pF1KB5557, Homo sapiens SRPX gene for sushi-repeat-containing protein, X-linked, without stop codon, in Flexi system.
LF379218 - JP 2014500723-A/186721: Polycomb-Associated Non-Coding RNAs.
MA614795 - JP 2018138019-A/186721: Polycomb-Associated Non-Coding RNAs.
LF379220 - JP 2014500723-A/186723: Polycomb-Associated Non-Coding RNAs.
MA614797 - JP 2018138019-A/186723: Polycomb-Associated Non-Coding RNAs.
CU676640 - Synthetic construct Homo sapiens gateway clone IMAGE:100022266 5' read SRPX mRNA.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K065, B4DQH5, ENST00000378533.1, ENST00000378533.2, ENST00000378533.3, ETX1, NM_006307, P78539, Q4VX66, Q99652, Q99913, SRPX_HUMAN, uc004ddy.1, uc004ddy.2, uc004ddy.3, uc004ddy.4
UCSC ID: ENST00000378533.4
RefSeq Accession: NM_006307
Protein: P78539 (aka SRPX_HUMAN)
CCDS: CCDS14245.1, CCDS55400.1

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