Sspo SCO-spondin [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Sspoprovided by RGD
Official Full Name: SCO-spondinprovided by RGD
Primary source: RGD:1549716
See related: EnsemblRapid:ENSRNOG00000025848 AllianceGenome:RGD:1549716
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Scospondin
Summary: Predicted to be involved in cell adhesion. Predicted to be located in cytoplasm. Predicted to be active in extracellular matrix and extracellular space. Orthologous to human SSPOP (SCO-spondin, pseudogene). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Kidney (RPKM 20.1), Thymus (RPKM 2.4) and 3 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 4q24

Exon count:: 104

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (78725829..78781330)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (77394915..77450526)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (78076695..78133676)

Chromosome 4 - NC_086022.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Results indicate that 5HT down-regulates SCO-spondin biosynthesis but apparently not its release, and suggest that 5HT may exert the effect on the SCO via the cerebrospinal fluid.
Title: Transcription of SCO-spondin in the subcommissural organ: evidence for down-regulation mediated by serotonin.

Submit: New GeneRIF Correction

General gene information

Go to the top of the page Help

Markers

AU049264 (e-PCR)
- UniSTS:145712

AU049114 (e-PCR)
- UniSTS:145562

Sspo (e-PCR), detects polymorphism
- UniSTS:532689

Gene Ontology Provided by RGD

Process	Evidence Code	Pubs
involved_in cell adhesion	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
is_active_in extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info

General protein information

Go to the top of the page Help

Preferred Names: SCO-spondin

Names: subcommissural organ spondin

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001007016.1 → NP_001007017.1 SCO-spondin precursor

See identical proteins and their annotated locations for NP_001007017.1

Status: PROVISIONAL

Source sequence(s)

AJ629845

UniProtKB/Swiss-Prot

Q700K0

Related

ENSRNOP00000037189.2, ENSRNOT00000035906.5

Conserved Domains (13) summary

smart00192
Location:1497 → 1528

LDLa; Low-density lipoprotein receptor domain class A

smart00209
Location:2543 → 2595

TSP1; Thrombospondin type 1 repeats

smart00215
Location:2932 → 2979

VWC_out; von Willebrand factor (vWF) type C domain

smart00216
Location:556 → 716

VWD; von Willebrand factor (vWF) type D domain

smart00231
Location:2070 → 2226

FA58C; Coagulation factor 5/8 C-terminal domain, discoidin domain

cd00057
Location:2111 → 2225

FA58C; Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes.

cd00112
Location:1421 → 1455

LDLa; Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about ...

pfam00057
Location:1568 → 1604

Ldl_recept_a; Low-density lipoprotein receptor domain class A

pfam00090
Location:2819 → 2867

TSP_1; Thrombospondin type 1 domain

pfam00094
Location:1019 → 1168

VWD; von Willebrand factor type D domain

pfam01826
Location:1280 → 1336

TIL; Trypsin Inhibitor like cysteine rich domain

pfam08742
Location:1206 → 1276

C8; C8 domain

cl17735
Location:4980 → 5035

VWC; von Willebrand factor type C domain