Tsku tsukushi, small leucine rich proteoglycan [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Tskuprovided by RGD
Official Full Name: tsukushi, small leucine rich proteoglycanprovided by RGD
Primary source: RGD:1359311
See related: EnsemblRapid:ENSRNOG00000027784 AllianceGenome:RGD:1359311
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: Eiih
Summary: Predicted to enable transforming growth factor beta binding activity. Predicted to be involved in several processes, including animal organ development; cholesterol efflux; and cholesterol homeostasis. Predicted to act upstream of or within several processes, including ciliary body morphogenesis; negative regulation of Wnt signaling pathway; and telencephalon development. Predicted to be active in extracellular matrix; extracellular space; and plasma membrane. Orthologous to human TSKU (tsukushi, small leucine rich proteoglycan). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Liver (RPKM 218.1), Kidney (RPKM 65.4) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q32

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (162071459..162082972, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (152660259..152671682, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (163317281..163328697, complement)

Chromosome 1 - NC_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The spatio-temporal expression of Decorin, Semaphorin6D, SPARC, Spry-1 and Tsukushi in developing prostate is described and observed similar mesenchymal expression patterns in rat and human.
Title: Stromal expression of decorin, Semaphorin6D, SPARC, Sprouty1 and Tsukushi in developing prostate and decreased levels of decorin in prostate cancer.
Tissue distribution of EIIH in adult rats revealed a pattern of expression mainly in the liver, intestine and islets of Langerhans, closely following that of the Glut2 (glucose transporter 2), suggesting that it may play a role in carbohydrate metabolism
Title: Identification of a novel rat hepatic gene induced early by insulin, independently of glucose.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables transforming growth factor beta binding	IEA Inferred from Electronic Annotation more info
enables transforming growth factor beta binding	ISO Inferred from Sequence Orthology more info
enables transforming growth factor beta binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in anterior commissure morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within anterior commissure morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in anterior commissure morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within anterior commissure morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in bone growth	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within camera-type eye development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within camera-type eye development	ISS Inferred from Sequence or Structural Similarity more info
involved_in cholesterol efflux	IEA Inferred from Electronic Annotation more info
involved_in cholesterol efflux	ISO Inferred from Sequence Orthology more info
involved_in cholesterol efflux	ISS Inferred from Sequence or Structural Similarity more info
involved_in cholesterol homeostasis	IEA Inferred from Electronic Annotation more info
involved_in cholesterol homeostasis	ISO Inferred from Sequence Orthology more info
involved_in cholesterol homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in cholesterol metabolic process	IEA Inferred from Electronic Annotation more info
involved_in cholesterol metabolic process	ISO Inferred from Sequence Orthology more info
involved_in cholesterol metabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in ciliary body morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within ciliary body morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ciliary body morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in corpus callosum morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within corpus callosum morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in energy homeostasis	IEA Inferred from Electronic Annotation more info
NOT involved_in energy homeostasis	ISO Inferred from Sequence Orthology more info
involved_in energy homeostasis	ISO Inferred from Sequence Orthology more info
involved_in energy homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in growth plate cartilage chondrocyte development	ISS Inferred from Sequence or Structural Similarity more info
involved_in hippocampus development	IEA Inferred from Electronic Annotation more info
involved_in hippocampus development	ISO Inferred from Sequence Orthology more info
involved_in hippocampus development	ISS Inferred from Sequence or Structural Similarity more info
involved_in inner ear receptor cell stereocilium organization	IEA Inferred from Electronic Annotation more info
involved_in inner ear receptor cell stereocilium organization	ISO Inferred from Sequence Orthology more info
involved_in inner ear receptor cell stereocilium organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in lateral ventricle development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within lateral ventricle development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of Wnt signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of myofibroblast differentiation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of myofibroblast differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of myofibroblast differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of neuron projection development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of neuron projection development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of neuron projection development	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of transforming growth factor beta1 production	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transforming growth factor beta1 production	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transforming growth factor beta1 production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of hair cycle	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of hair cycle	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of hair cycle	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within regulation of gene expression	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of gene expression	ISS Inferred from Sequence or Structural Similarity more info
involved_in wound healing	IEA Inferred from Electronic Annotation more info
involved_in wound healing	ISO Inferred from Sequence Orthology more info
involved_in wound healing	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
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
located_in extracellular space	IEA Inferred from Electronic Annotation more info
NOT located_in extracellular space	ISO Inferred from Sequence Orthology more info
located_in extracellular space	ISO Inferred from Sequence Orthology more info
located_in extracellular space	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: tsukushi

Names: early insulin-induced hepatic gene protein; hepatic protein EIIH; leucine-rich repeat-containing protein 54; tsukushin

NCBI Reference Sequences (RefSeq)

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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_001009965.3 → NP_001009965.2 tsukushi precursor

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000001

UniProtKB/Swiss-Prot

Q6QMY6

UniProtKB/TrEMBL

A0A8I6G739, A6I6D6

Conserved Domains (2) summary

COG4886
Location:39 → 286

LRR; Leucine-rich repeat (LRR) protein [Transcription]

sd00033
Location:90 → 110

LRR_RI; leucine-rich repeat [structural motif]

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086019.1 Reference GRCr8

Range

162071459..162082972 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006229759.5 → XP_006229821.1 tsukushi isoform X1

See identical proteins and their annotated locations for XP_006229821.1

UniProtKB/Swiss-Prot

Q6QMY6

UniProtKB/TrEMBL

A0A8I6G739, A6I6D6

Conserved Domains (2) summary

COG4886
Location:39 → 286

LRR; Leucine-rich repeat (LRR) protein [Transcription]

sd00033
Location:90 → 110

LRR_RI; leucine-rich repeat [structural motif]
XM_039113189.2 → XP_038969117.1 tsukushi isoform X1

UniProtKB/Swiss-Prot

Q6QMY6

UniProtKB/TrEMBL

A0A8I6G739, A6I6D6

Related

ENSRNOP00000093869.2, ENSRNOT00000114784.2

Conserved Domains (2) summary

COG4886
Location:39 → 286

LRR; Leucine-rich repeat (LRR) protein [Transcription]

sd00033
Location:90 → 110

LRR_RI; leucine-rich repeat [structural motif]
XM_006229761.5 → XP_006229823.1 tsukushi isoform X1

See identical proteins and their annotated locations for XP_006229823.1

UniProtKB/Swiss-Prot

Q6QMY6

UniProtKB/TrEMBL

A0A8I6G739, A6I6D6

Related

ENSRNOP00000103897.1, ENSRNOT00000125977.1

Conserved Domains (2) summary

COG4886
Location:39 → 286

LRR; Leucine-rich repeat (LRR) protein [Transcription]

sd00033
Location:90 → 110

LRR_RI; leucine-rich repeat [structural motif]
XM_063262800.1 → XP_063118870.1 tsukushi isoform X1

UniProtKB/TrEMBL

A0A8I6G739, A6I6D6

Related

ENSRNOP00000078677.1, ENSRNOT00000114498.2
XM_039113208.2 → XP_038969136.1 tsukushi isoform X1

UniProtKB/Swiss-Prot

Q6QMY6

UniProtKB/TrEMBL

A0A8I6G739, A6I6D6

Related

ENSRNOP00000090380.1, ENSRNOT00000099039.2

Conserved Domains (2) summary

COG4886
Location:39 → 286

LRR; Leucine-rich repeat (LRR) protein [Transcription]

sd00033
Location:90 → 110

LRR_RI; leucine-rich repeat [structural motif]
XM_039113213.2 → XP_038969141.1 tsukushi isoform X1

UniProtKB/Swiss-Prot

Q6QMY6

UniProtKB/TrEMBL

A0A8I6G739, A6I6D6

Related

ENSRNOP00000086216.1, ENSRNOT00000111957.2

Conserved Domains (2) summary

COG4886
Location:39 → 286

LRR; Leucine-rich repeat (LRR) protein [Transcription]

sd00033
Location:90 → 110

LRR_RI; leucine-rich repeat [structural motif]