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Tsku tsukushi, small leucine rich proteoglycan [ Mus musculus (house mouse) ]

Gene ID: 244152, updated on 12-May-2024

Summary

Official Symbol
Tskuprovided by MGI
Official Full Name
tsukushi, small leucine rich proteoglycanprovided by MGI
Primary source
MGI:MGI:2443855
See related
Ensembl:ENSMUSG00000049580 AllianceGenome:MGI:2443855
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Tsk; E2ig4; Lrrc54; 9530051K01Rik
Summary
Enables transforming growth factor beta binding activity. Involved in several processes, including cholesterol efflux; cholesterol homeostasis; and nervous system development. Acts upstream of or within several processes, including ciliary body morphogenesis; negative regulation of Wnt signaling pathway; and telencephalon development. Located in extracellular space. Is expressed in embryo and olfactory epithelium. Orthologous to human TSKU (tsukushi, small leucine rich proteoglycan). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in bladder adult (RPKM 55.7), duodenum adult (RPKM 40.7) and 19 other tissues See more
Orthologs
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Genomic context

See Tsku in Genome Data Viewer
Location:
7 E1; 7 53.66 cM
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 7 NC_000073.7 (97999875..98010602, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 7 NC_000073.6 (98350668..98361390, complement)

Chromosome 7 - NC_000073.7Genomic Context describing neighboring genes Neighboring gene UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6 Neighboring gene alkaline ceramidase 3 Neighboring gene STARR-seq mESC enhancer starr_19625 Neighboring gene STARR-seq mESC enhancer starr_19626 Neighboring gene STARR-positive B cell enhancer mm9_chr7:105457877-105458178 Neighboring gene STARR-seq mESC enhancer starr_19627 Neighboring gene STARR-seq mESC enhancer starr_19628 Neighboring gene predicted gene 44507 Neighboring gene predicted gene, 39053

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (2) 
  • Targeted (2)  1 citation

General gene information

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables transforming growth factor beta binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within anterior commissure morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in anterior commissure morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within camera-type eye development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cholesterol efflux IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cholesterol homeostasis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cholesterol metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within ciliary body morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within corpus callosum morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
NOT involved_in energy homeostasis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in energy homeostasis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in hippocampus development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in inner ear receptor cell stereocilium organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within lateral ventricle development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within negative regulation of Wnt signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of myofibroblast differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of neuron projection development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of transforming growth factor beta1 production IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within nervous system development IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of hair cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in wound healing IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
is_active_in extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
NOT located_in extracellular space IMP
Inferred from Mutant Phenotype
more info
PubMed 

General protein information

Preferred Names
tsukushi
Names
leucine rich repeat containing 54
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)

  1. NM_001024619.3NP_001019790.1  tsukushi precursor

    See identical proteins and their annotated locations for NP_001019790.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. All four variants encode the same protein.
    Source sequence(s)
    AC111084, AK137208
    Consensus CDS
    CCDS21469.1
    UniProtKB/Swiss-Prot
    Q4W655, Q8CBR6
    UniProtKB/TrEMBL
    Q08EE6
    Related
    ENSMUSP00000146025.2, ENSMUST00000206414.2
    Conserved Domains (2) summary
    COG4886
    Location:64317
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:6386
    LRR_RI; leucine-rich repeat [structural motif]
  2. NM_001168539.1NP_001162011.1  tsukushi precursor

    See identical proteins and their annotated locations for NP_001162011.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. All four variants encode the same protein.
    Source sequence(s)
    AC111084, AK137208
    Consensus CDS
    CCDS21469.1
    UniProtKB/Swiss-Prot
    Q4W655, Q8CBR6
    UniProtKB/TrEMBL
    Q08EE6
    Related
    ENSMUSP00000128431.2, ENSMUST00000165257.8
    Conserved Domains (2) summary
    COG4886
    Location:64317
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:6386
    LRR_RI; leucine-rich repeat [structural motif]
  3. NM_001168540.1NP_001162012.1  tsukushi precursor

    See identical proteins and their annotated locations for NP_001162012.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. All four variants encode the same protein.
    Source sequence(s)
    AC111084, AK053973
    Consensus CDS
    CCDS21469.1
    UniProtKB/Swiss-Prot
    Q4W655, Q8CBR6
    UniProtKB/TrEMBL
    Q08EE6
    Related
    ENSMUSP00000130917.2, ENSMUST00000164726.8
    Conserved Domains (2) summary
    COG4886
    Location:64317
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:6386
    LRR_RI; leucine-rich repeat [structural motif]
  4. NM_001168541.1NP_001162013.1  tsukushi precursor

    See identical proteins and their annotated locations for NP_001162013.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. All four variants encode the same protein.
    Source sequence(s)
    AC111084, AK053973
    Consensus CDS
    CCDS21469.1
    UniProtKB/Swiss-Prot
    Q4W655, Q8CBR6
    UniProtKB/TrEMBL
    Q08EE6
    Related
    ENSMUSP00000091713.5, ENSMUST00000094161.11
    Conserved Domains (2) summary
    COG4886
    Location:64317
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:6386
    LRR_RI; leucine-rich repeat [structural motif]

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000073.7 Reference GRCm39 C57BL/6J

    Range
    97999875..98010602 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006507835.4XP_006507898.1  tsukushi isoform X1

    See identical proteins and their annotated locations for XP_006507898.1

    UniProtKB/Swiss-Prot
    Q4W655, Q8CBR6
    UniProtKB/TrEMBL
    Q08EE6
    Conserved Domains (2) summary
    COG4886
    Location:64317
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:6386
    LRR_RI; leucine-rich repeat [structural motif]
  2. XM_006507832.4XP_006507895.1  tsukushi isoform X1

    See identical proteins and their annotated locations for XP_006507895.1

    UniProtKB/Swiss-Prot
    Q4W655, Q8CBR6
    UniProtKB/TrEMBL
    Q08EE6
    Conserved Domains (2) summary
    COG4886
    Location:64317
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:6386
    LRR_RI; leucine-rich repeat [structural motif]
  3. XM_006507837.2XP_006507900.1  tsukushi isoform X1

    See identical proteins and their annotated locations for XP_006507900.1

    UniProtKB/Swiss-Prot
    Q4W655, Q8CBR6
    UniProtKB/TrEMBL
    Q08EE6
    Conserved Domains (2) summary
    COG4886
    Location:64317
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:6386
    LRR_RI; leucine-rich repeat [structural motif]
  4. XM_036153119.1XP_036009012.1  tsukushi isoform X1

    UniProtKB/Swiss-Prot
    Q4W655, Q8CBR6
    UniProtKB/TrEMBL
    Q08EE6
    Conserved Domains (2) summary
    COG4886
    Location:64317
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:6386
    LRR_RI; leucine-rich repeat [structural motif]
  5. XM_006507833.2XP_006507896.1  tsukushi isoform X1

    See identical proteins and their annotated locations for XP_006507896.1

    UniProtKB/Swiss-Prot
    Q4W655, Q8CBR6
    UniProtKB/TrEMBL
    Q08EE6
    Conserved Domains (2) summary
    COG4886
    Location:64317
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:6386
    LRR_RI; leucine-rich repeat [structural motif]
  6. XM_036153118.1XP_036009011.1  tsukushi isoform X1

    UniProtKB/Swiss-Prot
    Q4W655, Q8CBR6
    UniProtKB/TrEMBL
    Q08EE6
    Related
    ENSMUSP00000127242.2, ENSMUST00000165901.8
    Conserved Domains (2) summary
    COG4886
    Location:64317
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:6386
    LRR_RI; leucine-rich repeat [structural motif]