Clec3b C-type lectin domain family 3, member B [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Clec3bprovided by RGD
Official Full Name: C-type lectin domain family 3, member Bprovided by RGD
Primary source: RGD:1311031
See related: Ensembl:ENSRNOG00000004540 AllianceGenome:RGD:1311031
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Tna
Summary: Predicted to enable calcium ion binding activity; heparin binding activity; and kringle domain binding activity. Involved in ossification. Predicted to be located in cytoplasm and granular component. Predicted to be active in extracellular space. Human ortholog(s) of this gene implicated in osteoarthritis. Orthologous to human CLEC3B (C-type lectin domain family 3 member B). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Lung (RPKM 73.7), Muscle (RPKM 50.2) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 8q32

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	8	NC_086026.1 (131687575..131693292)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	8	NC_051343.1 (122810120..122815837)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	8	NC_005107.4 (132241016..132248066)

Chromosome 8 - NC_086026.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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
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?

age-related changes in preadipocyte gene expression differ among depots, potentially contributing to fat redistribution and dysfunction.
Title: Aging, depot origin, and preadipocyte gene expression.

Submit: New GeneRIF Correction

General gene information

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Markers

AU049759 (e-PCR)
- UniSTS:146205

D8Rat71 (e-PCR), detects polymorphism
- UniSTS:119130

RH143893 (e-PCR)
- UniSTS:233139

Clec3b (e-PCR), detects polymorphism
- UniSTS:519415

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables calcium ion binding	ISO Inferred from Sequence Orthology more info
enables calcium ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables heparin binding	ISO Inferred from Sequence Orthology more info
enables heparin binding	ISS Inferred from Sequence or Structural Similarity more info
enables kringle domain binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in bone mineralization	IBA Inferred from Biological aspect of Ancestor more info
involved_in bone mineralization	ISO Inferred from Sequence Orthology more info
involved_in bone mineralization	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to organic substance	ISO Inferred from Sequence Orthology more info
involved_in cellular response to transforming growth factor beta stimulus	ISO Inferred from Sequence Orthology more info
involved_in ossification	IBA Inferred from Biological aspect of Ancestor more info
involved_in ossification	IEP Inferred from Expression Pattern more info	PubMed
involved_in ossification	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of plasminogen activation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of plasminogen activation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within skeletal system development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor 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
located_in granular component	ISO Inferred from Sequence Orthology more info
located_in granular component	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: tetranectin

Names: tetranectin (plasminogen binding protein); tetranectin-like

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_001398638.1 → NP_001385567.1 tetranectin precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000008

UniProtKB/TrEMBL

A6I4B3, D3ZUU6

Related

ENSRNOP00000006055.4, ENSRNOT00000006055.8

Conserved Domains (1) summary

cd03596
Location:71 → 199

CLECT_tetranectin_like; C-type lectin-like domain (CTLD) of the type found in the tetranectin (TN), cartilage derived C-type lectin (CLECSF1), and stem cell growth factor (SCGF)