Lum lumican [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Lumprovided by RGD
Official Full Name: lumicanprovided by RGD
Primary source: RGD:620984
See related: EnsemblRapid:ENSRNOG00000004610 AllianceGenome:RGD:620984
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
Summary: Predicted to enable collagen binding activity. Involved in cartilage development; response to growth factor; and response to organic cyclic compound. Predicted to be located in extracellular matrix. Predicted to be part of fibrillar collagen trimer. Predicted to be active in extracellular space. Biomarker of ureteral obstruction. Human ortholog(s) of this gene implicated in carotid artery disease; coronary artery disease; and pancreatic cancer. Orthologous to human LUM (lumican). [provided by Alliance of Genome Resources, Oct 2024]
Expression: Biased expression in Heart (RPKM 913.3), Uterus (RPKM 445.4) and 5 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 7q13

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	7	NC_086025.1 (34245323..34252510)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	7	NC_051342.1 (32358990..32365794)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	7	NC_005106.4 (38820058..38826862)

Chromosome 7 - NC_086025.1 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?

Immunolocalization of Keratan Sulfate in Rat Spinal Tissues Using the Keratanase Generated BKS-1(+) Neoepitope: Correlation of Expression Patterns with the Class II SLRPs, Lumican and Keratocan.
Title: Immunolocalization of Keratan Sulfate in Rat Spinal Tissues Using the Keratanase Generated BKS-1(+) Neoepitope: Correlation of Expression Patterns with the Class II SLRPs, Lumican and Keratocan.
These findings indicate that lumican is transiently synthesized by acinar cells and fibroblasts in acute pancreatitis.
Title: Transient and ectopic expression of lumican by acinar cells in L-arginine-induced acute pancreatitis.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables collagen binding	IBA Inferred from Biological aspect of Ancestor more info
enables collagen binding	IEA Inferred from Electronic Annotation more info
enables collagen binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cartilage development	IEP Inferred from Expression Pattern more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transforming growth factor beta1 production	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transforming growth factor beta1 production	ISO Inferred from Sequence Orthology more info
involved_in response to growth factor	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to organic cyclic compound	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
located_in extracellular matrix	ISO Inferred from Sequence Orthology 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
part_of fibrillar collagen trimer	IEA Inferred from Electronic Annotation more info
part_of fibrillar collagen trimer	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: lumican

Names: KSPG lumican; keratan sulfate proteoglycan lumican

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_031050.2 → NP_112312.1 lumican precursor

See identical proteins and their annotated locations for NP_112312.1

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000007

UniProtKB/Swiss-Prot

P51886

UniProtKB/TrEMBL

A6IG66

Related

ENSRNOP00000006109.2, ENSRNOT00000006109.6

Conserved Domains (4) summary

smart00013
Location:37 → 71

LRRNT; Leucine rich repeat N-terminal domain

cd00116
Location:66 → 267

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

sd00033
Location:68 → 91

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:66 → 128

LRR_8; Leucine rich repeat