Defb1 defensin beta 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Defb1provided by RGD
Official Full Name: defensin beta 1provided by RGD
Primary source: RGD:619943
See related: EnsemblRapid:ENSRNOG00000013768 AllianceGenome:RGD:619943
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: CDK4
Summary: Predicted to enable CCR6 chemokine receptor binding activity; double-stranded DNA binding activity; and identical protein binding activity. Involved in response to testosterone. Predicted to be located in membrane; microvesicle; and sperm midpiece. Predicted to be active in extracellular space. Biomarker of obesity and type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in asthma; chronic obstructive pulmonary disease; and lung disease. Orthologous to human DEFB1 (defensin beta 1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Restricted expression toward (RPKM 2123.5) See more
Orthologs: human all
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Genomic context

Location:: 16q12.5

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	16	NC_086034.1 (77001326..77016068, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	16	NC_051351.1 (70298862..70313604, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	16	NC_005115.4 (75294385..75309127, complement)

Chromosome 16 - NC_086034.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

expression perturbed in diabetes
Title: Tlr1-13, Nod1/2 and antimicrobial gene expression in the epididymis and testis of rats with alloxan-induced diabetes.
The -44CC SNP genotype was more common in endophthalmitis, and a mini-haplotype including this single-nucleotide polymorphism was associated strongly with endophthalmitis.
Title: β-Defensin 1 haplotype associated with postoperative endophthalmitis.
May play an antimicrobial role in the testis and epididymis.
Title: Messenger RNA (mRNA) expression for the antimicrobial peptides beta-defensin-1 and beta-defensin-2 in the male rat reproductive tract: beta-defensin-1 mRNA in initial segment and caput epididymidis is regulated by androgens and not bacterial lipopolysaccharides.
Overexpression of beta-defensin-1 mRNA in diabetic nephropathy.
Title: Elevated levels of beta defensin-1 mRNA in diabetic kidneys of GK rats.

Submit: New GeneRIF Correction

General gene information

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Markers

D16Got75 (e-PCR)
- UniSTS:115406

PMC96815P1 (e-PCR)
- UniSTS:273634

PMC96815P5 (e-PCR)
- UniSTS:273638

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables CCR6 chemokine receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables CCR6 chemokine receptor binding	ISO Inferred from Sequence Orthology more info
enables CCR6 chemokine receptor binding	ISS Inferred from Sequence or Structural Similarity more info
enables double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in antimicrobial humoral immune response mediated by antimicrobial peptide	ISO Inferred from Sequence Orthology more info
involved_in calcium-mediated signaling	ISO Inferred from Sequence Orthology more info
involved_in calcium-mediated signaling	ISS Inferred from Sequence or Structural Similarity more info
involved_in defense response to Gram-negative bacterium	IBA Inferred from Biological aspect of Ancestor more info
involved_in defense response to Gram-negative bacterium	ISO Inferred from Sequence Orthology more info
involved_in defense response to Gram-negative bacterium	ISS Inferred from Sequence or Structural Similarity more info
involved_in defense response to Gram-positive bacterium	IBA Inferred from Biological aspect of Ancestor more info
involved_in defense response to Gram-positive bacterium	ISO Inferred from Sequence Orthology more info
involved_in defense response to Gram-positive bacterium	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within defense response to bacterium	ISO Inferred from Sequence Orthology more info
involved_in innate immune response	ISO Inferred from Sequence Orthology more info
involved_in innate immune response in mucosa	IBA Inferred from Biological aspect of Ancestor more info
involved_in innate immune response in mucosa	ISO Inferred from Sequence Orthology more info
involved_in killing of cells of another organism	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of flagellated sperm motility involved in capacitation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of flagellated sperm motility involved in capacitation	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to bacterium	ISO Inferred from Sequence Orthology more info
involved_in response to testosterone	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
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 membrane	ISO Inferred from Sequence Orthology more info
located_in membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in microvesicle	ISO Inferred from Sequence Orthology more info
located_in microvesicle	ISS Inferred from Sequence or Structural Similarity more info
located_in sperm midpiece	ISO Inferred from Sequence Orthology more info
located_in sperm midpiece	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: beta-defensin 1

Names: BD-1; rBD-1

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.